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Abstract

RNA viruses are known to replicate by low fidelity polymerases and have high mutation rates whereby the resulting virus population tends to exist as a distribution of mutants. In this review, we aim to explore how genetic events such as spontaneous mutations could alter the genomic organization of RNA viruses in such a way that they impact virus replications and plaque morphology. The phenomenon of quasispecies within a viral population is also discussed to reflect virulence and its implications for RNA viruses. An understanding of how such events occur will provide further evidence about whether there are molecular determinants for plaque morphology of RNA viruses or whether different plaque phenotypes arise due to the presence of quasispecies within a population. Ultimately this review gives an insight into whether the intrinsically high error rates due to the low fidelity of RNA polymerases is responsible for the variation in plaque morphology and diversity in virulence. This can be a useful tool in characterizing mechanisms that facilitate virus adaptation and evolution.

Poliovirus (PV)

The poliovirus population diversity was evaluated in the brain of the murine model during viral spread. It was observed that only a fraction of the original injected viral pool was able to move from the initial site of inoculation to the brain via the 'bottleneck effect.' To determine the maintenance of the quasispecies during infection in vivo, 6-10 weeks old mice were inoculated in the leg with individual viruses. Total RNA recovered from the brain tissues revealed that four viruses were shown to be capable of spreading to the brain with their introduced mutations unchanged. Therefore, it was postulated that the innate immune response reduced the viral pathogenicity by limiting the diversity of viruses during spread to vulnerable tissues [16] . Two mechanisms to explain the bottleneck effect have been speculated, namely-the "tough-transit" model and the "burned-bridge" model. The "tough-transit" model suggests that virus trafficking within the murine model has a low probability of success passing the blood-brain barrier. However, once in the CNS, it acts as a founder virus and re-establishes a population with initial limited diversity. On the other hand, the "burned bridge" model stipulates that it is not tough for the virus to physically reach the blood-brain barrier. Thus, when the first few viruses reach the gateway to the brain, the host innate immune response triggers an antiviral state [16] .
The poliovirus population diversity was evaluated in the brain of the murine model during viral spread. It was observed that only a fraction of the original injected viral pool was able to move from the initial site of inoculation to the brain via the 'bottleneck effect.' To determine the maintenance of the quasispecies during infection in vivo, 6-10 weeks old mice were inoculated in the leg with individual viruses. Total RNA recovered from the brain tissues revealed that four viruses were shown to be capable of spreading to the brain with their introduced mutations unchanged. Therefore, it was postulated that the innate immune response reduced the viral pathogenicity by limiting the diversity of viruses during spread to vulnerable tissues [16] . Two mechanisms to explain the bottleneck effect have been speculated, namely-the "tough-transit" model and the "burned-bridge" model. The "tough-transit" model suggests that virus trafficking within the murine model has a low probability of success passing the blood-brain barrier. However, once in the CNS, it acts as a founder virus and re-establishes a population with initial limited diversity. On the other hand, the "burned bridge" model stipulates that it is not tough for the virus to physically reach the blood-brain barrier. Thus, when the first few viruses reach the gateway to the brain, the host innate immune response triggers an antiviral state [16] .

Hepatitis B Virus (HBV)

Another challenge to overcome is to accurately determine the origin and spread of a founder population of the virus. Hence, the discrepancies in the evolution of HBV was investigated. Eight related patients with acquired chronic HBV through mother-to-infant transmission were selected and the viral genomes isolated were analyzed. Sequence analysis indicated that the samples originated from a single source of HBV genotype B2 (HBV-B2) which diverged from a tiny common ancestral pool regardless of the route of acquisition. Between individuals, viral strains obtained from a time point showed evidence that they originated from a small pool of the previous time point. This conferred the strain an advantage over other strains with regards to the recovery of the founder state shortly after transmission to the new host and the adaptation to the local environment within the host. Natural selection rather than genetic drift was hypothesized to be the root cause for the evolution of HBV, due to the observed varying patterns of divergence at synonymous and non-synonymous sites. This was in line with the higher rate of substitutions within the host rather than between hosts. Approximately 85/88 amino acid residues changed from common to rare residues. Since these changes were shown not to be a random process, it is concluded that the HBV was able to evolve and change but was limited to a defined range of phenotypes. It can be argued that the mechanism observed thus far suggest that the adaptive mutations accumulated in one individual would not be maintained in another individual and might revert after transmission. Hence, within the host, substitutions were higher than between hosts [156] .

Introduction

With their diverse differences in size, structure, genome organization and replication strategies, RNA viruses are recognized as being highly mutatable [1] . Their high mutation rates make it very difficult for therapeutic interventions to work effectively and very often they develop resistance to antiviral drugs and antibodies elicited by vaccines [2, 3] . This poses a real threat to how emerging infectious agents could be prevented or treated [4] . The success of the evolution of RNA viruses arises from their capacity to utilize varying replication approaches and to adapt to a wide range of biological niches faced during viral spread in the host. One of the factors affecting the emergence or re-emergence of infectious diseases is the genetics of the infectious agents [1] .
Only about 15 viral diseases can be effectively prevented through FDA approved vaccinations [5] . This attests to the urgency to understand the mechanisms by which viruses can overcome the different pressures applied to restrict their replications. In the last four decades, breakthroughs in molecular biology have favored in-depth analysis of virus isolates. Findings from other studies have suggested that populations of RNA viruses are divergent and favor an active evolution of RNA genomes. The quick evolution of RNA genomes could lead to variant sequences that differ by one or two nucleotides from the wild-type sequence in the population. It is further suggested that each viral RNA population of 10 9 or more infectious particles was always a mixture of various variants despite being isolated from a single clone [6] .
Such heterogeneity within the virus population could be explained by the existence of not a single genotype within the species but rather an ensemble of related sequences known as the quasispecies [7] . Developed by Manfred Eigen and Peter Schuster, the concept of quasispecies was defined as a mutant distribution dominated by a primary sequence with the highest rates of replication between the components of the mutant distribution. The phenomenon of quasispecies was further supported by the "hypercycle" theory as a self-organization principle to include different quasispecies in a higher-order organization that eases evolution into more complicated forms such that the coding capacity and catalytic activities of proteins are taken into account [8] [9] [10] .
Mutants with varying levels of infectivity generated from a mutated gene occurred regularly in a virus population due to the high mutation rates [6] . The error-prone replication ability of RNA viruses and the shorter generation times can be used to explain the variations in evolution rates between DNA and RNA viruses. While mutation rates for DNA genomes have been estimated to be between 10 −7 and 10 −11 per base pair per replication [11] , the RNA dependent RNA polymerase (RdRp) showed typically low fidelity whereby the mutation rate is of roughly 10 −4 mutations per nucleotide copied, which is greater than that of almost all DNA viruses [7, 12, 13] . This characteristic of the RNA polymerase in RNA viruses led to the generation of diverse offspring with different genotypes in shorter generation times.
There is some general consensus regarding quasispecies that have been established. For instance, the presence of diverse mutants in a population of viruses is a reality which can affect the biological behavior of the virus in vivo due to the complexity and amplitude of the mutant spectra [14] . Moreover, interactions amongst variants of a quasispecies population was classified into three types namely-cooperation, interference and complementation. Cooperative interactions arise from those variants exhibiting advantageous phenotypes compared to the wild-type while interfering interactions are those exemplified in variants with detrimental effects on the replication of the virus. However, complementation interactions have no positive or negative effects on the virus population [15] .
Considerably less is known of the relationships between the evolution of RNA viruses with respect to virulence. The dynamics of quasispecies has explained the failure of monotherapy and synthetic antiviral vaccine but opened up new avenues for exploration [14] . Specifically, unanswered questions pertaining to quasispecies remain-What are the underlying mutations responsible for long term tenacity compared to those of extinction? Are there any molecular determinants which are the root cause of higher virulence in a quasispecies population?
Frequent occasional outbreaks of emerging and re-emerging viral diseases such as Dengue fever, West Nile Fever, Zika virus disease, Chikungunya disease, Middle east respiratory syndrome, Ebola virus disease and many others have been targets for therapeutic interventions. Long lasting protection against viral infections is best achieved via vaccinations through live attenuated viruses (LAVs). In order to generate stable vaccine strains, the evolution of these viruses must be properly understood. This review is centered on the examination of the evidence for the heterogeneous nature of RNA genomes (quasispecies), the factors leading to quasispecies formation and its implications on virulence.
The phenomenon of quasispecies has been well reported for many viruses belonging to different families and genera [16] [17] [18] . There is no clear idea whether emerging viruses such as Zika virus, Ebola virus, West Nile virus, Dengue virus and many others owe part of their evolution to higher virulence conferred by the presence of specific quasispecies within the viral population. Exploring the underlying mechanism of virulence stemming from a quasispecies population remains of interest. In this review, we examine reported cases of quasispecies and their implications on virulence.

Picornaviridae

Viruses of the family Picornaviridae can be classified into genera such as Enterovirus, Parechovirus, Aphotovirus and others. The virion is made up of a non-enveloped capsid of 30 nm surrounding a core positive stranded ssRNA genome ( Figure 1A ) [19] . The genome is approximately 7 kb in size and possesses a single long ORF flanked on both ends by the 5 -non-translated region (5 -NTR) and the 3 -non-translated region [20] . The 5 -NTR has an internal ribosome entry site (IRES) which controls cap-independent translation. The ORF comprising 6579 nucleotides can be classified into three polyprotein regions, namely, P1, P2 and P3. They encode for structural proteins (VP1 to VP4) in the P1 region and non-structural proteins in the P2 (2A-2C) and P3 regions (3A-3D) following proteolytic cleavage ( Figure 1B) . The viral capsid proteins VP1, VP2 and VP3 are displayed on the external structures of the EV-A71 viral particle whereas VP4 is found within the internal structures of the capsid [21] . (7.4 Kb) . The Open Reading Frame (ORF) contains the structural viral protein P1 which is cleaved to yield VP1, VP2, VP3 and VP4 and non-structural viral proteins P2 (cleaved to yield 2A, 2B and 2C) and P3 (cleaved to yield 3A, 3B, 3C and 3D). The 3′-NTR end of the genome contains the poly (A) tail.

Poliovirus (PV)

Poliovirus is found within the Human Enterovirus C species of the Picornaviridae family and can be classified into three distinct serotypes (1, 2 and 3). Most poliovirus infections cause an asymptomatic incubation period followed by a minor illness characterized by fever, headache and sore throat which mainly affects children. However, PV infections can lead to paralytic poliomyelitis which can result in death. Following the WHO 1988 polio eradication program, the number of poliomyelitis has been reduced by 99% worldwide but a small number of countries still have sporadic outbreaks of polio [22] .
In order to verify whether limiting the genomic diversity of a viral population has any effect on its evolution, a study was conducted on a strain of poliovirus with a substitution of Glycine 64 to Serine (G64S) in the RNA polymerase of the virus. The outcome of one-step growth curves and
Poliovirus is found within the Human Enterovirus C species of the Picornaviridae family and can be classified into three distinct serotypes (1, 2 and 3). Most poliovirus infections cause an asymptomatic incubation period followed by a minor illness characterized by fever, headache and sore throat which mainly affects children. However, PV infections can lead to paralytic poliomyelitis which can result in death. Following the WHO 1988 polio eradication program, the number of poliomyelitis has been reduced by 99% worldwide but a small number of countries still have sporadic outbreaks of polio [22] .
In order to verify whether limiting the genomic diversity of a viral population has any effect on its evolution, a study was conducted on a strain of poliovirus with a substitution of Glycine 64 to Serine (G64S) in the RNA polymerase of the virus. The outcome of one-step growth curves and northern blot analysis of genomic RNA synthesis confirmed that the G64S mutation showed greater fidelity without a considerable reduction in the overall efficiency of RNA replication. The study hypothesized that having greater heterogeneity within a viral population allows it to adapt better to changing environments encountered during an infection and indeed the finding showed that boosting the fidelity of poliovirus replication had a noticeable effect on viral adaptation and pathogenicity. The poliovirus strain with a mutated RNA polymerase carrying an altered amino acid residue (G64S) was observed to replicate similarly to the wild-type counterpart but produced lower genomic diversity and subsequently was incapable of adapting well under detrimental growth situations. This study showed that the diversity of the quasispecies was associated with increased virulence rather than selection of single adaptive mutations. Alongside previous observations, these findings indicated a rise in the error rate over the tolerable error threshold which induced viral extinction, suggesting that the rate of viral mutation was precisely modulated and most likely had been finely tuned during the evolution of the virus [7] . It was further revealed that curbing the diversity of a RNA viral population by raising the fidelity of the RNA polymerase had a direct effect on its pathogenicity and capacity of the viruses to escape antiviral immunity [23] . These findings support the fact that RNA viruses have developed minimal viral polymerase fidelity to facilitate quick evolution and adaptation to novel situations [24] .

Enterovirus 71 (EV-A71)

EV-A71 belongs to the genus Enterovirus within the family of Picornaviridae. It was first characterized in 1969 in California, USA [25] and is one of the main etiological agents of hand, foot and mouth disease (HFMD) [26] . Some cases of EV-A71 infections have been associated with neurological complications such as aseptic meningitis, brainstem encephalitis and acute flaccid paralysis [27] . In China, enteroviruses such as EV-A71 and CV-A16 have caused 7,200,092 cases of HFMD between 2008 to 2012. The mortality rate was highest among children below the age of five. It was further reported that 82,486 patients developed neurological complications and 1617 deaths were confirmed by the laboratory to be caused by EV-A71 [28, 29] .

Flaviviridae

Of the Flaviviridae family (genera Flavivirus, Pestivirus, Pegivirus and Hepacivirus), there are 89 animal viruses with a small, positive-sense, single stranded RNA genome [31] . The virions are 40-60 nm in diameter, spherical in shape and contain a lipid envelope (Figure 2A ). The majority of these viruses are arthropod-borne and transmitted via infected mosquitoes and ticks. They are considered as emerging and re-emerging pathogens such as dengue virus (DENV), West Nile Virus (WNV), Zika Virus (ZIKV) and these viruses pose a global threat to public health by causing significant mortality [32] . The flaviviral genome is approximately 11 kb and has a single open reading frame (ORF), which is flanked by untranslated regions (5 and 3 NTR). The ORF encodes three structural proteins (C, M and E) and 7 non-structural proteins (NS). The non-structural proteins include large, highly conserved proteins NS1, NS3 and NS5 and four small hydrophobic proteins NS2A, NS2B and NS4A and NS4B ( Figure 2B ) [33] . quasispecies utilized the dynamic proportion of varying haplotype populations to co-exist, sustained the ability of the population to adapt and enabled the propagation in different tissues. Lastly, the study concluded that the selection of haplotype(s) might be a driving factor in viral dissemination and severity of infections in humans as well as the virulence in EV-A71 infected patients [30] .
Of the Flaviviridae family (genera Flavivirus, Pestivirus, Pegivirus and Hepacivirus), there are 89 animal viruses with a small, positive-sense, single stranded RNA genome [31] . The virions are 40-60 nm in diameter, spherical in shape and contain a lipid envelope (Figure 2A ). The majority of these viruses are arthropod-borne and transmitted via infected mosquitoes and ticks. They are considered as emerging and re-emerging pathogens such as dengue virus (DENV), West Nile Virus (WNV), Zika Virus (ZIKV) and these viruses pose a global threat to public health by causing significant mortality [32] . The flaviviral genome is approximately 11kb and has a single open reading frame (ORF), which is flanked by untranslated regions (5′ and 3′ NTR). The ORF encodes three structural proteins (C, M and E) and 7 non-structural proteins (NS). The non-structural proteins include large, highly conserved proteins NS1, NS3 and NS5 and four small hydrophobic proteins NS2A, NS2B and NS4A and NS4B ( Figure 2B ) [33] .

Zika Virus (ZIKV)

Zika Virus was first discovered in 1947 when it was isolated from Aedes Africanus mosquitoes [42] . It belongs to the Flavivirus genus within the Flaviviridae family. Zika infections have been reported in Egypt [43] , East Africa [44] , India [45] , Thailand, Vietnam [46] , Philippines and Malaysia [47] .
An Asian/American lineage ZIKA virus (ZIKV) formed 2 types of plaques-large and small. The large plaque variant was observed to have faster growth kinetics compared to the small plaque variant. Sequencing of the plaque variants showed that the large plaque variant had a guanine nucleotide at position 796 (230 Gln ) while the small plaque clone had an adenine at the same position. A recombinant clone carrying the G796A mutation was produced using an infectious molecular clone of the ZIKV MR766 strain. The plaque size produced by the recombinant clone was smaller when compared to the parental strain and its growth rate was significantly reduced in Vero cells. In vivo studies demonstrated that the virulence of the MR766 strain in IFNAR1 mice had decreased, showing that the mutation at position 230 in the -M protein is a molecular determinant of plaque morphology, growth property and virulence in mice [48] .

West Nile Virus (WNV)

West Nile Virus was first characterized in 1937 in the West Nile district of Uganda and was taxonomically placed in the genus Flavivirus within the Flaviviridae family. The virus later appeared in New York in 1999, where it caused 59 hospitalized infections and 7 deaths before its spread to other parts of the USA between 1999-2001 [50] . WNV survives naturally in a mosquito-bird-mosquito transmission cycle involving the Culex sp. mosquitoes [51] .
The genetic diversity of WNV in the avian host was also investigated using next-generation sequencing. The aim was to explore whether the genetically homogeneous cloned virus would go through genetic diversification after passages in young SPF chickens and wild juvenile carrion crows. Data collected revealed that the WNV population showed significant heterogeneity diverging from the quasispecies structure of the initial viral inoculum in both animal models. However, in-depth analysis enacted a comparison between the infection model (SPF chicken and wild juvenile carrion crows) to assess the variations in genetic diversity. It was demonstrated that the WNV genetic diversifications varied significantly from the inoculum in crows with 18 genetic variants but exhibited suboptimal levels of diversifications among the chickens with only 3 single nucleotide variants (SNV) being detected. Hence, natural WNV-susceptible avian hosts could provide a selective setting and contributed to genetic diversifications. NGS technologies have enabled the analysis of WNV quasispecies dynamics, leading to a better understanding of the virus and shed some light on its mechanism of pathogenicity [53] .

Togaviridae

Viruses from the Togaviridae family can be further classified into the genus Alphavirus and Rubivirus. Alphaviruses are anthropod-borne viruses [54] and they formed icosahedral particles of about 70 nm with a lipid envelope ( Figure 3A ) [55] . The spikes of the virion are made up of E1 and E2 glycoproteins organized in a T4 icosahedral lattice of 80 trimers. The alphavirus virion carries a positive single stranded RNA of approximately 11-12 kb as the genetic material [54] . The RNA has a 5 -methylated nucleotide cap and a polyadenylated 3 end. The viral genome is translated into three structural proteins (CP, E2 and E1) and four non-structural proteins (NSP1, NSP2, NSP3 and NSP4) ( Figure 3B ). The genetic diversity of WNV in the avian host was also investigated using next-generation sequencing. The aim was to explore whether the genetically homogeneous cloned virus would go through genetic diversification after passages in young SPF chickens and wild juvenile carrion crows. Data collected revealed that the WNV population showed significant heterogeneity diverging from the quasispecies structure of the initial viral inoculum in both animal models. However, in-depth analysis enacted a comparison between the infection model (SPF chicken and wild juvenile carrion crows) to assess the variations in genetic diversity. It was demonstrated that the WNV genetic diversifications varied significantly from the inoculum in crows with 18 genetic variants but exhibited suboptimal levels of diversifications among the chickens with only 3 single nucleotide variants (SNV) being detected. Hence, natural WNV-susceptible avian hosts could provide a selective setting and contributed to genetic diversifications. NGS technologies have enabled the analysis of WNV quasispecies dynamics, leading to a better understanding of the virus and shed some light on its mechanism of pathogenicity [53] .
Viruses from the Togaviridae family can be further classified into the genus Alphavirus and Rubivirus. Alphaviruses are anthropod-borne viruses [54] and they formed icosahedral particles of about 70 nm with a lipid envelope ( Figure 3A ) [55] . The spikes of the virion are made up of E1 and E2 glycoproteins organized in a T4 icosahedral lattice of 80 trimers. The alphavirus virion carries a positive single stranded RNA of approximately 11-12kb as the genetic material [54] . The RNA has a 5′-methylated nucleotide cap and a polyadenylated 3′ end. The viral genome is translated into three structural proteins (CP, E2 and E1) and four non-structural proteins (NSP1, NSP2, NSP3 and NSP4) ( Figure 3B ).

Chikungunya Virus (CHIKV)

Chikungunya virus (CHIKV) is an arthropod-borne virus transmitted to humans by mosquitoes and has caused significant human morbidity in many parts of the world [56] . Chikungunya virus causes an acute febrile illness with high fever, severe joint pain, polyarthralgia, myalgia, maculopapular rash and edema. While the fever and rash are self-limiting and are able to resolve within a few days, arthralgia can be prolonged from months to years [57, 58] . Some cases of CHIKV
Chikungunya virus (CHIKV) is an arthropod-borne virus transmitted to humans by mosquitoes and has caused significant human morbidity in many parts of the world [56] . Chikungunya virus causes an acute febrile illness with high fever, severe joint pain, polyarthralgia, myalgia, maculopapular rash and edema. While the fever and rash are self-limiting and are able to resolve within a few days, arthralgia can be prolonged from months to years [57, 58] . Some cases of CHIKV disease were associated with neurological complications [59] . The virus has been associated with frequent outbreaks in tropical countries of Africa and Southeast Asia and also in temperate zones around the world. A major outbreak in 2013 affected several countries of the Americas, involving approximately 2 million people [60] .
The original geographical distributions of the CHIKV indicated that there are 3 distinct groups and phylogenetic analysis confirmed the West African, the Asian and the East/Central/South African (ECSA) genotypes. The ECSA virus with an A226V substitution in the E2 envelope gene had caused multiple massive outbreaks in various regions starting in the La Reunion Islands in 2005. The virus then spread to Asia and caused over a million cases in the following years [61] [62] [63] . The Asian genotype started invading the Americas in 2013, causing massive outbreaks in various countries in Central, South America and the Caribbean. The ECSA virus is now the dominant virus all over Africa and Asia and the Asian genotype is the dominant virus in the Americas [62, [64] [65] [66] [67] . Even though a number of CHIKV vaccine candidates are being developed, no effective vaccine is currently available for clinical use [68] .
Similar to other RNA viruses with extensive mutation rates, CHIKV produces populations of genetically diverse genomes within a host. Up to date, the role of several of these mutations and the influence of disease severity in vertebrates and transmission by mosquitoes have been studied. Riemersma et al. investigated the intra-host genetic diversity of high and low-fidelity CHIKV variants using murine models. Both the high and low fidelity variants were expected to lower the virulence of CHIKV as compared to the wild-type (CHIKV-WT). However, the high-fidelity variant caused more acute levels of infection such that the onset of the swelling in the footpad exhibited earlier than the CHIKV-WT at 3-and 4-days post-infection (dpi). Moreover, the high-fidelity CHIKV (CHIKV-HiFi) infected mice also displayed higher peaks of disease severity when compared to the CHIKV-WT 7 dpi. This enhanced diversification was subsequently reproduced after serial in vitro passages. In high-fidelity variants, nsp2 G641D and nsp4 C483Y mutations increased CHIKV virulence in the adult mice. The NGS data showed that the CHIKV-HiFi variant produced more genetically diverse populations than the CHIKV-WT in mice. However, the low-fidelity variant gave rise to reduced rates of replication and disease [69] .
The P5 CHIKV-NoLS clone remained genetically stable after five passages in Vero cells or insect cells when compared to the CHIKV-WT. Sequence analysis of the P5 CHIKV-NoLS plaques showed that the two plaque variants had no mutations in the capsid protein. A single non-synonymous change in the nucleotide of the capsid caused an alanine to serine substitution at position 101 in the third plaque variant. However, the substitution did not cause any change in the small plaque phenotype or replication kinetics of the CHIKV-NoLS clone after ten passages in vitro [74] . The in vivo study showed that the CHIKV-NoLS-immunized mice were able to produce long-term immunity against CHIKV infection following immunization with a single dose of the CHIKV-NoLS small plaque variant. Attenuation of CHIKV-NoLS through the NoLS mutation is most likely due to the disruption of the replication of viruses after viral RNA synthesis, however, the precise mechanism of reduced viral titer remained unsolved [76] . The NoLS mutation caused a considerable change in the very basic capsid region involving two nucleotides which could affect the structure of RNA binding, assembly of nucleocapsid and interaction with the envelope proteins [77] . Since the CHIKV-NoLS small plaque variant was attenuated in immunized mice and produced sera which could effectively neutralize CHIKV infection in vitro, it could serve as a promising vaccine candidate needed to control the explosive large-scale outbreaks of CHIKV [76] .

Filoviridae

Viruses found within the Filoviridae family can be further classified into five genera-Marburgvirus, Ebolavirus, Cuevavirus, Striavirus and Thamnovirus. The virions are 80 nm in diameter and appear as branched, circular or filamentous ( Figure 4A ). Filoviruses contain a linear negative sense single stranded RNA of approximately 19 kb. The genome of the filoviruses encodes for four structural proteins, namely nucleoprotein (NP), RNA-dependent RNA polymerase co-factor (VP35), transcriptional activator (VP30) and a RNA-dependent RNA polymerase (L). There are also three non-structural membrane-associated proteins, namely a spike glycoprotein (GP1,2), a primary matrix protein (VP40) and a secondary matrix protein (VP24) present within the virion membrane [78] ( Figure 4B ).

Ebola Virus (EboV)

The Ebolavirus genus belongs to the Filoviridae family within the order Mononegavirales. Five species have been identified within the genus of Ebolavirus-Zaire (EBOV), Bundibugyo (BDBV), Sudan (SUDV), Tai Forest (TAFV) and Reston (RESTV) [81] . Among them, only the Reston virus (RESTV) is assumed to be non-pathogenic for humans. The other four classified as Ebolaviruses are well-known to cause the Ebola virus disease (EVD). The virus causes a severe fever along with systemic inflammation and damage to the endothelial cell barrier, leading to shock and multiple organ failure with high mortality rates in humans and animals [82] . It is transmitted to people from wild animals and spreads in the human population through human-to-human transmission [83] . However, the natural host reservoirs of Ebola viruses are unknown. The average Ebola virus disease (EVD) case fatality rate is around 50%. So far, the largest recorded EVD with 28,652 infections had killed 11,325 people [84] . The Zaire, Bundibugyo and Sudan Ebola viruses are involved in large outbreaks in Africa.
The glycoprotein (GP) is responsible for cell attachment, fusion and cell entry. The broad cellular tropism of the GP resulted in multisystem involvement that led to high mortality [85] . The Ebola virus has a high frequency of mutation within a host during the spread of infection and in the reservoir in the human population [86] . Alignment of the Glycoprotein (GP) sequences of 66 Ebola virus isolates from the previous outbreaks (old Ebola outbreak of 1976 to 2005) with the new Ebola outbreak isolates (2014) showed some differences in the positions and frequency of the amino acid replacements. Comparative analysis between the isolates from the old epidemic with the new epidemic isolates showed that 19 out of the 22 amino acid mutations were consistently present in the latter [87] .
In addition, nucleotide mutations at positions A82V and P382T were present only in the Ebola virus glycoprotein from the new Ebola epidemic 2014 isolates. Mutation at position W291R was also found only in the 2014 isolate but at a very low frequency of occurrence [87] . Having a large number of mutations from previous outbreaks present with more than 90% frequency in the sequence of the new Ebola epidemic isolates as well as the emergence of new mutations (A82V, P382T and W291R) indicated the presence of viral quasispecies in the population. The high mutation rates found in a RNA quasispecies increased the probability of escape mutations and this could explain the escape of the 2014 viral isolates from neutralizing antibodies elicited by the old Ebola epidemic isolates. The structural analysis of the Ebola virus revealed the strong contribution of these residues in the three-
The Ebolavirus genus belongs to the Filoviridae family within the order Mononegavirales. Five species have been identified within the genus of Ebolavirus-Zaire (EBOV), Bundibugyo (BDBV), Sudan (SUDV), Tai Forest (TAFV) and Reston (RESTV) [81] . Among them, only the Reston virus (RESTV) is assumed to be non-pathogenic for humans. The other four classified as Ebolaviruses are well-known to cause the Ebola virus disease (EVD). The virus causes a severe fever along with systemic inflammation and damage to the endothelial cell barrier, leading to shock and multiple organ failure with high mortality rates in humans and animals [82] . It is transmitted to people from wild animals and spreads in the human population through human-to-human transmission [83] . However, the natural host reservoirs of Ebola viruses are unknown. The average Ebola virus disease (EVD) case fatality rate is around 50%. So far, the largest recorded EVD with 28,652 infections had killed 11,325 people [84] . The Zaire, Bundibugyo and Sudan Ebola viruses are involved in large outbreaks in Africa.
The glycoprotein (GP) is responsible for cell attachment, fusion and cell entry. The broad cellular tropism of the GP resulted in multisystem involvement that led to high mortality [85] . The Ebola virus has a high frequency of mutation within a host during the spread of infection and in the reservoir in the human population [86] . Alignment of the Glycoprotein (GP) sequences of 66 Ebola virus isolates from the previous outbreaks (old Ebola outbreak of 1976 to 2005) with the new Ebola outbreak isolates (2014) showed some differences in the positions and frequency of the amino acid replacements. Comparative analysis between the isolates from the old epidemic with the new epidemic isolates showed that 19 out of the 22 amino acid mutations were consistently present in the latter [87] .
In addition, nucleotide mutations at positions A82V and P382T were present only in the Ebola virus glycoprotein from the new Ebola epidemic 2014 isolates. Mutation at position W291R was also found only in the 2014 isolate but at a very low frequency of occurrence [87] . Having a large number of mutations from previous outbreaks present with more than 90% frequency in the sequence of the new Ebola epidemic isolates as well as the emergence of new mutations (A82V, P382T and W291R) indicated the presence of viral quasispecies in the population. The high mutation rates found in a RNA quasispecies increased the probability of escape mutations and this could explain the escape of the 2014 viral isolates from neutralizing antibodies elicited by the old Ebola epidemic isolates. The structural analysis of the Ebola virus revealed the strong contribution of these residues in the three-dimensional rearrangement of the glycoprotein and they played an important role in the re-emergence of the new epidemic Ebola isolates in 2014.
Several studies of the Ebola virus glycoprotein showed that the two mutations at positions A82V and T544I might have caused an increase in viral infectivity in humans [88] [89] [90] [91] [92] [93] . These two mutations reduced the stability of the pre-fusion conformation of the EBOV glycoprotein. Kurosaki et al. investigated the viral pseudotyping of EBOV glycoprotein derivatives in 10 cell lines from nine mammalian species and the infectivity of each pseudotype. The data showed that isoleucine at position 544 mediated membrane fusion and increased the infectivity of the virus in all host species, whereas valine at position 82 modulated viral infectivity but was dependent on the virus and the host. Analysis via structural modeling revealed that the isoleucine 544 changed the viral fusion. However, the valine 82 residue influenced the interaction with the viral entry receptor, Niemann-Pick C1 [94] . The frequency of these two amino acid substitutions (A82V and T544I) varied between different Ebolavirus species.
Dietzel et al. studied the functional significance of three non-synonymous mutations in the Ebola virus (EBOV) isolates from the outbreak in West Africa. Among 1000 sequenced Ebola virus genomes, approximately 90% carried the signature three mutations at positions 82, 111 and 759 of the Ebola virus genome. The impact of specific mutations on the role of each viral proteins and on the growth of recombinant EBOVs was analyzed by recently engineered virus-like particles and reverse genetics. A D759G substitution in proximity to a highly conserved region of the GDN motif in the enzymatically active center (amino acid 741 to 743) of the L polymerase was able to increase viral transcription and replication. On the other hand, a R111C substitution in the multifunctional region of the nucleoprotein which is essential for homo-oligomerization and nucleocapsid formation was found to reduce viral transcription and replication. Furthermore, the A82V replacement in the glycoprotein region was able to enhance the efficacy of GP-mediated viral entry into target cells. The combination of the three mutations in the recombinant Ebola virus affected the functional activity of viral proteins and enhanced the growth of the recombinant virus in the cell culture when compared to the prototype isolate [93] . A pilot epidemiological NGS study with a substantial sample size suggested that high mortality in the host was not changed by these three mutations since the rate of mortality in the overall study was not considerably altered throughout the outbreak [95] .
Furthermore, Fedewa et al. showed that genomic adaptation was not crucial for efficient infection of the Ebola virus. The genomes were characterized after serial-passages of EBOV in Boa constrictor kidney JK cells. Deep sequencing coverage (>×10,000) confirmed the presence of only one single nonsynonymous variant (T544I) of unknown significance within the viral population that demonstrated a shift in frequency of at least 10% over six serial passages. However, passaging the EBOV in other cell lines, such as HeLa and DpHt cheek cells, showed different mutations in the genomes of the viral population [96] . This brings forth the question as to whether the viral strains of the Ebola virus should be directly isolated from patients in order to determine the quasispecies of the Ebola virus.

Coronaviridae

Viruses within the Coronaviridae family are positive sense, single-stranded RNA viruses capable of infecting three vertebrate classes comprising mammals (Coronavirus and Torovirus), birds (Coronavirus) and fish (Bafinivirus). Coronaviruses are the largest RNA viruses identified so far with the enveloped spherical virions of about 120-160 nm and the viral genome is about 31 kb in length ( Figure 5A ) [97] . The genome consists of many ORFs. Two thirds of the 5 end is occupied by a replicase gene comprising two overlapping ORFs namely-ORF1a and ORF1b. The four structural proteins are spike glycoprotein (S), small envelope protein (E), membrane glycoprotein (M) and nucleocapsid (N). Accessory regions that are group specific ORFs are designated as ORF3, ORF4a, ORF4b and ORF5 [97] (Figure 5B ).

Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

Middle East respiratory syndrome (MERS) coronavirus is an enveloped, positive-sense, singlestranded RNA virus that was identified for the first time in 2012 in Saudi Arabia. The viral respiratory disease was caused by a novel coronavirus. The causative coronaviruses (CoV) belong to the lineage C of the Betacoronavirus within the family Coronaviridae. MERS-CoV can infect a broad range of mammals, including humans and is transmitted by the infected dromedary camels [98, 99] . Typical MERS symptoms are similar to the common flu but in some patients, pneumonia and gastrointestinal symptoms including diarrhea and organ failure were reported [100] . Since September 2012 to August 2018, 2253 MERS-CoV cases including 840 deaths were reported in 27 countries worldwide [101] . Approximately 35% of patients with MERS-CoV infection have died.
Alterations in the coronavirus spike glycoprotein by means of natural and experimentally induced mutations changed cell and organ tropism and virus pathogenicity. The wild-type MERS-CoV spike glycoprotein precursor contains 1353 amino acids arranged into two subunits-an aminoterminal subunit (S1) carrying the receptor binding domain (RBD) and a carboxy-terminal subunit (S2) containing the putative fusion peptide (FP/IFP), two heptad repeat domains (HR1/HR2) and the transmembrane (TM) and intracellular domains ( Figure 6 ).
Middle East respiratory syndrome (MERS) coronavirus is an enveloped, positive-sense, single-stranded RNA virus that was identified for the first time in 2012 in Saudi Arabia. The viral respiratory disease was caused by a novel coronavirus. The causative coronaviruses (CoV) belong to the lineage C of the Betacoronavirus within the family Coronaviridae. MERS-CoV can infect a broad range of mammals, including humans and is transmitted by the infected dromedary camels [98, 99] . Typical MERS symptoms are similar to the common flu but in some patients, pneumonia and gastrointestinal symptoms including diarrhea and organ failure were reported [100] . Since September 2012 to August 2018, 2253 MERS-CoV cases including 840 deaths were reported in 27 countries worldwide [101] . Approximately 35% of patients with MERS-CoV infection have died.
Alterations in the coronavirus spike glycoprotein by means of natural and experimentally induced mutations changed cell and organ tropism and virus pathogenicity. The wild-type MERS-CoV spike glycoprotein precursor contains 1353 amino acids arranged into two subunits-an amino-terminal subunit (S1) carrying the receptor binding domain (RBD) and a carboxy-terminal subunit (S2) containing the putative fusion peptide (FP/IFP), two heptad repeat domains (HR1/HR2) and the transmembrane (TM) and intracellular domains ( Figure 6 ).
Middle East respiratory syndrome (MERS) coronavirus is an enveloped, positive-sense, singlestranded RNA virus that was identified for the first time in 2012 in Saudi Arabia. The viral respiratory disease was caused by a novel coronavirus. The causative coronaviruses (CoV) belong to the lineage C of the Betacoronavirus within the family Coronaviridae. MERS-CoV can infect a broad range of mammals, including humans and is transmitted by the infected dromedary camels [98, 99] . Typical MERS symptoms are similar to the common flu but in some patients, pneumonia and gastrointestinal symptoms including diarrhea and organ failure were reported [100] . Since September 2012 to August 2018, 2253 MERS-CoV cases including 840 deaths were reported in 27 countries worldwide [101] . Approximately 35% of patients with MERS-CoV infection have died.
Alterations in the coronavirus spike glycoprotein by means of natural and experimentally induced mutations changed cell and organ tropism and virus pathogenicity. The wild-type MERS-CoV spike glycoprotein precursor contains 1353 amino acids arranged into two subunits-an aminoterminal subunit (S1) carrying the receptor binding domain (RBD) and a carboxy-terminal subunit (S2) containing the putative fusion peptide (FP/IFP), two heptad repeat domains (HR1/HR2) and the transmembrane (TM) and intracellular domains ( Figure 6 ). Lu et al. isolated a diverse population comprising the wild-type and a variant carrying a deletion of 530 nucleotides in the spike glycoprotein gene from the serum of a 75-year-old patient in Taif, Saudi Arabia. The patient subsequently died. Analysis of the MERS-CoV sequence showed an out of frame deletion which led to the loss a large part of the S2 subunit. It contained all the major structures of the membrane fusion in the S2 subunit preceding the early stop codon [103] and this also included the proposed fusion peptide (949-970 aa) [104] . The deletion resulted in the production of a shortened protein bearing only 801 amino acids. In the cell-free serum sample of the patient, mutant genomes with the S530∆ were abundant with an estimated ratio of 4:1 deleted to intact sequence reads. The spike gene deletion would cause the production of a defective virus which was incapable of causing infections or with a lowered rate of infection. Losing the S2 subunit caused a disruption in the membrane holding the spike protein and halted the fusion of the virus to the host. However, in the case of the mutant bearing the S530∆, the mutation helped to sustain the wild-type MERS-CoV infection by producing a free S1 subunit with a "sticky" hydrophobic tail and the additional disulfide bonds caused the aggregation and mis-folding of proteins. In addition, the mutated S530∆ could form steady trimer complexes that retained biding affinity for the dipeptidyl peptidase 4 (DPP4) and acted as a decoy such that the spike-specific MERS-CoV neutralizing antibodies were blocked.
Scobey et al. reported the T1015N mutation in the spike glycoprotein during 9 passages of the virus was able to alter the growth kinetics and plaque morphology in vitro. The mutated MERS-CoV virus (MERS-CoV T1015N) replicated approximately 0.5 log more effectively and formed larger plaques compared to the wild type (MERS-CoV). The data suggested that the mutation T1015N was a tissue culture-adapted mutation that arose during serial in vitro passages [107] . The whole genome sequencing of MERS-CoV revealed the presence of sequence variants within the isolate from dromedary camels (DC) which indicated the existence of quasispecies present within the animal. A single amino acid (A520S) was located in the receptor-binding domain of the MERS-CoV variant. Strikingly, when detailed population analysis was performed on samples recovered from human cases, only clonal genomic sequences were reported. Therefore, the study speculated that a model of interspecies transmission of MERS-CoV whereby specific genotypes were able to overcome the bottleneck selection. While host susceptibility to infection is not taken into account in this setting, the findings provided insights into understanding the unique and rare cases of human of MERS-CoV [108] .

Paramyxoviridae

Paramyxoviridae is a family of viruses in the order Mononegavirales that uses vertebrates as their natural hosts. Currently, 72 species are placed in this family and they are divided amongst 14 genera [109] . Diseases associated with Paramyxoviridae included measles (MeV), mumps and Newcastle disease (NDV). Paramyxoviridae virions are enveloped and pleomorphic which are presented as spherical or filamentous particles with diameters of around 150 to 350 nm ( Figure 7A ). The genome is linear, negative-sense single-stranded RNA, about 15-19 kb in length and encode 9-12 proteins through the production of multiple proteins from the P gene ( Figure 7B ) [110] . On the external surface of the virion, glycoproteins possessing hemagglutinin, neuraminidase and cell fusion activities are present. The middle component of the envelope is a lipid bilayer acquired from the host cell as the virus buds off the cytoplasmic membrane. The innermost surface of the envelope is a non-glycosylated membrane protein layer that maintains the outer structure of the virus. The paramyxoviruses can be characterized by the gene order of the viral proteins and by the biochemical characteristics of the proteins associated with viral attachment. Figure 7A ). The genome is linear, negative-sense single-stranded RNA, about 15-19 kb in length and encode 9-12 proteins through the production of multiple proteins from the P gene ( Figure 7B ) [110] . On the external surface of the virion, glycoproteins possessing hemagglutinin, neuraminidase and cell fusion activities are present. The middle component of the envelope is a lipid bilayer acquired from the host cell as the virus buds off the cytoplasmic membrane. The innermost surface of the envelope is a nonglycosylated membrane protein layer that maintains the outer structure of the virus. The paramyxoviruses can be characterized by the gene order of the viral proteins and by the biochemical characteristics of the proteins associated with viral attachment. The L protein which is the catalytic subunit of RNA-dependent RNA polymerase (RDRP) is associated with the nucleocapsid protein (N) and phosphoprotein (P) to form part of the RNA polymerase complex. The RNA polymerase complex is covered by the viral envelope consisting of a matrix protein (M) and two glycosylated envelope spike proteins, a fusion protein (F) and cell attachment protein. Cell attachment protein is different based on the genera and it could be hemagglutinin (H in Measles), hemagglutinin-neuraminidase (HN in Mumps and NDV viruses) or glycoprotein G (Henipavirus). Some genera within the Paramyxoviridae family also contain various conserved proteins including the non-structural proteins (C, NS1, NS2), a cysteine-rich protein (V), a small integral membrane protein (SH) and transcription factors M2-1 and M2-2 [111] .
Fusion and cell attachment proteins are large glycoprotein spikes that are present on the surface of the virion. Both of these proteins play important roles in the pathogenesis of viruses from Paramyxoviridae family and are responsible for attachment to the cellular receptor(s), whereas the F protein mediates cell entry by inducing fusion between the viral envelope and the host cell membrane. The matrix protein organizes and sustains the virion structure. The nucleocapsid associates with genomic RNA and protects the RNA from nucleases. Extracistronic (noncoding) regions include a 3′ leader sequence with 50 nucleotides in length, which works as a transcriptional promoter and a 5′ trailer with 50-161 nucleotides [111] .
The genomes of viruses within the family Paramyxoviridae are non-segmented and thus cannot undergo genetic reassortment. Like many other RNA viruses, the RNA-dependent RNA polymerase does not have an error proofreading capability and hence many mutations can occur when the RNA is processed. These mutations can build up in the genome and eventually give rise to new variants. Since each protein has an important function, the mutant viruses will exhibit a loss in viral fitness and are eliminated, leaving only those exhibiting good viral fitness [111] . Within the Paramyxoviridae family, mutations leading to a spectrum of mutant distributions among Measles virus, Mumps virus and Newcastle disease virus are reviewed. The L protein which is the catalytic subunit of RNA-dependent RNA polymerase (RDRP) is associated with the nucleocapsid protein (N) and phosphoprotein (P) to form part of the RNA polymerase complex. The RNA polymerase complex is covered by the viral envelope consisting of a matrix protein (M) and two glycosylated envelope spike proteins, a fusion protein (F) and cell attachment protein. Cell attachment protein is different based on the genera and it could be hemagglutinin (H in Measles), hemagglutinin-neuraminidase (HN in Mumps and NDV viruses) or glycoprotein G (Henipavirus). Some genera within the Paramyxoviridae family also contain various conserved proteins including the non-structural proteins (C, NS1, NS2), a cysteine-rich protein (V), a small integral membrane protein (SH) and transcription factors M2-1 and M2-2 [111] .
Fusion and cell attachment proteins are large glycoprotein spikes that are present on the surface of the virion. Both of these proteins play important roles in the pathogenesis of viruses from Paramyxoviridae family and are responsible for attachment to the cellular receptor(s), whereas the F protein mediates cell entry by inducing fusion between the viral envelope and the host cell membrane. The matrix protein organizes and sustains the virion structure. The nucleocapsid associates with genomic RNA and protects the RNA from nucleases. Extracistronic (noncoding) regions include a 3 leader sequence with 50 nucleotides in length, which works as a transcriptional promoter and a 5 trailer with 50-161 nucleotides [111] .
The genomes of viruses within the family Paramyxoviridae are non-segmented and thus cannot undergo genetic reassortment. Like many other RNA viruses, the RNA-dependent RNA polymerase does not have an error proofreading capability and hence many mutations can occur when the RNA is processed. These mutations can build up in the genome and eventually give rise to new variants. Since each protein has an important function, the mutant viruses will exhibit a loss in viral fitness and are eliminated, leaving only those exhibiting good viral fitness [111] . Within the Paramyxoviridae family, mutations leading to a spectrum of mutant distributions among Measles virus, Mumps virus and Newcastle disease virus are reviewed.

Measles Virus (MeV)

Measles virus belongs to the genus Morbillivirus within the family Paramyxoviridae of the order Mononegavirales. Measles is transmitted by air or by direct contact with body fluids. The initial site of viral infection is the respiratory tract, followed by dispersions in the lymphoid tissue, liver, lungs, conjunctiva and skin. The measles virus (MeV) may persist in the brain, causing fatal neurodegenerative diseases. This virus can only infect humans and causes subacute sclerosing panencephalitis and encephalitis [112] [113] [114] . Measles often lead to fatality in young children (below 5 years) due to complications in respiratory tract infections like pneumonia, brain swelling or encephalitis, dehydration, diarrhea and ear infections [115] .
The MeV is a negative sense single stranded RNA virus and the genome is composed of six contiguous, non-overlapping transcription units separated by three untranscribed nucleotides. The genes which code for eight viral proteins are in the order of 5 -N-P/V/C-M-F-H-L-3 [116] . The second transcription unit (P) codes for two non-structural proteins, C and V, which interfere with the host immune response [117] [118] [119] [120] .

Mumps

Mumps virus belongs to the genus nus Rubulavirus within the Paramyxoviridae family of the order Mononegavirales. Mumps is an extremely contagious, acute, self-limited, systemic viral infection that primarily affects swelling of one or more of the salivary glands, typically the parotid glands. The infection could cause pain in the swollen salivary glands on one or both sides of patient face, fever, headache, muscle aches, weakness, fatigue and loss of appetite. Complications of mumps are rare but they can be potentially serious involving inflammation and body swelling in testicles, brain, spinal cord or pancreas. Infections can lead to hearing loss, heart problems and miscarriage. In the United States, mumps was one of common disease prior to vaccination became routine. Then a dramatic decrease was observed in the number of infections. However, mumps outbreaks still occur in the United States and there was an increase in the number of cases recently. Majority of those who are not vaccinated or are in close-contact with the viruses in schools or college campuses are at high risk. There is currently no specific treatment for mumps [122] .
The strain Urabe AM9 is one of the mumps virus strains that was widely used in vaccines but this strain was associated with meningitis and was withdrawn from the market. Sauder et al. performed serial passaging of the strain Urabe AM9 in cell cultures and compared the whole nucleotide sequences of the parental (Urabe P-AM9) and passaged viruses (Urabe P6-Vero or Urabe P6-CEF) to investigate the attenuation process and to identify the attenuation markers [123] . Passaging of the Urabe AM9 mumps virus in Vero or chicken embryo fibroblast (CEF) cell lines caused changes in the genetic heterogeneity at particular regions of the genome through either changing of one nucleotide at locations where the starting material showed nucleotide heterogeneity or the presentation of an additional nucleotide to produce a heterogenic site. Virulence of the passaged virus was dramatically decreased in the murine model. Moreover, similar growth kinetics of the virulent Urabe P-AM9 and passaged attenuated variants in the rat brain suggested that the impaired replication ability of the attenuated variants was not the main cause of the neuroattenuation. However, in the rat brain, the peak titer of the neuroattenuated variant was almost one log lower than that of the neurovirulent parental strain. For instance, identical but independent induction of heterogeneity at position 370 of the F-gene by substitution of threonine to alanine in passaged virus in Vero and CEF cells suggested a correlation of this mutation to the neuroattenuation phenotype. There was lack of ability to identify heterogeneity for those regions with differences of more than 10% between the detected nucleotides in the consensus sequence. The heterogeneity could be the result of new mutations at these positions or the selection of pre-existing sequences within the minority quasispecies. In addition, passaging of the parental strain in CEF and Vero cells led to the observation of several amino acid alterations in the NP, P, F, HN and L proteins that could affect the virulence of the virus. Thus, the modifications of genetic heterogeneity at particular genome sites could have important consequences on the neurovirulence phenotype. Therefore, extra caution should be exercised in order to evaluate genetic markers of virulence or attenuation of variants based on only a consensus sequence [123] .

Newcastle Disease Virus (NDV)

Newcastle disease virus (NDV) belongs to the genus Avulavirus in the family Paramyxoviridae of the order Mononegavirales. NDV is an avian pathogen that can be transmitted to humans and cause conjunctivitis and an influenza like disease [124] . Clinical diseases affecting the neurological, gastrointestinal, reproductive and respiratory systems are detected in naïve, unvaccinated or poorly vaccinated birds [125] . NDV is a continuous problem for poultry producers since it was identified ninety years ago. It has negatively impacted the economic livelihoods and human welfare through reducing food supplies and many countries were affected since 1926 with NDV outbreaks [126] .
The NDV genome codes for seven major viral proteins in the order of 5 -N-P(V)-M-F-HN-L-3 . In NDV, the hemagglutinin neuraminidase (HN) and fusion (F) glycoproteins are presented on the surface of the virion envelope and contribute to viral infection [127] . The fusion protein is expressed as an inactive precursor (F0) prior to activation by proteolytic cleavage. The cleavage of F0 is crucial for infectivity and works as a key virulence indicator for certain viruses such as virulent strains of avian paramyxovirus 1 (NDV). The F0 cleavage site contains several basic residues which cause the cleavage of the F protein by furin, an endopeptidase present in the trans-Golgi network [110] .

Pneumoviridae

The Pneumoviridae family contains large enveloped negative-sense RNA viruses. Previously, this taxon was known as a subfamily of the Paramyxoviridae but it was reclassified in 2016 as a family of its own with two genera, Orthopneumovirus and Metapneumovirus. Some viruses belonging to Pneumoviridae family are only pathogenic to humans, such as the human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV). Human pneumoviruses do not have animal reservoirs and their primary site of infection is the superficial epithelial cells of the respiratory tract. There are no known vectors for pneumoviruses and transmission is thought to be primarily by aerosol droplets [132] .
The virions of the pneumoviruses are enveloped with a spherical shape and a diameter of about 150 nm. They have a negative-sense RNA genome of 13 to 15 kb ( Figure 8A ). The RNA-dependent RNA polymerase (L) binds to the genome at the leader region and sequentially transcribes each gene. The cellular translation machinery translates the capped and poly-adenylated messenger RNA of the virus in the cytoplasm. Members of the genus Orthopneumovirus possess 10 genes including NS1 and NS2 which are promoter proximal to the N gene. The gene order is NS1-NS2-N-P-M-SH-G-F-M2-L ( Figure 8B ). Alignment of the L proteins showed moderate conservation of the sequences between the human and bovine viruses. Bovine respiratory syncytial virus (BRSV) differs from HRSV in host range and the two viruses bear substantially similar sequences as well as antigenic relatedness [132] . Figure 8B ). Alignment of the L proteins showed moderate conservation of the sequences between the human and bovine viruses. Bovine respiratory syncytial virus (BRSV) differs from HRSV in host range and the two viruses bear substantially similar sequences as well as antigenic relatedness [132] .

Respiratory Syncytial Virus (RSV)

Respiratory syncytial virus (RSV) belongs to the genus Orthopneumovirus under the family Pneumoviridae of the order Mononegavirales. Human respiratory syncytial virus (HRSV) is the primary cause of infection of the upper and lower respiratory tracts with mild, cold-like symptoms in infants and young children. The virus spreads through tiny air droplets. Globally, there are 4-5 million children younger than 4 years with HRSV infections and more than 125,000 are hospitalized every year in the United States. Although the risk of hospital admission is higher in known risk groups such as prematurely born infants. RSV is also responsible for 14,000 deaths in the elderly > 65 years of age annually in the United State [133, 134] . On the other hand, bovine respiratory syncytial virus (BRSV) is a common source of pneumonia in calves. Clinical infections stem from yearly outbreaks of the disease during winter and primarily affect calves less than 6 months of age. The target infection site of the viruses are the epithelial layer of the upper and lower respiratory tracts that can damage the bronchioles, leading to severe onset of bronchiolitis in caws [135] .
Palivizumab (PZ) is the sole humanized monoclonal antibody against an infectious disease that recognizes the fusion protein of respiratory syncytial virus (RSV). Zhao et al. selected a PZ resistant virus by passaging of RSVA2 strain in the presence of PZ in HEp-2 cell culture [136] . Utilization of PZ provided the opportunities to gain new insights into the transmission dynamics and the quasispecies nature of RSV. Protein sequence analysis of a single plaque (MP4) isolated from the fifth passage revealed the substitution of lysine by methionine 272. The mutation caused the cell culturederived virus to be completely resistant to PZ prophylaxis in cotton rats. Dramatic reduction in replication of the parental strain A2 virus was observed at PZ concentrations ranging from 4 to 40
Respiratory syncytial virus (RSV) belongs to the genus Orthopneumovirus under the family Pneumoviridae of the order Mononegavirales. Human respiratory syncytial virus (HRSV) is the primary cause of infection of the upper and lower respiratory tracts with mild, cold-like symptoms in infants and young children. The virus spreads through tiny air droplets. Globally, there are 4-5 million children younger than 4 years with HRSV infections and more than 125,000 are hospitalized every year in the United States. Although the risk of hospital admission is higher in known risk groups such as prematurely born infants. RSV is also responsible for 14,000 deaths in the elderly > 65 years of age annually in the United State [133, 134] . On the other hand, bovine respiratory syncytial virus (BRSV) is a common source of pneumonia in calves. Clinical infections stem from yearly outbreaks of the disease during winter and primarily affect calves less than 6 months of age. The target infection site of the viruses are the epithelial layer of the upper and lower respiratory tracts that can damage the bronchioles, leading to severe onset of bronchiolitis in caws [135] .
Palivizumab (PZ) is the sole humanized monoclonal antibody against an infectious disease that recognizes the fusion protein of respiratory syncytial virus (RSV). Zhao et al. selected a PZ resistant virus by passaging of RSVA2 strain in the presence of PZ in HEp-2 cell culture [136] . Utilization of PZ provided the opportunities to gain new insights into the transmission dynamics and the quasispecies nature of RSV. Protein sequence analysis of a single plaque (MP4) isolated from the fifth passage revealed the substitution of lysine by methionine 272. The mutation caused the cell culture-derived virus to be completely resistant to PZ prophylaxis in cotton rats. Dramatic reduction in replication of the parental strain A2 virus was observed at PZ concentrations ranging from 4 to 40 µg/mL. The replication of the MP4 mutant was not affected by PZ. The growth kinetics of both the parental strain and the variant were almost similar with maximum titers above 10 7 PFU/mL during the third and fourth day post infection. Hence, it was proposed that the fusion protein supported the entry of the MP4 mutants in HEp-2 cells in an early phase of the replication cycle through a fusion step. The A2 parental strain exhibited limited growth in HEp-2 cells due to its reactivity with PZ. However, the lack of reactivity of the MP4 mutants with PZ suggested that the F1 protein of the MP4 mutant caused a loss of antigenic reactivity with the humanized monoclonal antibody. Preclinical studies in cotton rats predicted the efficacy of PZ in humans. However, the usage of PZ up to 40 µg/mL, especially in immunosuppressed patients, could provide opportunities for the emergence of resistant viruses. Therefore, the PZ resistant viruses in humans could cause the PZ prophylaxis to be ineffective.
Larsen et al. analyzed the nucleotides coding for the extracellular part of the G glycoprotein and the full SH protein of bovine respiratory syncytial virus (BRSV) from several outbreaks from the same herd in different years in Denmark. Identical viruses were isolated within a herd during outbreaks but viruses from recurrent infections were found to vary up to 11% in sequences even in closed herds. It is possible that a quasispecies variant of BRSV persisted in some of the calves in each herd and this persistent variant displayed high viral fitness and became dominant. However, based on the high level of diversity, the most likely explanation is that BRSV was reintroduced into the herd prior to each new outbreak. These findings are highly relevant to understand the transmission patterns of BRSV among calves [138] .

Orthomyxoviridae

The family Orthomyxoviridae belongs to the order of Articulavirales and contains seven genera-Influenza A-D, Isavirus, Thogotovirus and Quaranjovirus. The virions within the Orthomyxoviridae family are usually spherical but can be filamentous, 80-120 nm in diameter ( Figure 9A ). The influenza virus genome is 12-15 kb and contains 8 segments of negative-sense, single-stranded RNA which encodes for 11 proteins (HA, NA, NP, M1, M2, NS1, NEP, PA, PB1 and PB2) ( Figure 9B ). Influenza viruses are pathogenic and they can cause influenza in vertebrates, including birds, humans and other mammals [139] . The genome fragments contain both the 5 and 3 terminal repeats which are highly conserved throughout all eight fragments.

Influenza Virus (IV)

The epidemiology and molecular characterization of low and highly pathogenic avian influenza virus strains (LPAIV & HPAIV, respectively) isolated from Germany were investigated. The complete genome analysis of the two strains showed that both LPAIV and HPAIV had high nucleotide similarity with only ten mutations outside the hemagglutinin cleavage site (HACS) which were Orthomyxoviruses employ many different splicing techniques to synthesize their viral proteins while making full use of the coding capacity of the genome. The virion envelope originates from the cell membrane with the addition of one to three virus glycoproteins and one to two non-glycosylated proteins. The viral RNA polymerase (PB1, PB2 and PB3) is involved in the transcription of a single mRNA from every fragment of the genome. The transcription is triggered by cap snatching and the poly(A) tail is added by the viral polymerase stuttering on the poly U sequence. Alternative splicing of the MP and NS mRNA led to the mRNA coding for M2 and NEP proteins. PB1-F2 is translated by leaky scanning from the PB1 mRNA. The structural proteins common to all genera include three polypeptides, the hemagglutinin which is an integral type I membrane glycoprotein involved in virus attachment, the envelope fusion and the non-glycosylated matrix protein (M1 or M) [140] .
The epidemiology and molecular characterization of low and highly pathogenic avian influenza virus strains (LPAIV & HPAIV, respectively) isolated from Germany were investigated. The complete genome analysis of the two strains showed that both LPAIV and HPAIV had high nucleotide similarity with only ten mutations outside the hemagglutinin cleavage site (HACS) which were spread along the six genome segments of the HPAIV. Of the ten mutations, five were previously identified as minor variants in the quasispecies population of the progenitor virus, LPAIV, with 18-42% significant variable frequency [144] . However, studies focusing on the diversity of quasispecies of avian influenza in the human host are few. Watanabe et al. successfully demonstrated that infections caused by a single-virus in vitro produced an evident spectra of mutants in the H5N1 progeny viruses. Analysis of the genetic diversity of the hemagglutinin (HA) revealed that variants with mutated HA had lower thermostability leading to higher binding specificity. Both traits were deemed beneficial for viral infection. On the other hand, other variants with higher thermostability also emerged but were unable to thrive against mutants with lower thermostability [145] . The quasispecies population of influenza A virus was also reported to be in a state of continuous genetic drift in a given subtype population. A viral single nucleotide polymorphism (vSNP) was reported to be important and was shared by more than 15% of the variants within the quasispecies population of the subtype strain in a given season. However, between the season 2010-2011, various vSNPs in the PB2, PA, HA, NP, NA, M and NS segments were shared among variants with more than 58-80% of the sample population and less than 50% of the shared vSNPs were located within the PB1 segment [146] .

Hepadnaviridae

Hepadnaviruses can be found within the family Hepadnaviridae. They are further classified into two genera-the mammalian genus Orthohepadnavirus and the avian genus Avihepadnavirus [149] . These viruses are spherical with 42-50 nm diameter and replicate their genomes with the help of a reverse transcriptase (RT) ( Figure 10A ). The approximate size of the DNA genome is 3.3 kb with a relaxed circular DNA (rcDNA) supported by base pairing complementary overlaps [150] . The DNA genome is made up of four partly or completely overlapping ORFs that encode for the core protein (Core and preCore), surface antigen protein (PreS1, PreS2 and S), the reverse transcriptase (Pol protein) and the X transcriptional transactivator protein [151] (Figure 10B ). Replication occurs by reverse transcription of the progenitor RNA by the RNA polymerase II from the covalently close circular form of the HBV DNA [152] .

Hepatitis B Virus (HBV)

Hepatitis B virus (HBV) is the prototype of hepadnaviruses. It infects humans and can be classified into 8 genotypes. More than one billion people have contracted hepatitis B virus (HBV) and more than 200 million patients are chronically infected with hepatitis B (CHB) [153] . CHB infections result in the development of hepatocellular carcinoma and chronic liver failure [151] and every year CHB causes 880,000 deaths worldwide [153] . Analysis of the immunodominant motifs of the HBV core region from the amino acids 40 to 95 indicated that the positions exhibiting peak rates of variability were found in the main core epitopes, thereby confirming their role in stimulating the immune system. Moreover, the distribution of the variability was observed to occur in a genotypedependent manner. For instance, HBV isolated from genotype A had higher variability within the core epitope regions but no significant differences in genotype D were observed in the core epitopes and other positions. Further sequential analysis of the samples put forth the dynamic nature of the HBV quasispecies whereby a strong selection for a single baseline variant was linked to a lower variability within the core region pre-and post-treatment. Leucine (L) at position 76 was determined to be the most highly conserved residue and the role of this amino acid was assessed by substitutions of Valine (V) or Proline (P) at position 76. Proline at position 76 was shown to drastically lower the production of Hepatitis B core antigen protein (HBsAg), likely due to the chemical and physical properties of the amino acid. However, substitution with Valine (V) at a similar position brought about a four-fold increase in the Hepatitis B e antigen protein (HBeAg) production when compared to Leucine at position 76. The decrease in the variability observed was associated with a stable quasispecies population after positive selection of the variant exhibiting high fitness level [154] .
Although a significant number of RNA viruses demonstrated the existence of quasispecies in their populations due to their low-fidelity polymerases, the phenomenon of quasispecies has been reported to exist in DNA viruses such as Hepatitis B virus (HBV) that replicates via a RNA intermediate.
Hepatitis B virus (HBV) is the prototype of hepadnaviruses. It infects humans and can be classified into 8 genotypes. More than one billion people have contracted hepatitis B virus (HBV) and more than 200 million patients are chronically infected with hepatitis B (CHB) [153] . CHB infections result in the development of hepatocellular carcinoma and chronic liver failure [151] and every year CHB causes 880,000 deaths worldwide [153] . Analysis of the immunodominant motifs of the HBV core region from the amino acids 40 to 95 indicated that the positions exhibiting peak rates of variability were found in the main core epitopes, thereby confirming their role in stimulating the immune system. Moreover, the distribution of the variability was observed to occur in a genotype-dependent manner. For instance, HBV isolated from genotype A had higher variability within the core epitope regions but no significant differences in genotype D were observed in the core epitopes and other positions. Further sequential analysis of the samples put forth the dynamic nature of the HBV quasispecies whereby a strong selection for a single baseline variant was linked to a lower variability within the core region pre-and post-treatment. Leucine (L) at position 76 was determined to be the most highly conserved residue and the role of this amino acid was assessed by substitutions of Valine (V) or Proline (P) at position 76. Proline at position 76 was shown to drastically lower the production of Hepatitis B core antigen protein (HBsAg), likely due to the chemical and physical properties of the amino acid. However, substitution with Valine (V) at a similar position brought about a four-fold increase in the Hepatitis B e antigen protein (HBeAg) production when compared to Leucine at position 76. The decrease in the variability observed was associated with a stable quasispecies population after positive selection of the variant exhibiting high fitness level [154] .
Although a significant number of RNA viruses demonstrated the existence of quasispecies in their populations due to their low-fidelity polymerases, the phenomenon of quasispecies has been reported to exist in DNA viruses such as Hepatitis B virus (HBV) that replicates via a RNA intermediate.

Conclusions

RNA viruses are responsible for numerous outbreaks of viral infections with substantial levels of fatality. We discussed how genetic variants carrying spontaneous mutations could give rise to diverse plaque morphologies in different RNA viruses. How the specific mutations could affect viral replications and have an impact on the virulence of the plaque variants are reviewed. The existence of quasispecies in the viral RNA populations is also explored. Many of the RNA viruses displayed different plaque morphologies and these variants could have arisen from a genetically diverse quasispecies population. Such diverse quasispecies in a population could be a key contributing factor to elevated levels of virulence exhibited by the RNA viruses. Through an extensive analysis of different plaque variants and quasispecies within a population, this study could shed more light on the evolutionary pattern and virulence of RNA viruses. More intricate in vitro and in vivo examination of the phenomenon of quasispecies and the relationship between plaque size determinants and virulence should be undertaken to reveal if serious infections are caused by a single strain or through the combined action of diverse quasispecies carrying different mutations. This can be a valuable tool to characterize the mechanisms that led to viral evolution and adaptation in a host. Eventually, discovering an answer to these concerns might ultimately help to design effective vaccines against the ever-evolving RNA viruses.

Enterovirus 71 (EV-A71)

The course of evolution through which EV-A71 evolves to escape the central nervous system (CNS) was investigated by complete sequencing and haplotype analysis of the strains isolated from the digestive system and the CNS. A novel bottleneck selection was revealed in various environments such as the respiratory system and the central nervous system throughout the dissemination of EV-A71 in the host. Consequently, a dominant haplotype resulting from the bottleneck effect caused a change from viruses harboring VP1-3D to VP1-31G where the amino acid 31 was a favorable site of selection among the circulating EV-A71 sub-genotype C2. VP1-31G was present at elevated levels amongst the population of mutants of EV-A71 in the throat swabs of subjects with severe EV-A71 infections. Furthermore, in vitro studies showed that VP1-31D virus isolates had higher infectivity, fitness and virion stability, which sustained the virus infections in the digestive system. Speculations were that such factors benefitted the virus in gaining added viral adaptation and subsequently enabled viral spread to more tissues. These beneficial abilities could also justify the reduced number of VP1-31D viruses located in the brain following positive selection. The VP1-31G viruses presenting the major haplotype in the central nervous system displayed increased viral fitness and growth rates in neuronal cells. This implied that the VP1-31G mutations aided the spread of the mutant virus in the brain which resulted in serious neurological complications in patients. It was speculated that the fluctuating degree of tissue tropism of EV-A71 at diverse inoculation sites resulted in the bottleneck effect of the viral population having a mutant spectrum. Hence, the adaptive VP1-31G haplotype became dominant in neuronal tissues and once the infection was achieved, VP1-31G viruses expedited bottleneck selection and propagation into the skin and CNS. Among the three minor haplotypes (C to E) which co-existed in various tissues, the minor haplotype C was isolated in the intestinal mucosa and throat swab specimens. The minor haplotype D was isolated from specimens obtained from the respiratory and digestive systems. However, the minor haplotype E appeared in throat swabs and the basal ganglia but not the intestinal mucosa, hence, suggesting that the intestinal mucosa is the initial replication site of the EV-A71. Collectively, these data showed that the EV-A71 quasispecies utilized the dynamic proportion of varying haplotype populations to co-exist, sustained the ability of the population to adapt and enabled the propagation in different tissues. Lastly, the study concluded that the selection of haplotype(s) might be a driving factor in viral dissemination and severity of infections in humans as well as the virulence in EV-A71 infected patients [30] .

Dengue Virus (DENV)

From another perspective, differences in the envelope (E) gene sequence was investigated using the plasma samples of six DENV infected patients. The first account of viral quasispecies of DENV in vivo was reported using clonal sequencing analysis whereby the simultaneous occurrence of diverse variant genomes was observed. The degree of genetic diversity was revealed to fluctuate among patients with the mean proportion being 1.67%. Moreover, out of 10 clones derived from dengue infected plasma, 33 nucleotide substitutions were detected, of which 30 were non-synonymous mutations. Of particular interest, mutations at amino acid residues 290 and 301 resulted in the presence of two stop codons which indicated that genome-defective dengue viruses (5.8%) were also present within the quasispecies population. It was hypothesized that this might have significant impact on the pathogenesis of the dengue virus [39] . Recently, Parameswaran et al. profiled the intra-host viral diversity of samples from 77 patients via whole-genome amplifications of the entire coding region of the DENV-3 genome. A significant difference in the viral makeup between naïve subjects and patients with DENV-3 immunity revealed that the immune repertoire of the host is responsible for the degree of diversity exhibited by the viral population. Subsequently, identification of the hotspots responsible for the intra-host diversity revealed that few spots were crucial for intra-host diversity. The major hotspots for diversity were revealed in more than 59% of the samples at three codon coordinates-amino acid residues 100 and 101 in the M protein and residue 315 in the AB loop of the E Domain III. The residue E 315 was speculated to have arisen as an immune escape variant in response to the pressure exerted by the immune defense mechanism. These findings highlighted the importance of host-specific selection pressures in the evolution of DENV-3 viral population within the host and this could eventually lead to the intelligent design of a vaccine candidate identified from the prevalent escape variants such as those bearing the E 315 [40] . It was reported that within the quasispecies population, amino acid substitutions occurred on the surface of the E protein which was involved in interactions with other oligomers, antibodies and host cell receptors. In particular, two amino acid substitutions at positions E452 and E455 were mapped to the E protein transmembrane domain, E450 to E472, which functioned as the membrane anchor for E protein. Intra-host quasispecies analysis using the E gene sequences also identified several amino acids on the surface of the E protein which altered the properties of the virus. The conformational rearrangements that led to the fusion of the virus and the host cell membrane was altered. The amino acids detected in the quasispecies consensus sequence were observed to be less frequent in the E proteins from patients suffering from mild disease than from patients with severe onset of dengue infection. Thus, the quasispecies might harbor specific variants that are crucial for the pathogenesis of the disease [41] . Understanding the significant molecular determinant of pathogenesis through the analysis of quasispecies could lead to the rational design of a DENV vaccine.

West Nile Virus (WNV)

A small-plaque (SP) variant was picked from a mutant population of WNV isolated from an American crow in New York in 2000. Characterization of this variant in mammalian, avian and mosquito cell lines led to the discovery that the SP variant contained four nucleotides in its genome that differed from the wild-type genome. Two nucleotide changes led to non-synonymous mutations where there was a P54S change in the prM protein and a V61A change in the NS2A protein. Further analysis of the mutations revealed that deletion at the cleavage site of the prM site did not affect virus replication and its release from mammalian BHK cells. However, the progeny of this virus was no longer able to infect BHK cells. A mutation in the prM region of the TBEV was also reported to cause decreased secretion of virus particles with no effect on protein folding. Lower neurovirulence and neuroinvasiveness were reported when mutation A30P occurred in the NS2A region of the isolate. Further sequencing of the isolate showed that most of the small plaque clones initially isolated reverted back to their wild-type sequence at position 625 in the prM region. Remaining isolates reverted at position 3707 in the NS2A region. These findings suggested that the mutation present in the prM region could be responsible for the phenotype of the small plaque. It is probable that the mutation in the NS2A region was responsible for the determination of the plaque size as the mutation in the prM region was sufficient to revert the isolate to the wild-type phenotype [52] .

Chikungunya Virus (CHIKV)

Plaque size is a common feature of viral characterization. Primary isolates of CHIKV containing variants with different plaque sizes were previously reported [70, 71] . Viral variants with different plaque morphology such as small and large plaques had been reported in the 2005 CHIKV outbreak isolates [72] . It is curious how small plaque variants with lower fitness were maintained as a natural viral quasispecies. Plausible explanations indicated that the plaque size might not represent the in vivo growth conditions and that cooperation among variants with different plaque sizes might be required for optimal in vivo replication and transmission fitness. Jaimipak et al. reasoned that if the plaque size did not represent the in vivo growth conditions and the small plaque variants had a similar fitness as the large plaque variants, they would be similarly virulent in a murine model. In order to explore the virulence of the small plaque CHIKV variant in vivo, the pathogenicity of the purified small plaque variant of the CHIKV virus isolated from the sera of the patient in Phang-nga, Thailand in 2009, was tested in neonatal mice [73] . The small plaque variant (CHK-S) showed stable homogenous small plaques after 4 plaque purifications. It also grew slower and produced lower titers when compared with the wild-type virus. After 21 days of infection in the suckling mice with the wild-type and CHK-S variants (injected 103 pfu/mouse), mice which received the CHK-S virus showed 98% survival rate while only 74% of mice survived after infection with the wild-type virus. The small plaque variant of CHIKV obtained by plaque purifications exhibited decreased virulence that makes it appropriate to serve as candidates for live-attenuated vaccine development. The CHIKV variant with the small plaque size formed a major subpopulation in the CHIKV primary isolate during multiple passages in C6/36 cells. This is in line with the reduction of virulence in the suckling mice and indicated that the small plaque variant had reduced in vivo fitness. This suggested that replication cycles in mosquito vectors might play an important role in maintaining the small plaque variant in natural infections. The persistence of the small plaque variant CHK-S clone after multiple passages in C6/36 cells showed that the CHK-S variant might be able to outcompete the large plaque variant when infecting the same cell by an unknown mechanism. Alternatively, small and large plaque variants might cooperate in a way that provided a selective advantage for maintaining the small plaque variant [73] .

Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

The nsp1 was reported to suppress protein synthesis by degrading the host mRNA but viral RNA could circumvent the nsp-1 mediated translational shutoff. Terada et al. showed that the double mutations (A9G/R13A) in the non-structural protein 1a (nsp1) affected viral propagation and the plaque morphology. The size of the plaque in the mutated MERS-CoV was smaller and the infectious titers and intracellular viral RNA were decreased in infected Huh7 or Vero cells when compared to the wild-type virus. The formation of the small plaque variant was due to impairment of viral replication via the disruption of the stem-loop (SL) structure of the RNA. In addition, analysis of the biological properties of the nsp1-A9G/R13A mutant showed that the mutant virus possessed low binding activity at the 5′-UTR and promoted translational shutoff against reporter plasmids with or without 5′-UTR [102] .
The nsp1 was reported to suppress protein synthesis by degrading the host mRNA but viral RNA could circumvent the nsp-1 mediated translational shutoff. Terada et al. showed that the double mutations (A9G/R13A) in the non-structural protein 1a (nsp1) affected viral propagation and the plaque morphology. The size of the plaque in the mutated MERS-CoV was smaller and the infectious titers and intracellular viral RNA were decreased in infected Huh7 or Vero cells when compared to the wild-type virus. The formation of the small plaque variant was due to impairment of viral replication via the disruption of the stem-loop (SL) structure of the RNA. In addition, analysis of the biological properties of the nsp1-A9G/R13A mutant showed that the mutant virus possessed low binding activity at the 5 -UTR and promoted translational shutoff against reporter plasmids with or without 5 -UTR [102] .
The nsp1 was reported to suppress protein synthesis by degrading the host mRNA but viral RNA could circumvent the nsp-1 mediated translational shutoff. Terada et al. showed that the double mutations (A9G/R13A) in the non-structural protein 1a (nsp1) affected viral propagation and the plaque morphology. The size of the plaque in the mutated MERS-CoV was smaller and the infectious titers and intracellular viral RNA were decreased in infected Huh7 or Vero cells when compared to the wild-type virus. The formation of the small plaque variant was due to impairment of viral replication via the disruption of the stem-loop (SL) structure of the RNA. In addition, analysis of the biological properties of the nsp1-A9G/R13A mutant showed that the mutant virus possessed low binding activity at the 5′-UTR and promoted translational shutoff against reporter plasmids with or without 5′-UTR [102] .

Newcastle Disease Virus (NDV)

NDV strains are categorized based on their pathogenicity in chickens as highly virulent (velogenic), intermediately virulent (mesogenic) or nonvirulent (lentogenic). These levels of pathogenicity can be differentiated by the amino acid sequence of the cleavage site in the fusion protein (F0). Lentogenic NDV strains have dibasic amino acids at the cleavage site whereas the velogenic strains contain polybasic residues. Meng et al. studied the changes in virulence of NDV strains, leading to a switch in lentogenic variant (JS10) to velogenic variant (JS10-A10) through 10 serial passages of the virus in chicken air sacs [128] . However, the lentogenic variants (JS10) remained lentogenic after 20 serial passages in chicken embryos (JS10-E20). The nearly identical genome sequences of JS10, JS10-A10 and JS10-E20 showed that after passaging, both variants were directly generated from the parental strain (JS10). Genome sequence analysis of the F0 cleavage site of the parental strain and the passaged variants revealed that the rise in virulence observed in the parental strain (JS10) stemmed from a build-up of velogenic quasispecies population together with a gradual disappearance of the lentogenic quasispecies. The decline of the lentogenic F0 genotypes of 112 -E(G)RQE(G)RL-117 from 99.30% to 0.28% and the rise of the velogenic F0 genotypes of 112 -R(K)RQR(K)RF-117 from 0.34% to 94.87% after 10 serial passages in air sacs was hypothesized to be due to the emergence of velogenic F0 genotypes. Subsequently, this led to the enhancement of virulence in JS10-A10. The data indicated that lentogenic NDV strains circulating among poultry could lead to evolution of the velogenic NDV strain. This velogenic NDV strain has the potential to cause outbreaks due to the difficulty in preventing contact between natural waterfowl reservoirs and sensitive poultry operations.
NDV quasispecies comprised lentogenic and velogenic genomes in various proportions. The change in virulence of the quasispecies composition of JS10 and its variants was investigated by analysis of viral population dynamics. The F0 cleavage site was reported to be the main region in which the majority of amino acid changes had occurred and resulting in an accumulation of variants exhibiting velogenic properties due to serial passages. Furthermore, passaging of the virus caused a transition in the degree of virulence of NDV strains from lentogenic to mesogenic and ultimately an increase of the velogenic type. Therefore, NDV pathogenesis could be controlled by the ratio of avirulent to virulent genomes and their interactions within the chicken air sacs and the embryo. The data clearly demonstrated that the status of the quasispecies population is dependent on the pathogenicity of the NDV [128] . Gould et al. reported the presence of the F0 cleavage sequences of 112 -RRQRRF- 117 and HN extensions of 45 amino acids in virulent Australian NDV strains [129] . Furthermore, the genome analysis of the avirulent field isolates of NDV puts forth the existence of viruses with virulent F0 sequences without causing obvious clinical signs of the disease [130] . Subsequently, Kattenbelt et al. studied the underlying causes that could affect the balance of virulent (pp-PR32 Vir) and avirulent (pp-PR32 Avir) variants throughout viral infections. The variability of the quasispecies population and the rate of accumulation of mutations in vivo and in vitro were analyzed. The in vivo analysis showed that both virulent and avirulent plaque-purified variants displayed a rise in the variability of quasispecies from 26% and 39%, respectively. The error rate in the viral sequences was observed to increase as well, such that one bird out of three displayed virulent viral characteristics ( 112 -RRQRRF-117 ) after passaging of the PR-32 Avir variant. Genome analysis following the in vivo study revealed that a single base mutation occurring in the F0 region led to the switch from RRQGRF to RRQRRF.
On the other hand, in vitro studies showed that the quasispecies distribution of the avirulent isolate harbored 10% of variants bearing the virulent F0 region (RRQRRF). Gene sequence analysis of Australian NDV isolates showed the existence of a novel clade of NDV viruses with the F0 cleavage site sequence of 112 -RKQGRL-117 and the HN region bearing seven additional amino acids. Four field isolates (NG2, NG4, Q2-88 and Q4-88) belonging to the novel clade were propagated for a longer time period in CEF cells prior to sequencing. Analysis revealed the existence of 1-2% of virulent strains with the F0 cleavage site of 112 -RKGRRF-117 in the population [131] .
Quasispecies analysis of all the NDV field isolates in this study showed variable ratios (1:4-1:4000) of virulent to avirulent viral F0 sequences. However, these sequences remained constant in the quasispecies population during replication. It was concluded that the virulent strains present in the quasispecies population did not emerge from an avirulent viral population unless the quasispecies population was placed under direct selective pressure, either by previous infection of the host by other avian viruses or by transient immunosuppression [131] .

Influenza Virus (IV)

The annual influenza epidemics caused about 3 to 5 million cases of severe illness with 290,000 to 680,000 deaths worldwide [141] . Current influenza vaccines have sub-optimal efficacy, as there was a lack of antigenic proximity between the vaccine candidate and the circulating seasonal influenza virus strains. During the 2016-2017 influenza epidemic, the influenza A (H3N2) viruses from the clade 3c.2a were dominant and was associated with severe onset of the disease. The low vaccine efficacy of the 2016-2017 egg-adapted H3N2 (clade 3c.2a) vaccine strain A/Hong Kong/4801/2014 was reported to be due to altered antigenicity [142] . To understand the pathogenesis of A(H3N2) viruses from the 3a.2c clade, it would be of great interest to consider if each infection was being caused by an individual strain or by a swarm of genetically related viruses (quasispecies). This would help to provide an insight into the vaccine coverage and efficacy.
A study investigated the impact of antigenic proximity, genomic substitutions, quasispecies, diversity and reassortment in order to understand the molecular evolution of the influenza A (H3N2) isolated directly from clinical samples. Of the 155/176 whole genomes analyzed, several amino acid substitutions were found to substantially affect the severity of the infection caused by the clade specific viruses. Within the sample, 121 viruses belonged to the genetic clade 3c.2a.1 and eight belonged to 3c.2a2, twenty-four belonged to 3c.2a3, one belonged to 3c.2a4 and one belonged to a different clade 3c.3a. Many distinct substitutions spanning across the whole influenza proteome, HA, NA and non-structural protein 1 were found to be responsible for causing mild and severe disease. Interestingly, two substitutions, V261I and K196E, were found in the NA and the NS1, respectively. These two mutations were found to be particularly significant as they showed the distinction between the strains causing mild and severe infections. Analysis of the clinical isolates showed a difference in a single amino acid residue, 160K within the HA, whereby 14 cases of glycosylation loss was observed within the quasispecies population linked to severity of infection. Moreover, the degree of diversity within the quasispecies population was reported to be elevated in severe cases when compared to mild ones [143] .
The annual influenza epidemics caused about 3 to 5 million cases of severe illness with 290,000 to 680,000 deaths worldwide [141] . Current influenza vaccines have sub-optimal efficacy, as there was a lack of antigenic proximity between the vaccine candidate and the circulating seasonal influenza virus strains. During the 2016-2017 influenza epidemic, the influenza A (H3N2) viruses from the clade 3c.2a were dominant and was associated with severe onset of the disease. The low vaccine efficacy of the 2016-2017 egg-adapted H3N2 (clade 3c.2a) vaccine strain A/Hong Kong/4801/2014 was reported to be due to altered antigenicity [142] . To understand the pathogenesis of A(H3N2) viruses from the 3a.2c clade, it would be of great interest to consider if each infection was being caused by an individual strain or by a swarm of genetically related viruses (quasispecies). This would help to provide an insight into the vaccine coverage and efficacy.
A study investigated the impact of antigenic proximity, genomic substitutions, quasispecies, diversity and reassortment in order to understand the molecular evolution of the influenza A (H3N2) isolated directly from clinical samples. Of the 155/176 whole genomes analyzed, several amino acid substitutions were found to substantially affect the severity of the infection caused by the clade specific viruses. Within the sample, 121 viruses belonged to the genetic clade 3c.2a.1 and eight belonged to 3c.2a2, twenty-four belonged to 3c.2a3, one belonged to 3c.2a4 and one belonged to a different clade 3c.3a. Many distinct substitutions spanning across the whole influenza proteome, HA, NA and non-structural protein 1 were found to be responsible for causing mild and severe disease. Interestingly, two substitutions, V261I and K196E, were found in the NA and the NS1, respectively. These two mutations were found to be particularly significant as they showed the distinction between the strains causing mild and severe infections. Analysis of the clinical isolates showed a difference in a single amino acid residue, 160 K within the HA, whereby 14 cases of glycosylation loss was observed within the quasispecies population linked to severity of infection. Moreover, the degree of diversity within the quasispecies population was reported to be elevated in severe cases when compared to mild ones [143] .
A study aimed to identify the key mechanisms contributing towards co-pathogenesis of BALB/c mice infected with the A(H1N1) quasispecies. It was revealed that the co-evolution of the quasispecies brought about a complex response due to different expressions of the biphasic gene. A significant upregulation of the Ifng was associated with an increased majority of mutants expressing a differentially expressed gene (DEG) named HA-G222 gene. This correlated with the increased levels of pro-inflammatory response observed in the lungs of the mice infected with the quasispecies A(H1N1) [147] . Serial passages of the H1N1 virus was also carried out prior to the analysis of its sequential replication, virulence and rate of transmission. Sequence analysis of the quasispecies in the viral population revealed that from the ninth passage onwards, the presence of five amino acid mutations (A469T, 1129T, N329D, N205K and T48N) in the various gene segments (PB1, PA, NA, NS1 and NEP) was detected. Furthermore, mutations located within the HA region indicated that the genetic makeup of the viral quasispecies was distinctly different in the upper and lower respiratory tracts of the infected pigs [148] .
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Abstract

Oncolytic viruses (OVs) are engineered and/or evolved to propagate selectively in cancerous tissues. They have a dual mechanism of action; direct killing of infected cancer cells crossprimes anticancer immunity to boost the killing of uninfected cancer cells. The goal of the field is to develop OVs that are easily manufactured, efficiently delivered to disseminated sites of cancer growth, undergo rapid intratumoral spread, selectively kill tumor cells, cause no collateral damage and pose no risk of transmission in the population. Here we discuss the many virus engineering strategies that are being pursued to optimize delivery, intratumoral spread and safety of OVs derived from different virus families. With continued progress, OVs have the potential to transform the paradigm of cancer care.

viruses as anticancer drugs

Oncolytic viruses (OVs), evolved and engineered for cancer specificity, are gaining momentum as a new drug class in the fight against cancer. Besides, causing the death of virus-infected cancer cells, the spreading intratumoral (IT) infection can also boost the anticancer immune response, leading to immune destruction of uninfected cancer cells. The paradigm of OVs has been reviewed extensively [1] [2] [3] [4] [5] [6] [7] .
It is well established in several rodent cancer models that a single dose of an effective OV can completely cure disease [8, 9] . This has been shown for DNA and RNA viruses in diverse tumor models. However, while the single shot cure is an exciting prospect for cancer therapy, to date clinical outcomes have typically fallen short of this, and repeat IT virus administration has proven to be a more reliable approach [6, 10] . But there are a number of anecdotal case reports that give credence to the idea that a single shot OV cure may be achievable in clinical practice [4, 11] suggesting that OVs have the potential to transform the practice of oncology.
Based on these clinical advances, development of OVs is rapidly accelerating. The purpose of this review is to discuss the virus engineering approaches and OV performance optimization strategies that are being pursued in the field, and to point out some of the challenges that remain. We believe this perspective will be particularly valuable to virologists entering the field. We apologize to the numerous investigators whose work has not been acknowledged; we are well aware of these omissions but due to space constraints our approach has been choosing illustrative examples that demonstrate the key principles. The review is divided into five main sections: (i) an introduction to viruses and virus engineering, (ii) delivery, (iii) spread, (iv) arming and (v) safety. All five topics are highly interdependent.

engineering viruses: a diversity of platforms

In nature, viruses are continuously evolving and adapting to occupy almost every imaginable biological niche. Viruses infect bacterial, archaea, protist, fungal, plant and animal cells. Their genomes are composed of DNA or RNA, which may be single or double stranded, positive or negative sense, ranging in size from 2 to 300 kb, in complexity from 1 to 300 genes and in capacity for foreign genetic material from a few hundred bases to several kilobases. The particles of viruses from different families also vary enormously in size and structure, ranging from 20 to 1000 nm, from icosahedral to helical symmetry, with or without lipid envelope, integument or matrix and with variable susceptibility to physical disruption. Naturally occurring viruses also offer a vast diversity of virus life cycles, cell entry and replication mechanisms, cell and species tropisms, cycle times, burst sizes, innate immune evasion, apoptosis, antiviral state prevention and immune combat strategies, modes of transmission and pathogenic mechanisms. The diversity of viruses that have been investigated as oncolytic platforms and the different strategies used to improve their efficacy continue to be expanded (Table 1) .
Aside from their differences, viruses share fundamental similarities including their dependence on the host cell to provide a suitable environment for genome amplification, gene expression and progeny virus production and their adaptation to a specific set of host cell conditions and factors such that propagation is precluded in cells that fail to provide the necessary environment. These characteristics allow viruses to be targeted to cancer cells as a self-replicating antineoplastic therapy.

Delivery of Ovs

OV therapy begins with the administration of the virus to the patient just as with any other drug. Several approaches can be taken, each with to optimize oncolytic virotherapy indicated that maximizing delivery, so more tumor cells are infected, has a profound impact on the degree to which the virus must propagate from each infected cell for curative therapy [60] . The higher the number and the more random the dispersion of infectious centers established in a tumor after delivery of virus, the more effective the virus will be, although these parameters must be optimized for each virus and model [61] . IV and IT administrations of OVs are common delivery methods that introduce large amounts of virus into one compartment in a very short time. This rapid delivery of a massive virus inoculum does not parallel what typically occurs in a natural infection and potentially allows the IT spread of the OV infection to outpace host defenses. Successful delivery in the context of an OV infection requires that a critical viral concentration is achieved within the tumor to allow for sufficient oncolysis and systemic spread of the virus to all sites of disease in a safe and reproducible pattern.
• • iv delivery IV delivery of an OV seems advantageous in the setting of metastatic disease, allowing the virus to potentially access all sites of disease via the circulation soon after infusion. In a clinical setting, systemic delivery may be preferred since it is more broadly applicable than IT inoculation, regardless of tumor location and total tumor burden. Yet, attempts at systemic delivery have shown limited success; the administered virus is immediately diluted in the circulating blood volume (∼5 l), so extremely high doses are needed to achieve meaningful circulating titers. A clinical trial using an oncolytic pox virus, JX-594, demonstrated that virus could only be detected in tumors of patients that received at least 10 9 p.f.u. per IV dose without any virus being detected in tumors of the lower dose cohorts of patients [62] . Because of this important dilution effect, doses required for IV therapy may have to be up to 1000-fold higher than for IT administration, which results in significant manufacturing challenges as well as a unique set of toxicities [2] . Administration of high titers of virus intravenously can lead to hepatotoxicity, thrombocytopenia and lymphopenia [33, 63] .
Following the path of an OV from the IV line to the tumor will quickly illustrate some of the challenges for IV delivery. First, the virus is rapidly diluted in the circulation, where its infectivity is neutralized by serum proteins including antibodies and complement, and a large proportion is sequestered by reticuloendothelial phagocytes in the spleen and liver. Any virus particles that reach the tumor vasculature without first being neutralized must then extravasate through fenestrations, and pores between the vascular endothelial cells of the tumor capillaries, and once in the interstitial space of the tumor, must negotiate the extracellular matrix (ECM) to reach and infect the resident cancer cell [64] .
Tumor vasculature can both aid and limit viral access. Tumors typically have an unorganized growth pattern, producing vasculature that is tumultuous and insufficient resulting in heterogeneous perfusion throughout the parenchyma [65] . Decreased perfusion limits the formation of infectious centers evenly throughout a tumor. Manipulating physiological parameters such as blood pressure and systemic vascular resistance can preferentially increase tumor perfusion and promote better delivery of viral vectors [66] . Once in a tumor vessel, the virus must move from the intravascular compartment into the interstitium by crossing the vascular endothelium to continue its journey through the interstitial space until finally reaching a permissive tumor cell.
At least in theory, viruses can cross the endothelial lining of tumor neovessels by diffusion, active infection, or by trafficking inside of or on the surface of marrow-derived cells that are capable of diapedesis. Tumors generally have poor lymphatic drainage and can have leaky blood vessels with a wide range of pore sizes which helps to explain the phenomenon of enhanced permeability and retention of nanoparticles such as OVs in the tumor parenchyma [67] . In some tumors, the pores and fenestrations in tumor capillaries may be large enough to permit passive diffusion of viruses (depending on their size) but in many tumors review Maroun, Muñoz-Alía, Ammayappan, Schulze, Peng & Russell future science group the endothelium is sufficiently organized that this type of extravasation is simply not possible.
Another approach to help OVs' extravasate is by temporally creating pores throughout the tumor microvasculature to enhance transport of the virus into tumor interstitium. This can be done through application of focused ultrasound in the presence of a contrast agent or a polymer. The microbubbles or polymers are injected intravenously and can freely circulate without harming tissues, but when they are exposed to ultrasound waves they can oscillate and induce pore formation or cavitation in the surrounding tissue. The ultrasound can be focused on a tumor just after the infusion of the virus to increase viral extravasation. This has been shown to enhance vaccinia virus delivery to tumor xenografts and can increase viral transgene expression by more than a 1000-fold in the tumor [71, 72] . Many strategies are being developed to enhance OV IV delivery.
• • iT delivery IT administration directly delivers a high concentration of the OV into the parenchyma of the injected tumor but may not result in spread of the virus to distant sites of metastasis. T-Vec is administered by IT injection to accessible skin tumors of patients with metastatic malignant melanoma. The injection is repeated every 2 weeks until lesions have resolved or failed to respond [12, 73] . Interestingly, viremia was not documented in patients, suggesting that the regression of noninjected lesions was likely immune-mediated and not due to direct oncolysis [74] .
Immediately following IT delivery, small levels of virus can be detected in the blood from leakage through injured tumor vasculature [75] , but that small amount of virus is quickly cleared from the system. Also, virus that has been injected into a tumor is frequently extruded immediately from the injection track once the syringe is removed, especially in smaller higher pressure tumors. However, systemic viral spread can occur following IT administration if the initially exposed tumor cells are capable of amplifying the input virus and releasing progeny into the bloodstream. Such secondary viremia may not peak until several days after IT virus delivery and, with currently used OVs, is often not detected. Secondary viremia, when it occurs, more closely mimics the natural propagation of a viral infection from the site of inoculation to more distant target organs.

• Other routes of delivery

Intraperitoneal virus administration is often pursued in virotherapy studies aiming to impact ovarian cancer and other disseminated intraperitoneal malignancies, while intrapleural administration is pursued for mesothelioma therapy. Both of these approaches are similar to IT administration in that the virus comes into direct contact with tumor cells in the injected cavity, although there is a greater risk that input virus will be immediately neutralized by antibodies and other proteins in ascites or pleural fluid. Intravesical instillation of virus is the favored route of administration for treatment of early-stage bladder cancer, requiring only that future science group www.futuremedicine.com the input virus be stable in urine. Also, immediately after brain cancer surgery, in an attempt to control residual disease, virus is often instilled directly into the resection cavity.

• Limiting viral neutralization & clearance

Perhaps the most significant barrier to widespread OV delivery is rapid neutralization and clearance of circulating virus particles. Antibodies and complement proteins can coat the virus blocking its ability to interact with its cellular receptor and accelerate Fc receptor-mediated clearance by splenic macrophages and hepatic Kupffer cells.
For high seroprevalence viruses, one approach to circumvent viral neutralization by preformed antibodies is to engineer or switch the viral coat proteins. Some OVs (e.g., adenovirus) offer a menu of different serotypes, providing a basis for serotype switching between successive doses of the therapy to avoid antibody neutralization, although this does greatly complicate the product development pathway since each serotype is considered to be a distinct pharmaceutical product [82] . For monotypic viruses such as measles, serotype switching is not an option, but antimeasles antibodies can be circumvented by substituting the surface glycoproteins of measles with those of a related but noncross-reactive morbillivirus such as canine distemper virus [83] . Alternatively, the immunodominant epitopes of the measles surface glycoproteins can be modified by mutating key surface residues to eliminate them, or by introducing glycosylation signals so they are shielded by N-linked glycans [84] . It is worth noting that all of these virus engineering strategies have the potential to alter viral receptor usage and hence tumor cell tropism which may limit their utility [83, 85] .
Mengovirus, VSV and Newcastle disease virus are examples of animal pathogens being developed as oncolytic agents. Their appeal as oncolytic platforms is due to the coupling of their ability to selectively propagate in human tumors with their low seroprevalence in the human population [77] . Unlike viruses such as measles which have almost exclusively human cell tropism, these zoonotic viruses are capable of infecting both rodent and human tumor cells allowing preclinical testing in more informative immunocompetent mouse cancer models.
Virus-infected cell carriers can also be used to transport viruses via the bloodstream to sites of tumor growth. In part, this is possible because there is an 'eclipse period' after the cell carriers have been infected during which they do not display viral proteins on their surface and are therefore not bound by virus neutralizing antibody, but are still able to extravasate from tumor neovessels and release infectious progeny into the tumor parenchyma. Several cell carrier/OV combinations have been used including mesenchymal stem cells, dendritic cells, T cells and endothelial progenitor cells [89] [90] [91] [92] . Some carrier cells are believed to home more efficiently to tumors responding to chemotactic signals arising from hypoxia or IT inflammation.

Ov spread

Replication and amplification in the tumor is the major feature that sets OVs apart from other anticancer drugs. No traditional chemotherapy, immunotherapy or small molecule inhibitor can target tumor cells and then amplify at the site of action and spread to other sites of tumor growth. Specificity as well as speed and extent of IT virus replication are the key determinants of therapeutic index (efficacy/toxicity ratio) for an OV therapeutic, and each of these parameters can be modified by virus engineering. Additionally, the kinetics of spread can be impacted by combining the virus with immunomodulatory drugs. The idea of a virus with selective tropism for cancerous tissue has obvious appeal. Even for naturally occurring viruses that have not been tropism modified, a tumor offers a favorable environment to support a productive infection, and this is borne out by case reports of temporary remission or regression of different cancers concurrent with viral infections [4, 93] . There are several reasons why tumors are generally more susceptible than normal tissues to virus attack; poorly developed lymphatics, high nonsuppressible metabolic activity, resistance to apoptosis, poor responsiveness to interferon and intrinsic suppression of immune effector cells. But as we move in the direction of intentionally using virus infections to mediate tumor destruction, it is apparent that a targeted virus with exquisite tumor specificity will be superior to its non targeted counterpart, allowing for the administration of higher tumor destructive doses without toxicity to normal tissues.
Virus tropism is determined by many factors, most of which, if understood sufficiently, can be manipulated to enhance tumor specificity. The receptor tropisms of naturally occurring viruses are rarely of interest for tumor targeting, but this is not true for tissue-culture-adapted vaccine lineage viruses, some of which have evolved in the laboratory to use receptors more abundantly expressed on cancer cells. Examples include the CD46 receptor tropism of vaccine lineage measles virus and the heparan sulfate tropism of laboratory-adapted Sindbis virus [94, 95] . Where greater specificity is desired, it may be possible to engineer new receptor tropisms by modifying the structure of a viral attachment protein, for example, by displaying polypeptide ligands at the extreme C-terminus of the measles H glycoprotein [96, 97] . However, for many viruses, displaying a polypeptide ligand on the surface does no more than redirect attachment and does not confer a new receptor tropism [98] [99] [100] . This remains an area of active investigation.
In addition to their dependence on specific entry receptors, the surface glycoproteins of many enveloped viruses (and sometimes other critical viral proteins) must be proteolytically activated before they are competent to mediate virus entry [101] . By engineering the protease target sequences in these viral glycoproteins it is possible to generate viruses whose propagation is now dependent on exposure to a specific protease with high IT abundance, such as urokinase, matrix metalloproteinase 1 or cathepsin D [102] [103] [104] .
Beyond the step of cell entry, viruses are exquisite sensors of intracellular processes and can therefore be adapted or engineered in several ways for intracellular targeting of cancer cells. This is best understood by considering some fundamental aspects of the interplay between a virus and an infected cell. The incoming virus aims to usurp the cellular synthetic machinery for generation of progeny viruses. The cell resists this takeover bid by rapidly detecting virus invasion, then triggering a signaling cascade that leads to establishment of an antiviral state and release of interferon which induces an anti viral state in adjacent cells [105, 106] . The antiviral state is very complex but suppression of protein translation is a key component. Apoptosis is also triggered by the virus detection machinery so that the infected cell dies before it is able to manufacture virus progeny [107] .
For a virus to be 'successful' it must combat these host cell responses, avoiding detection, as long as possible, for suppressing the establishment of an antiviral state and preventing apoptosis. Virtually all naturally occurring viruses therefore encode proteins that inhibit apop tosis and the antiviral state [108] . Removing these accessory functions from the viral genome leads to virus attenuation in normal tissues, but to a much lesser degree in cancerous tissues. This is because cancer cells are intrinsically resistant to apoptosis and to the establishment of an antiviral state, making them highly susceptible to attenuated viruses that are no longer able to control those processes. This has provided a mechanistic basis for physiologic targeting of several viruses; VSV by mutating the matrix gene whose encoded protein blocks the interferon response [109] ; HSV by mutating both copies of the γ-34.5 gene which interferes with interferonmediated shutoff of host protein synthesis and enhances neurovirulence [110, 111] ; adenovirus by mutating the E1B protein, one of whose actions is to inhibit the apoptotic activity of p53 [112] .
Viruses can be further engineered to exclusively replicate in tumor cells by combining a virus' needs with physiologic peculiarities intrinsic in tumorigenesis. For example, a virally encoded thymidine kinase (TK) is required for HSV and vaccinia virus infection to increase the supply of deoxynucleotide triphosphates required for synthesis of progeny virus genomes [113, 114] . Elimination of the TK future science group www.futuremedicine.com gene from the viral genome restricts viral replication to cancer cells where there is an upregulation of human TK [115, 116] . Another example of a virus that exploits the high replication rate of tumor cells is Toca-511, a replication competent C-type retrovirus encoding the drug activating enzyme cytosine deaminase (CD) [117] . Since the integration of C-type retroviruses is S-phase dependent [118] , this virus is selectively amplified in rapidly proliferating tumor tissue.
Engineering tumor specificity can also be achieved by detargeting viruses to ablate unwanted tropisms that can cause off target pathology in normal tissues. MircroRNA targeting is the best example of this approach. For example, miRNA targeting was used to control the tropism of an oncolytic coxsackievirus A21 virus which caused rapid tumor regression followed by fatal myositis in murine models of myeloma and melanoma [119] . Insertion of muscle-specific miRNA targets into the viral genome eliminated muscle toxicity but left the antitumor potency of the virus intact. This was shown to be due to miRNA-mediated recognition and rapid destruction of the viral genome in muscle cells. miRNA targeting has since been applied to many OVs from diverse virus families and provides a convenient and economical strategy (using sequence insertions of only ∼100 bases) to control unwanted virus tropisms [25] .

• viral amplification & spread

After an appropriately targeted virus has infected a tumor cell, it is the extent of its subsequent propagation that becomes the key driver of potency. Data-driven mathematical models of systemic oncolytic virotherapy indicate that tumor eradication is dependent on two major parameters: the initial density and distribution of infectious foci in the tumor; and the ultimate size of the infectious centers arising from each individual infected cell (i.e., virus spread) [120] . Viral spread may occur by various mechanisms. Local spread may occur by intercellular fusion, by direct transfer of virus from infected to adjacent cells, or by release and local migration of progeny virions through the interstitial space. Systemic spread as free virus particles or as virusinfected migratory cells occurs via lymphatic channels or via the bloodstream.
Direct cell-to-cell transfer of viruses has the advantage of stealth as the virus cannot be neutralized by antiviral antibodies in the interstitial fluid [121] . Nonfusogenic viruses can be armed with fusogenic membrane glycoproteins (FMGs) to enable stealthy spread through intercellular fusion leading to the formation of large, nonviable multinucleated syncytia which may also serve as excellent antigen presenting cells for amplification of the antitumor immune response [122] . By way of example, VSV encoding measles fusogenic glycoproteins and HSVs encoding the fusogenic gibbon ape leukemia virus glycoproteins have shown superior efficacy when compared with their corresponding parental viruses [123, 124] .
In the case of free virus particles, which are susceptible to antibody neutralization, the stroma of the tumor also has the potential to limit IT diffusion and block systemic release. Fibroblasts, endothelial cells, immune cells and the ECM make up the tumor stroma, and the exact composition varies widely depending on tumor type [125] . The ECM is a collagenous matrix of protein fibrils, adhesive proteins and proteoglycans that create a web with pore sizes similar or slightly smaller than virions [126] . Destruction of ECM components can facilitate viral spread throughout the tumor and can be achieved using conventional chemoradiotherapy or by delivering matrix-degrading enzymes such as collagenase and hyaluronidase [127] . An alternative approach is to encode a matrix-degrading enzyme or inducer of matrixdegrading enzymes in the viral genome. For example, hyaluronidase and relaxin encoding oncolytic adenoviruses have each been shown to spread more efficiently in experimental tumors [128] [129] [130] .
Another factor that significantly impacts the kinetics of virus spread is the burst size, or the number of progeny viruses released by a productively infected cell, which varies widely between viral families. Picornaviruses, VSV and vaccinia virus can release up to 10,000 progeny from a single infected cell after a delay of only 6-18 h [131] [132] [133] . In addition to innate antiviral immunity, adaptive cell-mediated immune responses are typically required for the complete elimination of a viral infection and act by eliminating infected cells before progeny can be released. Oncolytic virotherapy can therefore be viewed as a race between the spreading virus and the responding immune system. For this reason, faster moving viral infections are often considered capable of inflicting greater damage to an infected tumor before they can be contained by the immune system [134] . However, in defense of the viruses with smaller burst sizes, or which release progeny by budding, they tend to be less review Maroun, Muñoz-Alía, Ammayappan, Schulze, Peng & Russell future science group rapidly controlled both by the innate and adaptive host immune responses [135] . Therefore, as with the classic race between the hare and the tortoise, it is very difficult to predict whether a fast or slow replicating virus will show superior efficacy in a given preclinical cancer model.

• • Secreted toxins

As a general rule, if a virus is to be armed with a gene encoding a secreted toxin, that toxin should be targeted so that it can kill only cancer cells. In the absence of such targeting, there would be little prospect of avoiding off-target toxicities. Immunotoxins are bifunctional proteins in which plant or bacterial toxins (typically ribosomal inhibitors) are fused to a single chain antibody or other polypeptide domain to target endocytosis in cancer cells [136] . In theory, such molecules that have been extensively investigated and advanced to human clinical trials particularly for the treatment of B-cell and T-cell malignancies [137] , could be expressed from an engineered OV genome.

• • Fusogenic membrane glycoproteins

Fusion of the lipid envelope of an incoming virus with the limiting membrane of its target cell is a necessary step in the life cycle of an enveloped virus, to deliver the encapsidated viral genome into the target cell cytoplasm. This virus-to-cell fusion reaction is mediated by FMGs embedded in the envelope of the virus, and may occur at the cell surface at neutral pH, or in the endo-somal compartment at acidic pH [150] . Neutral pH fusion is triggered by receptor attachment. Cells expressing certain virally encoded, neutral pH-active FMGs on their surface may fuse with neighboring receptor positive cells (cell-to-cell fusion), giving rise to multinucleated syncytia, the hallmark cytopathic signature of a fusogenic virus (e.g., measles) [151] . But more often the FMG is activated only after its incorporation into a budding virus particle, so cannot cause cell-tocell fusion, and must be modified, for example, by cytoplasmic tail truncation, to render it constitutively fusogenic. Either way, FMG-driven fusion of OV-infected cells with uninfected neighboring cells leads to increased bystander killing because multinucleated syncytia are nonviable as well as being highly immunogenic [152] . Based on these observations, nonfusogenic OVs have been armed with FMGs thereby conferring superior oncolytic potency [123, 153] . In one example, an oncolytic herpes virus was rendered highly fusogenic when engineered to encode a cytoplasmically truncated gibbon ape leukemia virus envelope glycoprotein [154] [155] [156] while in another study, an oncolytic VSV was rendered highly fusogenic by replacing its surface glycoprotein (G) with the hemagglutinin and fusion glycoproteins of measles virus.

• • Arming Ovs to amplify antitumor immunity

Each step of the above process can be impacted by virus engineering. Not only can the kinetics and mode of cell killing be manipulated (see the previous section on virus spread), but also the OVs can be armed with a wide variety of immunoregulatory genes whose products will be secreted into the interstitial fluid space. Thus, OVs have been engineered to express the following: high levels of type I interferons to better drive the early innate/inflammatory response; GM-CSF to stimulate the phagocytic activity and lymph node trafficking of professional antigen presenting cells; chemokines to enhance the IT recruitment of immune and inflammatory effector cells, especially cytotoxic T cells; cytokines to drive the activation and proliferation of tumor-resident cytotoxic T cells; bispecific T-cell engagers to enable tumor cell killing by T cells not recognizing tumor antigens; checkpoint inhibitor antibodies to block the protective PD-L1/B7.1 shield that protects tumor cells from T-cell attack; cytokines to increase MHC-peptide neoantigen expression on uninfected tumor cells; or cloned tumor antigens to further amplify tumor-specific immunity [165] .
While each of these approaches has proven beneficial in selected preclinical animal models where immune destruction of the tumor is the dominant OV effect, they are equally likely to decrease potency by speeding virus elimination in situations where the spread of the virus is dominant.

Safety

Engineering viruses for increased stealth, greater specificity, faster spread and enhanced potency is not without risk. As OVs gain new properties, checks and balances must be applied to assure that they do not readily evolve into pathogens, let alone transmissible pathogens that could pose a risk not only to immediate contacts of the treated patient, but also to the greater population.

• • Limiting pathogenicity

Viral cytotoxicity is the basis of tumor cell death necessary for oncolytic activity. Off-target infection and killing of normal cells by poorly targeted OVs or by OVs that have evolved new tropisms in a treated patient can cause unwanted normal tissue pathology. OVs are therefore delicately balanced between retaining enough virulence to substantially decrease tumor burden versus being sufficiently targeted (or attenuated) to not cause a new disease in the patient. Cancer-specific targeting is the most critical safety feature, but viruses evolve and viral populations are dynamic [172] . Evolution is a constant accompaniment of a spreading virus infection, whether or not the virus is oncolytic; in vivo progeny of the therapeutic OV differs on average by a single -point mutation per genome from the input virus [173] . Hence, as the input virus is amplified, it generates a swarm of quasispecies viruses, each one a slightly imperfect replica of the input virus. This swarm of progeny viruses is subjected to selective pressure as it encounters new biological niches in the treated cancer patient. Thus, if it so happens that a member of the swarm is capable of infecting a normal host tissue, the virus may have gained a new foothold from which to further evolve. Gaining new cell tropisms or losing restriction factors is therefore a significant theoretical concern in oncolytic infections, but has not yet been documented in human trials, nor in preclinical models. However, given the importance of this particular scenario, a great deal of attention is paid to the problem not just by investigators, but also by regulatory agencies.
Polymerase infidelity is not the sole driver of virus genome diversification and evolution. For many viruses, recombination between homologous viral genomes can occur when two related viruses infect the same cell [178] . This type of recombination is not a feature of negative strand RNA virus evolution because the nascent progeny viral genomes are cotranscriptionally incorporated into a helical ribonucleocapsid structure which prevents recombination. However, for positive sense RNA picornaviruses, and DNA viruses such as adenovirus, HSV and vaccinia, it is important to consider the possibility that the input virus may encounter and recombine with a homologous 'wild-type' virus in a treated patient. While such recombination has never been documented in OV trials, there are well described examples in the field of vaccinology, such as the re-emergence of pathogenic polioviruses through the recombination of vaccine genomes and naturally circulating picornavirus genomes [179] . In view of these risks, it is generally considered inadvisable to arm viruses with therapeutic transgenes that have theoretical potential to increase pathogenicity if transferred to a related naturally circulating virus. Genes encoding immunosuppressive, antiapoptotic or directly cytotoxic proteins are on this list.
Certain viruses with segmented genomes, most notably the orthomyxoviruses (e.g., influenza), are capable of rapid evolution by genome fragment reassortment in multiple infected cells. Reassortment of genome fragments in virus-infected birds and pigs is considered to be a key driver of the antigenic shifts that occur during evolution of new pathogenic influenza virus strains [180] . This important safety concern may explain why oncolytic influenza viruses have not yet been advanced to human clinical trials [181] . Because of the toxicity risks associated with the proliferative and evolutionary capacity of OVs, there is considerable interest in contingency plans to terminate the spread and/or transmission of an OV infection. Reliable antiviral medications are available for TK-expressing herpes viruses, but this is not the case for the majority of viruses being developed as OV platforms [182, 183] . Attention has therefore been directed to the development of safety switches that can be engineered into the OV genome and triggered on demand to terminate in vivo replication.

• Limiting transmissibility

For obvious reasons OV transmission from a treated patient to a caregiver, family member, coworker, pet or other species is highly undesir-able. Infectious virus particles may be present in the blood of a treated patient, and may be shed into the environment in urine, feces, saliva and other bodily secretions. Contact with the body fluids of an OV-treated patient therefore may have the potential to spread an infection to new hosts [190] .
Because the risks of OV transmission are typically unknown when first-in-human Phase I trials are initiated, it is usual to implement standard infection containment measures throughout these studies and to carefully monitor body fluids for the appearance and disappearance of viral genomes and infectious virus progeny [191] . For certain viruses, containment may be considered unnecessary, particularly when there is already widespread population immunity to the OV in question (e.g., measles) or when there has been extensive human experience of exposure to a related virus in the form of a live viral vaccine (e.g., vaccinia). Contingency plans may also be required calling for quarantine of OV-treated patients if treatment toxicity is associated with a longer period of shedding. In reality, to date there has been no instance in which transmission of an OV from a patient to a caregiver or other contact has been demonstrated, and there are no examples of long-term virus persistence or shedding in a treated patient.
In light of the inconvenience and undesirability of OV shedding, there is interest in engineering strategies that may selectively interfere with the process. As one example, wild-type measles virus is a highly transmissible airborne virus that uses the nectin-4 receptor to enter into airway epithelial cells from whence its progeny are shed into respiratory secretions [192, 193] . Eliminating the nectin-4 tropism by strategically mutating key surface residues in the hemagglutinin attachment protein results in a virus that still causes measles in nonhuman primates, but which is no longer shed into respiratory secretions or urine [194] . Measles virus RNA (but not infectious virus) was detected in the blood, urine and saliva of myeloma patients up to 3 weeks after IV administration of an oncolytic measles virus, especially at higher dose levels, and it is possible that this shedding might be eliminated by using a nectin-4 blind version of the virus [195] . Virus shedding has also been detected in human clinical trials of HSV, reovirus, vaccinia, reovirus and adenovirus oncolytics, but was less readily detected following IT therapy with oncolytic VSV and polioviruses [167] . However, future science group www.futuremedicine.com it should be noted that while genome sequences have been detected in shed material, infectious virus particles have not been recovered.
In an OV-treated patient pre-existing antiviral immunity can be a formidable barrier to efficacy, particularly if the virus is administered intravenously. However, pre-existing antiviral immunity in caregivers and patient contacts provides reassuring protection against virus transmission. Conversely, when this particular efficacy barrier is circumvented by using OVs engineered for antibody evasion or selected for low seroprevalence, the risk of epidemic spread in the human population, unchecked by pre-existing herd immunity, looms larger.
An alternative strategy often used to side step antibody neutralization, at least of the first dose of virus administered, is to use OVs derived from zoonotic animal viruses such as New Castle disease virus (chicken), VSV (cattle), myxomavirus (rabbit), Seneca Valley virus (pig) or mengovirus (e.g., mouse and monkey). Additional regulatory executive summary viruses as anticancer drugs • Viruses naturally possess many properties that favor infection of cancer cells. Enhancing these natural properties and adding new properties through directed evolution and genetic engineering are used to create oncolytic viruses (OVs), which are emerging as a new anticancer drug class.
• The diversity of virus families and engineering techniques allows for the creation of OVs with a wide range of properties that can be tailored for each type of cancer.

Delivery of Ovs

• Intravenous delivery allows a virus to reach distant sites of metastasis via the circulation, but extravasation into the tumor parenchyma is inefficient.
• Intratumoral injection can concentrate virus at a site of tumor growth, but regression of distant tumors requires that the virus spread systemically or induce a systemic antitumor immune response.
• Neutralizing antibodies, hepatosplenic sequestration of the virus by macrophages and dilution of the virus in blood or tissue may limit the effectiveness of treatment.

viral spread

• Targeting viral spread to tumor cells can be accomplished by transductional targeting (modifying receptor tropism), transcriptional targeting (controlling virus gene expression with tumor-specific promoters), physiologic targeting (disrupting viral immune combat proteins), apoptosis targeting (disrupting viral antiapoptotic proteins) or miRNA targeting.

Safety

• Ideally, OVs should be nontransmissible. scrutiny is generally required for these viruses (e.g., from the US Department of Agriculture) to address the additional risks of environmental release and epidemic spread in domestic animals, particularly as they relate to agricultural livestock.

Conclusion & future perspective

Viruses are at last being harnessed for the benefit of cancer patients. The OV field has moved well beyond proof of principle in human studies, and virus engineering will be the key to its continued advancement in the coming years. Virtually every component of every naturally occurring or laboratory-adapted virus can be engineered and/or evolved to enhance its suitability for cancer therapy and we are currently witnessing unstoppable creative activity in this area. Safety is obviously of paramount importance in this relatively new field, and is therefore closely regulated from the design stage to clinical implementation. Considering the current trajectory of OV research, there can be little doubt that viruses are on their way to becoming one of the foundational modalities of future cancer treatment regimens.

viruses as anticancer drugs

In light of recent clinical progress, interest in the approach is burgeoning. One critical milestone was the 2015 marketing approval granted in Europe and the USA for talimogene laherparepvec (T-Vec, Imlygic™), an engineered HSV encoding GM-CSF. This virus, administered intratumorally every 2 weeks for malignant melanoma, led to complete resolution in 47% of injected tumors and boosted systemic antitumor immunity leading to resolution of 9% of distant un infected visceral tumors [12] . Subsequent clinical studies have shown that responses are more frequent and more durable when T-Vec (and other OVs such as coxsackievirus A21) is combined with immune checkpoint For reprint orders, please contact: reprints@futuremedicine.com review Maroun, Muñoz-Alía, Ammayappan, Schulze, Peng & Russell future science group inhibitor antibody therapy [13] . Another significant milestone was the demonstration that a systemically administered oncolytic measles virus can target and destroy disseminated cancer in a human subject [11] .

engineering viruses: a diversity of platforms

As might be expected, proponents of a given OV are typically able to advance strong arguments to support their choice of platform, emphasizing unique features such as replication kinetics, genome plasticity, targetability, seroprevalence and stability that may lead to superior oncolysis. However, it is too early to determine which unique viral characteristics will be the critical drivers of clinical success for a given cancer type. Reverse genetics systems are available for virtually all virus families, and the rules of engagement for new virus creation are well established. In general, the most effective strategy is to combine rational design with evolution, allowing each engineered virus to mutate and fully adapt to its intended target cells after it has been rescued. Biosafety oversight is in place at all academic centers responsibly engaging in virus engineering activities, and it is now a relatively straightforward matter to generate and test new virus configurations using what now amounts to the world's best lego set. Viral gene and noncoding sequences can be modified in a variety of ways to add or eliminate functions and nonviral genes or noncoding regulatory elements, whether synthetic or naturally occurring, can be added into viral genomes to confer additional desirable properties. The overarching engineering goal for the oncolytic virotherapy field is to generate viruses that can be efficiently delivered to disseminated tumors in the body where they will spread and selectively kill both infected and uninfected tumor cells, without causing collateral damage and posing no risk of transmission to the population.

Delivery of Ovs

Viral infections are well understood but for OV applications must be viewed as drugs obeying pharmacological principles. A drug is typically administered to a patient in an extremely controlled way to produce a reliable, consistent and predictable pharmacokinetic profile (absorption, biodistribution, metabolism and excretion) and bioavailability. Natural viral infections do not obey these rules since the inoculum is of variable size; host resistance varies from person to person; and the kinetics of the adaptive immune response differ greatly between individuals. Thus, the outcomes of natural infections with a given pathogenic virus range from asymptomatic seroconversion to full blown disease. The primary virus inoculum must contain sufficient virus particles to overcome initial host defenses at the site of entry. Some viruses enter through mucous membranes in the GI or respiratory tracts, while others enter via direct inoculation into the blood stream following a needle stick or arthropod blood meal [58] . OVs are delivered in the same way as traditional drugs, by introducing a highly concentrated virus inoculum into the body via oral, intravenous (IV), intranasal, transdermal, subcutaneous or intramuscular routes whereupon the dispersion of the inoculated virus, or its progeny, takes it to the targeted cancerous tissues. A major factor distinguishing OVs from traditional drugs is that they self-amplify and spread after delivery so their peak concentration may not be reached until sometime after the treatment is administered. Biological amplification by viral replication is the most important difference between viral therapies and traditional drugs. The concentration of a drug diminishes over time at a very well described rate depending on the clearance and elimination from the body. Through the course of a viral infection the viral load is initially small and then increases and finally decreases rather than just following a specific rate law of elimination. Limited amounts of virus particles replicate at the site of inoculation [59] . Input or progeny viruses then can either drain with the lymphatic fluid to the nearest lymph node, go directly into circulation or spread locally before spreading systemically to eventually arrive at a specific target organ. Pathology is induced by high levels of viral replication in the target organ directly killing infected cells or recruiting the immune system to kill them, at the same time provoking a local inflammatory response.
Clearly, the ability to infect the activated endothelial cells of tumor neovessels would be an attractive targeting property for OVs to enhance entry into the tumor parenchyma by releasing viral progeny on the ablumenal side of the blood vessel. Intravascular coagulation in the capillary could also be provoked by virusinfected endothelial cells reacting with clotting and inflammatory factors. Virus engineering strategies have been pursued to achieve this goal, for example, by displaying polypeptide ligands echistatin and urokinase plasminogen activator on the surface of measles virus to target integrin αVβ3 and UPaR endothelial cell surface receptors, respectively [68, 69] . Also, at least one OV (vesicular stomatitis virus VSV) has been shown naturally capable of infecting neovessel endothelium in implanted mouse tumors, but the study did highlight the potential toxicity of the approach, namely intravascular coagulation requiring heparin therapy for its prevention [70] .
Mouse models with implanted flank tumors provide a convenient model for IT injection as the tumor is superficial, but in human patients with spontaneous malignancies tumors often develop internally in visceral organs. Melanoma, head and neck cancer, and lower gastrointestinal malignancies may be better suited for IT injections due to anatomical position, although with advanced interventional radiology using computed tomography or MRI image guidance to place the needle many more tumors may be accessible for IT virotherapy. One additional advantage of IT injection over the IV route is that the threshold concentration of input virus required to initiate a spreading infection in the tumor tissue can be more easily achieved.

• Limiting viral neutralization & clearance

Antibody neutralization has been shown to reduce the efficacy of systemically administered OVs such as measles, VSV and vaccinia in preclinical models [76] [77] [78] . When previous exposure has occurred, preformed antibody reduces the effectiveness of the initial treatment. However, the situation is typically far more problematic for second and subsequent doses, even for low seroprevalence viruses, because the first dose induces a powerful primary antiviral antibody response or boosts the pre-existing response [79, 80] . These troublesome responses can be constrained by coadministering immunosuppressive drugs such as cyclophosphamide. Cyclophosphamide administered concurrently with an OV has been shown to suppress or delay the development of humoral and cytotoxic antiviral T-cell responses [81] .
Another strategy for avoiding neutralization is to block the reticuloendothelial system with polyinosinic acid or with clodronate-loaded liposomes which poison or deplete splenic macrophages and Kupffer cells. This approach has been shown to slow the clearance of circulating virus particles that have been coated with antibodies or complement [86] [87] [88] .

Arming Ovs: extending the range

No matter how extensively an OV infection spreads through a tumor, a sizable percentage of the cancer cells will escape infection [61] . Killing of these uninfected (bystander) cancer cells is therefore critical if oncolytic virotherapy is to become a curative, as opposed to just a tumor debulking strategy. Bystander killing can be achieved, both locally at the site of a spreading infection and systemically at uninfected tumor sites, by genetically arming the virus using one of several possible approaches. For example, an OV can be engineered to encode a secreted protein that selectively mediates the destruction of neighboring and/or distant cancer cells. Alternatively, it can be armed with a 'suicide gene' or prodrug convertase whose encoded protein converts a harmless prodrug to a diffusible anticancer drug. In a third approach, the OV can be armed with a 'radioconcentrator gene' so that infected tumor cells are able to concentrate a β-emitting radioisotope whose emitted electrons damage adjacent uninfected tumor cells. Fourth, it can be engineered to fuse infected tumor cells with uninfected neighboring cells. And last, but by no means least, it can be engineered to express one or more genes capable of amplifying immune-mediated killing of uninfected tumor cells. Each of these approaches is discussed below using specific examples to illustrate the concepts.

• • Prodrug convertases

CD converts 5-flurocytosine (5-FC), an inert small molecule that is administered intravenously, to 5-flurouracil (5-FU), an antimetabolite that irreversibly inhibits thymidylate synthase and is an approved chemotherapeutic agent for a variety of cancers (anal, breast, colorectal, esophageal, stomach, pancreatic and skin) [29] . The argument supporting the CD/5-FC system is that local production of 5-FU in the OV-infected tumor will create a 5-FU concentration gradient that will expose tumor cells to a higher concentration of the drug compared with distant tissues, thereby ameliorating toxicity and enhancing the therapeutic index of the drug. However, 5-FU is freely diffusible so local production of the drug in a CD-positive tumor exposed to high concentrations of 5-FC can lead to systemic toxicity [140] . The dose of 5-FC must therefore be adjusted accordingly. CD has been incorporated into several OVs including adenoviruses, paramyxoviruses and poxviruses, but the one that has advanced ahead of all others in clinical testing is a C-type retrovirus, Toca-511, which is currently being evaluated in a Phase III clinical trial for the treatment of patients with malignant glioma [141] [142] [143] . Besides the TK and CD prodrug convertase systems, there are reports of OVs engineered to express the cyclophosphamide-activating protein CYP2B1, future science group www.futuremedicine.com the CPT11-activating secreted human intestinal carboxylesterase (shiCE) and the fludarabine phosphate activating purine nucleotide phosphorylase [144, 145] .

• • Sodium iodide symporter (radioconcentrator)

Iodide is a critical component of thyroxine and is concentrated in thyroid follicular cells by the thyroidal sodium iodine symporter (NIS), a cell surface glycoprotein with 13 transmembrane domains [146] . Radioiodine is therefore used routinely in the clinic for thyroid imaging and for ablation of overactive thyroid tissue, including metastatic thyroid cancer. This is facilitated by the ready availability of several iodine radioisotopes, most notably 123 Ifor γ camera and single-photon emission computed tomography imaging, 124- for PET imaging and 131 I -, a β-emitting isotope, for thyroid ablation. Besides radioiodine, NIS can concentrate several related anions, of equal or greater value for single-photon emission computed tomography ( 99m TcO 4 -, pertechnetate), PET (B 18 F 4 -, tetrafluoroborate) and tissue ablation ( 211 At -, astatide, 188 ReO 4 -, perrhenate) [147] . The β emissions of 131 Ihave an average path length of approximately 1.8 mm in tissue and can therefore inflict significant damage on cells adjacent to an 131 I --loaded NIS expressing cell. For 188 ReO 4 the β emission path length is longer such that NIS negative tumor cells are even more likely to be damaged in the β particle crossfire when this radioisotope is used. Unsurprisingly, therefore, the NIS gene has been engineered into several OVs whose IT spread has been elegantly mapped and monitored in tumor-bearing mice by serial radiotracer imaging, and whose potency has been substantially boosted by appropriately timed administration of 131 I - [148] . At least two NIS-expressing OVs, a prostate-targeted oncolytic adenovirus and a CD46-targeted measles virus, have been advanced to human clinical trials with positive imaging data reported [11, 149] .

Safety

So far OVs have an exceptional safety record in the clinic with few serious adverse events and minimal mortality reported from human trials [166, 167] . However, since efficacy has also been limited, it remains possible that toxicity profiles may appear less favorable as doses are increased and as newer OVs or virus-drug combinations are advanced to clinical testing. Currently, there are over 40 active clinical trials ongoing using OVs alone or in combination with other therapies [168] . As the number of patients participating in trials grows so will the insight into rare adverse effects. The most common adverse effects reported in recent OV trials are fever and flu-like symptoms [169] . However, the potential for severe adverse reactions was much more clearly demonstrated in the earliest virotherapy trials undertaken in the 1950s and 1960s when deaths and severe adverse reactions were not infrequently recorded due to presumed OV replication in normal tissues, notably the brain, especially in immunocompromised cancer patients [4, 170, 171] .

• • Limiting pathogenicity

Understanding the selective pressures that operate within the tumor and the host, as well as the role of viral quasispecies in treatment outcomes is an active area of research. RNA and DNA viruses exist as a population of quasispecies or collections of related viral genomes undergoing variation and selective pressure [174] . Generation of quasispecies occurs when viral genomes are copied during the replication cycle. Viral polymerases typically have an error rate that introduces an average of one or more base mutations per progeny genome [175] . In general, the larger the virus genome, the lower the polymerase error rate. Picornaviruses are among the smallest viruses being developed for oncolytic therapy with positive sense RNA genomes ranging from 7 to 9 kb in length, and their RNA polymerases have a correspondingly high intrinsic error rate. Production of a virus for clinical application is a highly regulated process and involves multiple rounds of replication to achieve enough virus for patients. The viral product is therefore already a swarm of quasispecies at the time it is administered to the patient and mutates further as it undergoes additional rounds of replication in vivo. Studies of the mutation rates of viral polymerases, the generation of quasi species, the evolution of viral populations and the evolution between dominant subspecies within a virus population are therefore of great interest and relevance to the OV field.
Two so-called suicide genes, TK and inducible caspase 9, are of interest in this regard. Both of these genes have been used as a safety switches to eliminate genetically modified T cells that were causing graft versus host disease in human clinical trials [184] [185] [186] . Viruses engineered to encode TK have also been controlled with ganciclovir therapy [187] , but this cannot be considered a reliable safety switch because of the ever-present risk of the emergence of viral quasispecies with TK inactivating mutations. The development of a universal and highly reliable safety switch remains one of the significant research challenges facing the field of oncolytic virotherapy.

• • Prodrug convertases

Unlike secreted toxins, prodrug convertases do not pose a risk of increasing OV virulence because their toxic potential is manifest only in the presence of an exogenously added prodrug. For this reason, the approach has been extensively studied. Perhaps the most well-known convertase-prodrug combination is HSV TK, used with ganciclovir. TK converts ganciclovir to ganciclovir monophosphate which is further processed intracellularly to ganciclovir triphosphate, a DNA synthesis chain terminator that kills dividing cells as they enter S phase [138] . A major weakness of the TK-ganciclovir system, aside from its inability to kill nondividing tumor cells, is that it has very limited bystander killing potential. This is because ganciclovir monophosphate is not released from the cell in which it is generated, so does not impact uninfected tumor cells unless they are connected to the infected cell via gap junctions through which it can pass [139] . Encoding connexin, a gap junction protein, in the OV genome can enhance the bystander killing effect of TK, but attention is shifting to other convertases, most notably CD.

Arming viruses with transgenes

• Secreted toxins, prodrug convertases and immunostimulatory proteins have been incorporated into OVs to increase treatment efficacy.
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Abstract

Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and the therapeutic success mainly depends on early detection of the infective agent. Over the last years, aptamer technology has been used in a wide range of diagnostic and therapeutic applications and, concretely, several strategies are currently being explored using aptamers against virus proteins. From a diagnostics point of view, aptamers are being designed as a bio-recognition element in diagnostic systems to detect viral proteins either in the blood (serum or plasma) or into infected cells. Another potential use of aptamers is for therapeutics of viral infections, interfering in the interaction between the virus and the host using aptamers targeting host-cell matrix receptors, or attacking the virus intracellularly, targeting proteins implicated in the viral replication cycle. In this paper, we review how aptamers working against viral proteins are discovered, with a focus on recent advances that improve the aptamers' properties as a real tool for viral infection detection and treatment.

Introduction

Viruses are infectious agents that enter and replicate only inside the living cells of other organisms. Once the virus replicates inside the cell, it may remain dormant for long periods of time or be released immediately and attach to other healthy cells to begin the infection process again. Many diseases are caused by viruses such as the influenza, hepatitis, human immunodeficiency virus (HIV) or emerging viral diseases. While they differ in symptoms such as fever and weakness, some present no symptoms at all. Rapid and secure diagnosis of viral infections is a key factor for treatment of these diseases avoiding new spread.
Viruses cause different types of damage to the body which, if left untreated, can lead to death. There are many antiviral drugs that block the infection process at different stages. Some drugs prevent the virus from interacting with the healthy cell by blocking a receptor that helps internalize the virus into the cell. Other drugs inhibit the proliferation of the virus within the cell. The simultaneously use of several drugs affecting different processes increases the probability of recovery of the patient. Although some viral infections such as hepatitis or HIV remain latent for a long time current treatments control the virus and prevent further damage to the body. Viral infections usually produce an immune response in the host that eliminates the infecting virus. The same protective effect is produced by vaccines, which confer an artificially acquired immunity to the viral infection. However, some viruses including those that cause acquired immune deficiency syndrome (AIDS) and viral hepatitis evade these immune responses and result in chronic infections. Antibiotics have no effect on viruses, but several antiviral drugs have been developed. Because viruses use vital metabolic pathways within host cells to replicate, they are difficult to eliminate without using drugs that cause toxic effects to host cells in general. The most effective medical approaches to viral diseases are vaccinations to provide immunity to infection, and antiviral drugs that selectively interfere with viral replication.
Most of the antiviral drugs are nucleoside analogues which lack the hydroxyl groups. Viruses mistakenly incorporate these analogues into their genomes during replication and, in consequence, the newly synthesized DNA is inactive and the life-cycle of the virus is then halted. Some of the most frequently prescribed antiviral nucleoside analogues based-drugs are aciclovir for Herpes simplex virus infections and lamivudine for HIV and Hepatitis B virus infections [1] . During the last years, the nucleoside analogue drug ribavirin combined with interferon has been used for hepatitis C treatment [2] , although currently there is a more effective treatment that includes simeprevir available for patients with genotype 1 and genotype 4 [3] . The treatment of chronic carriers of the hepatitis B virus by means of a similar strategy using lamivudine has been developed [4] . Today, the first line treatment of choice includes one of three drugs: Peg-IFN, entecavir or tenofovir because of their greater power and because they produce a very low rate of resistance.

Aptamers against Human Immunodeficiency Virus (HIV)

Human immunodeficiency virus is a lentivirus (a subgroup of retrovirus) that causes HIV infection and over time AIDS [21] . HIV infects essential cells in the human immune system such as CD4 + T cells, macrophages, and dendritic cells. When CD4 + T cell numbers decline below a critical level, cell-mediated immunity is lost, and the body becomes progressively more susceptible to opportunistic infections. HIV enters cells by endocytosis through the interaction of gp120 viral surface protein (SU) with CD4 host cell. The subsequent interaction of this complex with chemokine coreceptors produces a conformational change in viral protein gp41 that promotes the fusion of virion and target cell membranes leading to the release of HIV particles into the cell. Once inside the cell, viral uncoating generates the viral reverse transcription complex, and the reverse transcription gives the HIV preintegration complex (PIC). The PIC gets into the nucleus and the HIV DNA (provirus) is integrated into the cellular chromosome. Integration can lead to either latent or transcriptionally active forms of infection. The latent form gives the viral latency in cells that can replicate in new infected cells; this provirus can remain hidden during years or replicate and form new viral particles in any moment. The transcriptional active forms are transcript and translated forming new viral particles that dead the host cell and goes to infect new cells. Great efforts are being made to get sensitive, fast and simple diagnostic methods and effective therapies.

Aptamers to Nucleocapsid Protein

Aptamers to Surface Glycoprotein (gp 120) Gp120 is essential for virus entry into cells as it plays a vital role in attachment to specific cell surface receptors mainly on helper T-cells. Several small aptamers containing G-quadruplex selected against gp120 have demonstrated antiviral activity [33] . The first of these molecules was the phosphorothioate 8-mer d(TTGGGGTT), named ISIS 5320, which forms a tetrameric G-quadruplex structure that binds the V3 loop of gp120 inhibiting virus entry [48] . Later on, Koizumi et al. synthesized a set of G-rich oligonucleotides and identified the hexadeosyribonucleotide d(TGGGAG), known as Hotoda's sequence, [49, 50] . Several authors have used the Hotoda's sequence as a lead sequence to make a series of modifications at the 5 and 3 ends of the molecule or mutations in the sequence that allowed to find molecules with high anti-HIV activity [50] [51] [52] [53] [54] [55] [56] .

Aptamers against HBV

Hepatitis B virus (HBV) is a partially double-stranded DNA virus of the Hepadnaviridae family classified into eight genotypes from A to H. The main element of the viral particle of HBV virus and also the most characterized component is the hepatitis B surface antigen (HBsAg) [72] .

Aptamers to 5′ and 3′ Untranslated Regions (5′ and 3′UTR)

Non-translated 5′ and 3′ regions have highly conserved sequences and structured regions closely related with transcription and replication of the HCV virus. Specifically, 5′ end contains the Internal

Aptamers to 5 and 3 Untranslated Regions (5 and 3 UTR)

Non-translated 5 and 3 regions have highly conserved sequences and structured regions closely related with transcription and replication of the HCV virus. Specifically, 5 end contains the Internal Ribosome Entry Site (IRES) domain responsible of transcription initiation by ribosome recognition of HCV viral genome. However, 3 UTR includes a region essential for viral replication named cis-acting replication element (CRE).

Aptamers to Nonstructural Protein 3 (NS3)

Multifunctional enzyme NS3 is an essential protein for virus survival and it is considered a good target for the development of new antiviral-drugs. The protease activity of the protein is found in the N-terminal domain and the helicase activity is present in the C-terminal domain of the enzyme. During the last years, the group of Nishikawa has been working with different sets of RNA aptamers against the full-length or truncated NS3 protein to inhibit its dual-activity. Initially, they isolated NS3-specific aptamers that inhibited the protease activity (10-G1) or the dual activity, protease/helicase, of the enzyme NS3 (G6-16 and G6-19) [101, 102] . Afterward, new RNA aptamers against the helicase domain of NS3 protein, named G9-I, II and III, were able to inhibit protease activity in vitro [103] . Later on, the authors described the interaction between G9-I aptamer with Arg161/Arg130 residues in the truncated NS3 form as a putative target for protease activity inhibition [104] . To stabilize and protect G9 aptamers against exonuclease activity in vivo, Nishikawa et al. conjugated G9-II aptamer to the stem IV region of the Hepatitis delta virus (HDV) ribozyme. In addition, to allow nuclear export of the aptamer, the chimeric molecule HDV-G9-II (HA) was fused to a constitutive transport element (CTE) generating HAC molecule. Finally, the protease-inhibition capability of G9-II aptamer was checked, using HA and HAC expression vector in vivo [105, 106] . In order to inhibit the dual activity of NS3, a poly U tail in the 5 or 3 ends of G9-I aptamer (5 -14U-NEO-III or NEO-III-14U) was added. The two constructions were able to inhibit with high efficiency of the protease and helicase activities of NS3. Moreover, NEO-III-14U decreased the interaction between NS3 protein and the 3 end of the positive or negative sense HCV RNA and inhibited protease activity of NS3 in vivo [107] . Next, a new set of RNA aptamers were selected against the helicase domain using the truncated NS3 protein (NS3h) and the aptamer with greatest capability to deplete helicase activity in vitro was identified and named aptamer #5 [108] . Finally, a dual-functional aptamer named G925-s50 was designed using a truncated version of aptamer #5 plus G9-II aptamer linked by 50 mer poly(U) spacer. The designed molecule G925-s50 showed a significant inhibition of NS3 helicase-protease activity in vivo and is proposed by Nishikawa group as the best candidate for anti-HCV therapy [109] .

Aptamers against Human Papilloma Virus (HPV)

Human papillomavirus (HPV) is a DNA virus from the papillomavirus family. Most HPV infections cause no symptoms and resolve spontaneously, but some of them persist and result in warts or precancerous lesions which increase the risk of cancer of the cervix, vulva, vagina, penis, anus, mouth, or throat [119, 120] .

Aptamers to HPV in Diagnostics

Several proteins from human papillomavirus, particularly E6 and E7, promote tumor growth and malignant transformation and are frequently associated with cervical cancer. Thus, these proteins represent ideal targets for diagnostic and therapeutic strategies. Belyaeva et al. reported two RNA aptamers to E6, named F2 and F4, which induced apoptosis in cells derived from an HPV16-transformed cervical carcinoma. This aptamers were able to inhibit the interaction between E6 and PDZ1 from Magi1, with F2 being the most effective inhibitor, while none of them inhibited E6-p53 interaction or p53 degradation [121] .
Toscano-Garibay et al. isolated an aptamer (G5α3N.4) that exhibited specificity for E7 with a Kd comparable to aptamers directed to other small targets [122] that may be used for the detection of papillomavirus infection and cervical cancer. The same group characterized an RNA aptamer, named Sc5-c3, that recognized baculovirus-produced HPV-16 L1 virus-like particles (VLPs) with high specificity and affinity (Kd = 0.05 pM). This aptamer produced specific and stable binding to HPV-16 L1 VLPs even in biofluid protein mixes and thus it may provide a potential diagnostic tool for active HPV infection [123] . Recently, Graham and Zarbl identified several DNA aptamers that have high affinity and specificity to the non-tumorigenic, revertant of HPV-transformed cervical cancer cells, which can be used to identify new biomarkers that are related to carcinogenesis produced by HPV [124] .

Aptamers to Herpes Simplex Virus (HSV)

Herpes simplex virus 1 and 2 (HSV-1 and HSV-2) are two members of the herpesvirus family, Herpesviridae, that infect epithelial tissues before invading the nervous system, where it becomes latent. Unfortunately until now, it has not found any treatment to eradicate the virus [128] . Table 5 shows information on the aptamers described against HPV and HSV. Aptamer technology has been used by Corbin-Lickfett et al. to identify RNA sequences capable of being recognized by HSV-1 ICP27 protein, an important regulator for viral gene expression. After SELEX procedure, GC-rich RNA sequences were isolated, which did not form stable secondary structures [129] . With a therapeutic purpose, Gopinath et al isolated two RNA aptamers (aptamer-1 and aptamer-5) against the ectodomain of the gD protein of HSV-1, which plays an important role in viral entry to the host cells. These aptamers specifically bind to gD protein of HSV-1 with high affinity but not the gD protein of HSV-2. Furthermore, aptamer-1 efficiently blocked the interaction between the gD protein and the HSV-1 target cell receptor (HVEM) in a dose-dependent manner with a EC 50 in the nanomolar range. Anti-HSV-1 activity of aptamer-1 was analyzed by using plaque assays and the results showed that this aptamer efficiently inhibited viral entry. A shorter variant of aptamer-1 named mini-1 aptamer (44-mer) had at least as high an affinity, specificity, and ability to interfere with gD-HVEM interactions [130] . In a similar way, Moore et al. have reported the isolation and characterization of one aptamer, G7a, that binds the gD protein of HSV-2 and neutralizes infection through the Nectin1 and HVEM entry receptors with IC 50 of 20 nM [131] . Interestingly, aptamers that prevent HSV-2 infection may also reduce the morbidity associated with HIV-1 as HSV-2 is a major risk factor for the acquisition of HIV-1.

Aptamers to Influenza

Influenza is considered the most prevalent infectious disease in humans. Three emerging influenza viruses were responsible for major pandemics in the twentieth century: the 1918 Spanish influenza virus, the 1957 Asian influenza virus, and the 1968 Hong Kong influenza virus [132] . Indeed, the 1918 Spanish influenza virus was estimated to have killed 20-50 million people worldwide [133] . More recently, a highly pathogenic avian virus of the H5N1 subtype has produced sporadic infections in humans and, while it is associated with high rates of mortality, its poor transmission in humans prevented a more extensive spread among human populations. However, in 2009, a new influenza A virus of the H1N1 subtype emerged (pH1N1) that possessed high transmissibility but relatively low virulence, rapidly spreading across the entire globe and causing the first pandemic of the 21st century [134, 135] . Subsequently, 2013 witnessed the appearance of a new highly pathogenic avian virus of the H7N9 subtype in China [136] .
Influenza viruses are enveloped RNA virus of the family Orthomyxoviridae. The virion surface carries two membrane glycoprotein components, hemagglutinin (HA) and neuraminidase (NA) and, in the central core, the viral RNA (negative-sense) genome fragmented into eight single-stranded molecules and viral proteins that package and protects this RNA. Each segment contains one or two genes that code for the 15 viral proteins. Highly variable surface proteins, HA and NA, are used to classify influenza subtypes. The combination of hemagglutinin and neuraminidase mainly determines the host organism and the viral infectiousness. Currently, 18 HA and 11 NA types have been identified being the subtypes H1, H2 and H3, and N1 and N2 commonly found in humans.

Aptamers to Influenza Virus in Diagnostics

The detection rapid of influenza virus as well as the categorization of these viruses is particularly important due to the high risk of infection, the rapid propagation and the high frequency of mutation that often induces the arrival of new strains that can cause epidemics and even pandemics. An extensive review about the diagnostic strategies for influenza has been recently published [137] .
The recent advances in the development of rapid, automatic, point of care devices for the diagnosis and subtyping of influenza virus are sustained in two facts: (i) the rapid spread of influenza-associated H1N1 viruses that has caused serious concern in recent years; and (ii) H5N1 subtype of the avian influenza virus (AIV) caused the most lethal outbreaks of highly pathogenic avian influenza (HPAI) in poultry and fatal infections in human cases for over a decade. Thus, aptamers have been generated and found to be specific against these recent pandemic influenza viruses A/H1N1pdm [142] and H5N1 [143] .
Lee et al. developed an integrated microfluidic system that was used to screen a specific aptamer for the influenza A/H1N1 virus in an automated and highly efficient manner [144] . The selected aptamer showed a specific and sensitive detection of the influenza A/H1N1 virus, even in biological samples such as throat swabs. Later, they used a new approach for fluorescence-based detection of the influenza A H1N1 virus using a sandwich-based aptamer assay that is automatically performed on an integrated microfluidic system [145] . The entire detection process was shortened to 30 min using this chip-based system which is much faster than the conventional viral culture method. The limit of detection was significantly improved due to the high affinity and high specificity of the H1N1-specific aptamers. In addition, this two-aptamer microfluidic system had about 10 3 times higher sensitivity than the conventional serological diagnosis. The conformation of the aptamers changes in response to the solvent composition, including ion type and concentration, pH, and temperature. On the basis of this, Wang et al. have developed a microfluidic system that exploited the predictable change in conformation of the aptamer previously used in the group, exposed to different ion concentrations in order to detect multiple types of the influenza virus [146] . Thus, a single fluorescent-labelled aptamer is able to identify three different influenza viruses (influenza A H1N1, H3N2, and influenza B) at the same time, by modifying operating conditions, in 20 min. This chip-based aptamer-binding assay has several important advantages; it is rapid, accurate, and cheaper than multiple-aptamer screening.
Current methods for H5N1 AIV detection are virus isolation and RT-PCR that requires several days and expensive equipment and reagents. Rapid detection assays are also available (such as ELISA or immunochromatographic strips) but are less sensitive and specific. The alternative approach is biosensors technology, several biosensors have been developed to detect AIV among them biosensors using as probe aptamers (aptasensors) (reviewed in [147] . In the Li's lab, a highly specific DNA aptamer that can bind H5N1 virus with high affinity was selected. Using this aptamer, other authors have developed different aptasensors based on Surface Plasmon Resonance (SPR) [148] , a quartz crystal microbalance (QCM) aptasensor crosslinked polymer hydrogel [149] and several aptasensors based on impedance methods [150] [151] [152] . These aptasensors were able to detect H5N1 quickly and/or with more sensitivity than antibody-based biosensors.
The impedance-based aptasensor described Fu et al. has the lowest detection limit, however, it requires signal amplification with labels and a prolonged detection limit [150] . The impedance aptasensor with microfluidics chips has a lower detection limit than the SPR-based aptasensor [148] and the same sensitivity as the QCM aptasensor [149] , but the QCM-based aptasensors are not practical for in-field use due to the QCM's predisposition to environmental noise. The major advantage of the impedance aptasensor with gold nanoparticles for signal amplification described by Karash et al. is that it requires a small sample volume and is cheaper than the detection platforms based on QCM or that use interdigitated electrode microfluidic chips [152] . Recently, Nguyen et al. developed a sandwich-type SPR-based biosensor for the detection of H5Nx viruses using a pair of aptamers selected against a mixture of H5Nx whole viruses using Multi-GO SELEX [153] . The sensitivity of the dual aptamer-based system increased by more than 50-fold than for single-aptamers. In addition, the sensitivity was additionally enhanced when the secondary aptamer was conjugated with gold nanoparticles.

Aptamers to Influenza Virus as Antiviral Agents

Several aptamers against influenza virus have been developed for therapeutics purposes, mainly targeting hemagglutinin (reviewed in [5] ) (Figure 4) . These aptamers are able to inhibit the entry of the virus of the cells by blocking hemagglutinin activity. The common technique to measure the inhibitory activity of the aptamers in vitro is the hemagglutination inhibition assay. The model was more extensively used to test the effect of the aptamers on the viral infection involving the use of cell cultures, mainly Madin-Darby canine kidney (MDCK) cells. The cells are infected with the virus and incubated with the aptamers and the inhibition of viral infectivity is tested. Using these assays, DNA and RNA aptamers selected against HA from Influenza A virus [142, [154] [155] [156] [157] [158] or avian influenza virus [159] [160] [161] , able to significantly decrease the viral infection in cells, have been described. However, only a few studies have described aptamers capable of mediating a reduction in viral pathogenicity in mice models. Jeon et al. evaluated the effect of the administration intranasal of the A22 aptamer, a DNA aptamer selected against the HA-(91-261) peptide, in mice before, at the same time and after virus infection [154] . The aptamer-induced inhibition of viral infection was determined by prevention of weight loss, decrease of viral load in the lungs and restriction of the level of inflammation and cellular infiltration. A22 reduced up to 95% of infection in all the strains tested (H1N1, H2N2 and H3N2). A22 was most effective when administered concomitantly with the viral infection leading to 95% reduction in viral burden. The administration of A22 one day prior to infection (preventive treatment) was less effective, probably because the DNA is partially degraded. Interestingly, the treatment with A22 two days following the infection (therapeutic treatment) still leads to almost 95% reduction in viral titer in the lungs of the mice. In 2014, Musafia et al. used A22 aptamer as a starting point and the quantitative structure-activity relationship (QSAR) tool to produce aptamers with 10-15 times more potent antiviral activity in animal models than A22 aptamer. The binding of these aptamers to the virus (20 times higher than A22) may not necessarily be sequence-specific being the most important properties the aptamer length, 2D-loops and repeating sequences of C nucleotides [157] .
Another antiviral strategy is the inhibition of the enzymes involved in the viral replication, transcription and translation. The polymerase complex of Influenza virus catalyzes the viral replication and transcription. This heterotrimer is composed of three subunits named PA, PB1 and PB2 [164] [165] [166] . PA plays the role of an endonuclease, cleaving host mRNAs downstream of their mRNA cap structures, which are recognized and bound by PB2 [167] . The N-terminal of the PA subunit (PA N ), which holds the endonuclease activity site, is highly conserved among different subtypes of influenza virus, which suggests it is an attractive target in the development of anti-influenza agents. Yuan et al. selected DNA aptamers against both PA protein (three aptamers), and the PA N domain (six aptamers) of an H5N1 virus strain [168] . Four of the six PA N selected aptamers inhibited both endonuclease activity and H5N1 virus infection whereas the three PA-selected aptamers did not inhibit endonuclease activity and virus infection. Finally, one of the four effective aptamers, exhibited cross-protection against infections of H1N1, H5N1, H7N7, and H7N9 influenza viruses, with a 50% inhibitory concentration (IC 50 ) around 10 nM.
Pharmaceuticals 2016, 9, 78 19 of 33 aptamers, exhibited cross-protection against infections of H1N1, H5N1, H7N7, and H7N9 influenza viruses, with a 50% inhibitory concentration (IC50) around 10 nM. The association of the viral polymerase, bound to the cap, and eIF4GI may be involved in the preferential translation of viral mRNAs during influenza infection. In addition, the interaction of NS1, bound to a conserved 5untranslated region (UTR) element of the viral mRNA, with eIF4GI and PABP1 could promote the formation of a "closed loop" between the 5′ and 3′ ends of the viral mRNA; (4) RIG-I is a cytosolic receptor for non-self RNA that mediates immune responses against viral infections through IFNα/β production. Mitochondrial antiviral-signaling (MAVS) protein. Table 6 shows information on the aptamers described against influenza virus. Vaccination is a powerful approach to diminish the effects of influenza epidemics, but the use of antiviral drugs can also be very useful, particularly in delaying the spread of new pandemic viruses. Neuraminidase inhibitors like oseltamivir, laninamivir, zanamivir, and peramivir are commonly used as antiviral agents to treat influenza infection, especially in Japan. However, because of the rapid increases in drug-resistant influenza virus, it is essential to develop new antiviral drugs as an emerging strategy to block cellular factors important for the infective cycle. The advantage of blocking important cellular pathways for the virus inhibitory effect is that, in principle, it is not specific of influenza strain and the emergence of resistant virus is minimized. A limited number of aptamers targeting host cell factors have been described. Of these, the use of RIG-I as a target for aptamers to control viral infection should be emphasized [169] . RIG-I is a cytosolic receptor for nonself RNA that mediates immune responses against viral infections through IFNα/β production [170] . The use of a specific RIG-I aptamer that activates RIG-I efficiently blocks the replication of the Newcastle disease virus, vesicular stomatitis virus and influenza virus in infected cells, evidencing that aptamers targeting cellular factors can act as efficient antiviral agents [169] . The association of the viral polymerase, bound to the cap, and eIF4GI may be involved in the preferential translation of viral mRNAs during influenza infection. In addition, the interaction of NS1, bound to a conserved 5-untranslated region (UTR) element of the viral mRNA, with eIF4GI and PABP1 could promote the formation of a "closed loop" between the 5 and 3 ends of the viral mRNA; (4) RIG-I is a cytosolic receptor for non-self RNA that mediates immune responses against viral infections through IFNα/β production. Mitochondrial antiviral-signaling (MAVS) protein. Table 6 shows information on the aptamers described against influenza virus. Vaccination is a powerful approach to diminish the effects of influenza epidemics, but the use of antiviral drugs can also be very useful, particularly in delaying the spread of new pandemic viruses. Neuraminidase inhibitors like oseltamivir, laninamivir, zanamivir, and peramivir are commonly used as antiviral agents to treat influenza infection, especially in Japan. However, because of the rapid increases in drug-resistant influenza virus, it is essential to develop new antiviral drugs as an emerging strategy to block cellular factors important for the infective cycle. The advantage of blocking important cellular pathways for the virus inhibitory effect is that, in principle, it is not specific of influenza strain and the emergence of resistant virus is minimized. A limited number of aptamers targeting host cell factors have been described. Of these, the use of RIG-I as a target for aptamers to control viral infection should be emphasized [169] . RIG-I is a cytosolic receptor for non-self RNA that mediates immune responses against viral infections through IFNα/β production [170] . The use of a specific RIG-I aptamer that activates RIG-I efficiently blocks the replication of the Newcastle disease virus, vesicular stomatitis virus and influenza virus in infected cells, evidencing that aptamers targeting cellular factors can act as efficient antiviral agents [169] . However, aptamers directed against cellular factors that establish essential interactions with influenza virus proteins had not been reported before. The mRNAs of influenza virus possess a 5 cap structure and a 3 poly (A) tail that makes them structurally indistinguishable from cellular mRNAs. However, selective translation of viral mRNAs occurs in infected cells through a discriminatory mechanism, whereby viral polymerase and NS1 interact with components of the translation initiation complex, such as the eIF4GI and PABP1 proteins [171] [172] [173] . Thus, the inhibition of viral protein-translation factor interactions or their destabilization can be potentially used as an antiviral strategy. Recently, Rodriguez et al. studied whether two aptamers which bind hPABP1 with high affinity (ApPABP7 and ApPABP11) are able to act as anti-influenza drugs [174] . Both aptamers inhibit influenza virus replication of H1N1 or H3N2 subtypes at high and low multiplicity of infection and the viral polymerase-eIF4GI interaction. In addition, aptamer ApPABP11 inhibits the interactions between NS1 and eIF4GI or PABP1. These results indicate that aptamers targeting the host factors that interact with viral proteins may potentially have a broad therapeutic spectrum, reducing the appearance of escape mutants and resistant subtypes.

Aptamers against Other Emerging Viruses

An emergent virus is a virus that has adapted and emerged as a new disease/pathogenic strain, with attributes facilitating pathogenicity in a field not normally associated with that of virus. This includes viruses that are the cause of a disease which has notably increased in incidence; this is often a result of a wide variety of causes from both the influence of man and nature. Most emergent viruses can be categorized as zoonotic (an animal disease that can be transmitted to humans), and this has the advantage of possibly having several natural reservoirs for the disease.
Most of these viruses have newly appeared in a population or have existed but are rapidly increasing in incidence or geographic range and only recently aptamers against emergent viruses such as Rift Valley Fever, Tick-borne encephalitis, Dengue, Ebola viruses or other arboviruses have been developed [175] .

Aptamers to Rift Valley Fever Virus (RVFV)

Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus (genus Phlebovirus) responsible for widespread outbreaks of severe disease such as hepatitis, encephalitis and hemorrhagic fever in humans [176] . The virus is endemic throughout much of the African continent. However, the emergence of RVFV in the Middle East, northern Egypt and the Comoros Archipelago has highlighted that the geographical range of RVFV may be increasing, and has led to the concern that an incursion into Europe may occur. At present, there is no licensed human vaccine [177] .
The nucleocapsid protein (N) of RVFV is an RNA binding protein required for the production of viable virus because of its involvement in several stages of viral replication. This protein protects the viral genome from degradation and prevents the formation of double stranded RNA intermediates during replication and transcription by encapsidating viral genomic and antigenomic RNA [178] . Ellenbecker et al. isolated RNA aptamers that bound N with high affinity and identified GAUU and pyrimidine/guanine motifs in their sequences, which are also present within the coding region of the RVFV genome. Furthermore, the authors developed a truncated RNA aptamer labeled with fluorescein using a fluorescence polarization (FP) system. Titration of N with the 3 -FAM-labeled RNA aptamer gave an apparent Kd of 2.6 µM. Competitive binding experiments were conducted with four different aptamers and the apparent Ki values were all in the~200 nM range. These data demonstrate that these aptamers might be used to construct a sensitive fluorescence based sensor of N binding with potential applications for drug screening and imaging methodologies [179] .

Aptamers to Tick-Borne Encephalitis Virus (TBEV)

Tick-borne encephalitis virus (TBEV) belongs to the family Flaviviridae, genus Flavivirus. This virus produces tick-borne encephalitis (TBE), an important emerging infectious disease that targets the central nervous system (CNS) [180] . There is currently no specific antiviral treatment for TBE because the specific immunoglobulin used in clinical practice has several disadvantages. The purpose of Kondratov et al. was to obtain an aptamer population against a fragment of the surface protein E of the TBEV, since it is available for aptamers outside of the host cell [181] . Authors showed that the treatment with the library of aptamers produced a TBEV neutralization index comparable with the results of neutralization of the commercial human immunoglobulin against tick-borne encephalitis (NPO Microgen, Russia). In addition, the enzyme immunoassay systems based on the immobilization of viral particles on antibodies are most commonly used for the TBEV diagnosis and the authors claim that protein E aptamers could substitute antibodies in these systems.

Aptamers to Dengue Virus (DENV)

Dengue viruses (DENVs) belong to the Flaviviridae family, and contain four serologically and genetically distinct viruses, termed DENV-1, DENV-2, DENV-3 and DENV-4. The envelope (E) protein plays an important role in viral infection but, however, there is no effective antibody for clinical treatment due to antibody dependent enhancement of infection. Chen et al. identified an aptamer (S15) that can bind to DENV-2 envelop protein domain III (ED3) with a high binding affinity. S15 aptamer was found to form a parallel quadruplex structure that together with the sequence on 5 -end were necessary for the binding activity to a highly conserved loop between βA and βB strands of ED3. Although S15 aptamer was selected against DENV-2, the authors demonstrated that this aptamer can neutralize the infections by all four serotypes of DENVs [182] .
The DENV capsid (C) protein functions as a structural component of the infectious virion but it may also have additional functions in the virus replicative cycle [183] . Balinsky et al. showed that the DENV C protein interacts and colocalizes with the multifunctional host protein nucleolin (NCL) and that this interaction can be disrupted by the addition of a NCL binding aptamer (AS1411), developed as AGRO100 by Aptamera (Louisville, KY, USA). Treatment of cells with AS1411 produced a significant reduction of viral titers after DENV infection. Moreover, the authors showed that treatment with AS1411 affected the migration characteristics of the viral capsid and identified a critical interaction between DENV C protein and NCL that represents a potential new target for the development of antiviral therapeutics [184] .

Aptamers to Ebola Virus (EV)

Ebola virus belong to the genus Ebolavirus. Four of five known viruses in this genus cause a severe and often fatal hemorrhagic fever in humans and other mammals, known as Ebola virus disease (EVD). Ebola virus has caused the majority of human deaths from EVD, and is the cause of the 2013-2015 Ebola virus epidemic in West Africa.
In many cases, aptamers have been used as a technological and research tool to identify RNA sequences that are recognized by different virus proteins. The zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of Moloney murine leukemia virus (MLV), Sindbis virus (SIN) and Ebola virus [187] , by targeting the viral mRNAs for degradation and preventing the accumulation in the cytoplasm. With the aim to identify RNA sequences that could be a target of ZAP, Huang et al. used aptamer technology identifying G-rich RNA aptamers that contained conserved "GGGUGG" and "GAGGG" motifs in the loop region. Interestingly, overexpression of the aptamers significantly reduced ZAP's antiviral activity and the substitution of the conserved motifs of the aptamers significantly impaired their ZAP-binding ability and ZAP-antagonizing activity, suggesting that the RNA sequence is important for specific interaction between ZAP and the target RNA [188] .

Aptamers to Severe Acute Respiratory Syndrome (SARS)

Severe acute respiratory syndrome (SARS) is a disease caused by SARS coronavirus (SARS-CoV) that caused a pandemic pneumonia in 2002-2003, with a total of 8096 reported cases, including 774 deaths in 27 countries. SARS-CoV belongs to the Coronavirus genus in the Coronaviridae family and is an enveloped, positive-sense RNA virus with a genome of 27.9 kilobases. This RNA encodes two large polyproteins, pp1a and pp1ab, and four structural proteins including spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. Pp1a and pp1ab are proteolytically cleaved into 16 non-structural proteins (nsps) that form the viral replicase-transcriptase complex (reviewed in [189] ).
Only a few studies have been focused on the development of aptamers against SARS-CoV as antivirals, in spite of the fact that there is still no effective therapeutic treatment against the virus. Two studies have selected DNA and RNA aptamers against the non-structural nsp13 protein. This protein possesses NTPase, duplex RNA/DNA-unwinding and RNA-capping activities that are essential for viral replication and proliferation. These aptamers inhibited helicase activity with subnanomolar IC 50 , while the ATPase activity was not affected, suggesting that the aptamers may bind to the nucleic acid binding site of the helicase and block the unwinding activity [192, 193] . Table 7 shows information on the aptamers described against emerging viruses. [190, 191] Severe acute respiratory syndrome n.d. DNA/RNA non-structural nsp13 protein [192, 193] n.d. = not determined.

Perspectives

The success of treatment in viral diseases depends on the early detection of the infective agent. The most probable use of aptamers in virus diagnostics involves the development of more simple, fast and cheap diagnostics devices. One of these simple detection systems can be the Lateral Flow Immunoassays (LFIAs) which are currently used for qualitative monitoring in resource-limited or non-laboratory environments. The LFIA biosensing platform mainly comprises the sample pad and test pad, which is generally composed of nitrocellulose membrane, and provides a platform for both reaction and detection where the capturing molecules are antibodies [197] . Lateral Flow biosensing platform has been developed using an aptamer against hepatitis C virus (HCV) core antigen [83] and could be applied for HIV or emerging virus detection using aptamers against specific proteins. This method allows detection of viruses in endemic or transit of human areas. Another interesting approach to obtaining cheaper diagnostics/genotyping devices is using only one aptamer to detect several targets. From this point of view, the strategy by Wang et al. [146] , in which they use the conformational change of one aptamer exposed to different ion concentrations to detect multiple types of the influenza virus could be used for genotyping of other viruses such as HBV or HCV.
From a therapeutic point of view, aptamers offer a hopeful solution in viral diseases because they can target elements of the virus or the infected host cell easier than the antibodies mainly due to their small size. The potential design of aptamers working against different targets might block the virion penetration into the cells or inhibit enzymes responsible for viral replication or other critical processes. In the case of HIV-1, despite efficient antiretroviral therapy, eradication of latent HIV-1 provirus is challenging and requires novel biological insights and therapeutic strategies. For this aim, novel target proteins should be chosen in HIV reservoir organs for the isolation of aptamers that could be applied to drug delivery or targeting of nanoparticles loaded with drugs to obtain HIV transcriptional activation.
As already mentioned above, RIG-I has been used as a target for aptamers to control viral infection [169] . Recently, Olagnier et al. investigated the inhibitory effect of a RIG-I agonist on the replication of Dengue and Chikungunya viruses [198] . The authors demonstrated that RIG-I stimulation generated a protective antiviral response against both pathogens. It would be motivating to study the use of RIG-I aptamers developed by Hwang for Dengue and Chikungunya therapy. Likewise, the effect of the aptamers developed by Guerra et al. against PABP in decreasing replication of influenza virus [174, 199] could be studied in other viruses that also use the PABP of the infected cell [200] .

Aptamers to HIV as Antiviral Agents

At present, the treatment HIV-1/AIDS is by a combination of several antiretroviral drugs (cART), which can slow the progress of the disease and reduce the risk of death and disease complication, but it is not curative. Moreover, many patients do not tolerate cART because it has severe side effects, and it is too expensive for patients in developing countries. In this regard, aptamers have been considered an alternative or adjuvant to the chemical antiviral agents in cART to overcome these limitations. To date, highly specific, nucleic acid-based aptamers that target various parts of HIV-1 genomes, HIV-1 proteins (including HIV-1 protease (PR), reverse transcriptase (RT), nucleocapsid, gp120, and Gag) and cellular proteins (nucleolin, CD4 or CCR5) have been isolated and shown to effectively suppress viral replication to apply in HIV therapy [5, [25] [26] [27] (Figure 2 ). (1) The HIV viral particle has an inner capside containing ssRNA viral genome and integrase and retro-transcriptase proteins, mainly; (2) The outer envelope has gp120 and gp40 proteins involved in interaction with cellular receptors (CD4, CCR5, NLS) and fusion to cellular membrane; (3) In the cytoplasm the ssRNA viral genome is released and the retro-transcription step is produced; (4) The integrase protein binds to dsDNA viral genome by LTR ends sequences and other cellular proteins forming the pre-integration complex (PIC); (5) The PIC goes into nucleus through the nuclear pore and is integrated in the cellular genome by the integrase protein activity (provirus); (6) The viral RNAs are transcripted from proviral DNA and exported to cytoplasm to translate viral proteins as protease and a big pre-protein that are assembled to new RNA viral genomes and leave the cell with outer envelope from the cellular membrane; (7) After the budding viral particle, the proteases process the big pre-protein and get a mature viral particle.

Aptamers to HIV Genome

(2) The outer envelope has gp120 and gp40 proteins involved in interaction with cellular receptors (CD4, CCR5, NLS) and fusion to cellular membrane; (3) In the cytoplasm the ssRNA viral genome is released and the retro-transcription step is produced; (4) The integrase protein binds to dsDNA viral genome by LTR ends sequences and other cellular proteins forming the pre-integration complex (PIC); (5) The PIC goes into nucleus through the nuclear pore and is integrated in the cellular genome by the integrase protein activity (provirus); (6) The viral RNAs are transcripted from proviral DNA and exported to cytoplasm to translate viral proteins as protease and a big pre-protein that are assembled to new RNA viral genomes and leave the cell with outer envelope from the cellular membrane; (7) After the budding viral particle, the proteases process the big pre-protein and get a mature viral particle.

Aptamers to Reverse Transcriptase (RT)

Reverse transcriptase has two enzymatic activities, a DNA polymerase activity that can copy either a DNA or an RNA template, and an RNase H that cleaves RNA only if the RNA is part of an RNA/DNA duplex. The two enzymatic functions of RT, polymerase and RNase H, cooperate to convert the RNA into a double-stranded linear DNA [40] . DeStefano and Nair confirmed in vitro effectiveness of DNA aptamer, named 37NT, directed against the reverse transcriptase of HIV HXB2 strain. The aptamer competed with the natural template for the binding site in the enzyme, subsequently producing inhibition of the viral replication [41] . In parallel, Michalowski et al. identified three aptamers (RT5, RT6 and RT47) which contained a bimodular structure comprising a 5 -stem-loop module linked to a 3 -G-quadruplex. In addition, the authors demonstrated that this DNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC 50 values [42] .

Aptamers to CCR5

HIV-1 commonly uses C-C chemokine receptor type 5 (CCR5) or C-X-C chemokine receptor type 4 (CXCR-4) as co-receptors along with CD4 to enter target cells. Human CCR5 is an important co-receptor for macrophage-tropic virus expressed by T-cells and macrophages. Differences in CCR5 are associated with resistance or susceptibility to HIV-1. As an essential factor for viral entry, CCR5 has represented an attractive cellular target for the treatment of HIV-1. Thus, Zhou et al. have reported the selection of RNA aptamers against CCR5 using high throughput sequencing (HTS) to analyze the RNA pools from selection rounds 5 to 9. The individual sequences were classified into six major groups (Group 1-6). Group 2, 4 and 5 shared a conserved sequence, which is comprised of 10 nucleotides UUCGUCUG(U/G)G, named G3. The G3 activity was studied by a "prophylactic" HIV-1 experiment determining whether the aptamer would block HIV infectivity of R5 viruses in cell culture. The results showed that the G3 aptamer efficiently neutralized HIV-1 infectivity of R5 strains with IC 50 about 170~350 nM [25] .

Aptamers HBV in Diagnostics

One of the current objectives in the diagnostic of HBV is to develop a daily screening assay with a short period of detection between infection and recognition. Therefore, Suh et al. have developed a fast and low cost detection test based on competitive binding assay combined with fluorescence resonance energy transfer (FRET) [73] . The assay was built with an aptamer selected against the hepatitis B virus surface antigen (HBsAg), the best characterize and most frequently used HBV marker [74] . The described aptasensor was approximately 40-fold more sensitive than the conventional method. In 2015, a new set of three different DNA aptamers was selected against HBsAg and applied to develop a chemiluminescence platform. The new aptasensor was designed with aptamers-conjugated to magnetic nanoparticles reaching a detection limit five-fold better than the current enzyme-linked immunosorbent assay (ELISA) kits used in hospitals [75] .

Aptamers HCV in Diagnostics

Aptamer-based biosensors are a promising diagnostic platform to allow HCV infection detection in early stages or in immunosuppressed patients. Thus, different groups have developed diverse aptasensors to improve diagnostic assay of HCV infection. First, Lee et al. developed a biosensor prototype that specifically recognizes the HCV core protein from sera of an infected patient using selected RNA aptamers against core antigen. The HCV viral particles were retained by the 2 -F aptamers immobilized in a 96-well plate and detected by sequential steps with anti-core and Cy3-labeled secondary antibodies [80] . Later on, Chen et al. developed an early diagnostic assay based on sandwich-ELISA to recognize HCV viral proteins using biotin-labelled DNA aptamers against HCV Envelope glycoprotein E2. The obtained results from infected patients showed a good correlation between viral genome quantification assay, HCV antibody detection and sandwich-ELISA aptasensor [81] . Afterwards, Shi et al. developed a similar platform for early detection, coating the bottom of the well with C7, a DNA aptamer against HCV core labelled with biotin, and HCV-core antibody conjugated with horseradish peroxidase (HRP) is applied over the surface. The platform was applied to the detection of the protein in sera from HCV-infected patients and showed a proportional relationship between amplified RNA copies and HCV core protein concentration [82] . Moreover, Wang et al. designed a rapid, easy-to-use diagnostic platform composed of lateral flow strips treated with thiol-DNA aptamers against HCV core antigen. HCV ELISA assay and core aptamer lateral flow strips showed positive coincidence rates when compared with HCV RNA amplification assay [83] . In an effort to develop a diagnostic test to monitor the infectivity of HCV samples, Park et al. have designed an ELISA-like assay replacing the capture and detection antibodies for DNA aptamers selected against HCV E2. The Enzyme Linked Apto-Sorbent Assay (ELASA) has been described to be used for qualitative and quantitative analysis of virus in infected samples [84] . Further, two laboratories have developed label-free aptasensor to eliminate the labelling step and simplify the HCV detection method. Hwang et al. have described a highly sensitive label-free aptasensor based on nanomechanical microcantilevers. The biosensors were able to measure the surface stress due to the interaction between immobilized RNA aptamers and the HCV helicase [85] . On the other hand, Roh et al. have developed a label-free diagnostic platform to detect and quantify the presence of HCV polymerase NS5B viral protein using conjugated streptavidin-biotin RNA aptamers on an Octet biosensor [86] .

Aptamers to HCV as Antiviral Agents

Eradication of HCV disease is one of the main objectives of global public health. Currently, HCV infected patients are treated combining protease inhibitors, as Telaprevir (TVR) and Boceprevir (BOC), with pegylated-interferon and Ribavirin. However, the new direct-acting antivirals (DAA), TVR and BOC, generate a high rate of side effects, are too expensive and are also susceptible to new resistant viruses [87] . Therefore, it is necessary to develop new DAA treatments that are more effective and with fewer side effects than current therapies. To this end, different advances have been made based on aptamers against HCV and host cell proteins as therapy [88] (Figure 3 ). amplification assay [83] . In an effort to develop a diagnostic test to monitor the infectivity of HCV samples, Park et al. have designed an ELISA-like assay replacing the capture and detection antibodies for DNA aptamers selected against HCV E2. The Enzyme Linked Apto-Sorbent Assay (ELASA) has been described to be used for qualitative and quantitative analysis of virus in infected samples [84] . Further, two laboratories have developed label-free aptasensor to eliminate the labelling step and simplify the HCV detection method. Hwang et al. have described a highly sensitive label-free aptasensor based on nanomechanical microcantilevers. The biosensors were able to measure the surface stress due to the interaction between immobilized RNA aptamers and the HCV helicase [85] .
Eradication of HCV disease is one of the main objectives of global public health. Currently, HCV infected patients are treated combining protease inhibitors, as Telaprevir (TVR) and Boceprevir (BOC), with pegylated-interferon and Ribavirin. However, the new direct-acting antivirals (DAA), TVR and BOC, generate a high rate of side effects, are too expensive and are also susceptible to new resistant viruses [87] . Therefore, it is necessary to develop new DAA treatments that are more effective and with fewer side effects than current therapies. To this end, different advances have been made based on aptamers against HCV and host cell proteins as therapy [88] (Figure 3) .

Aptamers to 5 and 3 Untranslated Regions (5 and 3 UTR)

In 2003, Toulmé et al. decided to use subdomain IIId of IRES element as an antiviral target. They selected RNA aptamer and verified that isolated aptamers inhibit HCV translation in vitro and in cell culture [89] . In the same year, Kikuchi et al. isolated RNA aptamers capable of binding to the domain II of HCV IRES and showed that IRES-mediated in vitro translation was reduced from 20% to 40% by using the 2-02 aptamer [90] . Later, they isolated a new RNA aptamer population against the HCV IRES domains III-IV and corroborated that 3-07 aptamer had a high inhibitory effect on IRES-mediated translation in vitro and in vivo [91] . To improve the inhibitory effect of selected aptamers, they constructed two new molecules, named 0207 and 0702, composed by 2-02 and 3-07 aptamers linked by their ends. The fused aptamers recognized two different subdomains of IRES element and are at least 10 times more efficient than the parental aptamers in the inhibition of mRNA IRES-dependent translation in vitro [92] . Following with IRES as an anti-viral target, Romero-López et al. described an innovative in vitro selection method to isolate aptamers fused to a hammerhead ribozyme with capacity to inhibit RNA translation mediated by IRES. Selected chimeric aptamer-ribozymes were able to recognize the IRES element and cleavage the 5 end at nucleotide position 363 [93] . The success of combining two functional elements in the same molecule was shown in the selected chimeric molecule HH363-50. Thus, the aptamer-ribozyme chimera did anchor to domain IV of the IRES element and inhibited in vitro and in vivo IRES-mediated translation [94] . Therefore, recruitment of ribosomal particles mediated by the IRES element was inhibited by the chimera HH363-24 that prevented both translation and replication in a hepatic cell line [95] . Moreover, to avoid HCV genome replication, Konno et al. isolated RNA aptamers against the 3 end of the negative strand of the virus genome [96, 97] . Interestingly, a RNA aptamer, named AP30, was able to recognize this minus-IRES region and reduce positive-strand genomic RNA synthesis [96] . To inhibit HCV replication, Marton et al. selected RNA aptamers against CRE element that were able to repress replication of HCV replicon in hepatic cells [98] . Subsequently, two selected aptamers, P58 and P78, interact with subdomain 5BSL3.2 of the CRE element and produce a structural reorganization of the 3 end HCV genome and a significant decrease of HCV replication in vivo [99] .

Aptamers to Nonstructural Protein 5A (NS5A)

It has been reported that NS5A protein is essential for HCV production and replication. Recently, Yu et al. have isolated and characterized DNA aptamers against HCV NS5A protein. Particularly, selected aptamer NS5A-5 was able to inhibit HCV virus infection by prevention of protein-protein interactions between NS5A and core protein [110] .
Aptamers to Nonstructural Protein 5B (NS5B) HCV nonstructural protein 5B (NS5B) is a RNA-dependent RNA polymerase protein (RdRp) responsible to the generation of positive-sense genomic HCV RNA and negative-sense RNA template. Reduction of HCV NS5B polymerase activity affects HCV viral life cycle and is one of the main objectives to isolate aptamers against NS5B. Thus, Biroccio et al. identified specific RNA aptamers against a truncated protein NS5B-∆55 without the C-terminal region. One of the selected aptamers, B.2, blocked RNA transcription but not competed with the complex RdRp-RNA, using different binding site than RNA template to the NS5B protein [111] . In the same way, Bellecave et al. selected DNA aptamers against the NS5B viral protein. One of the chosen aptamers, 27v, competed with positive and negative sense HCV viral RNA to bind RdRp polymerase and blocked initiation and elongation steps of RNA transcription [112] . However, 127v aptamer partially competes to dissociate RdRp-RNA complex formation and only inhibited initiation steps of HCV transcription [113] . Moreover, interference of viral production and transcription inhibition of HCV virus was confirmed in vivo using 27v aptamer. Table 4 shows information on the aptamers described against HCV. Five years later, another set of RNA aptamers against NS5B protein were obtained by Lee et al. [114] . To avoid aptamer degradation, oligonucleotides were modified with 2 hydroxyl (R-OH) or fluoropyrimidines (R-F). The R-OH aptamers blocked RNA synthesis of HCV replicon in cell culture without emergence of virus escape mutant or cellular toxicity. On the other hand, R-F oligonucleotides were truncated and conjugated with cholesterol-or galactose-PEG molecules to allow direct and specific liver delivery into cells or tissue. Cholesterol-and Gal-PEG-R-F t2 conjugated aptamer blocked RNA synthesis of HCV genome [115] . The above mentioned aptamers were non-genotype-specific; however, Jones et al. described for the first time aptamers against NS5 protein that exclusively recognized and inhibited RNA-polymerase activity of HCV virus subtype 3a [116] .

Aptamers to Structural Proteins E1, E2 and Core

Envelope E1 and E2 glycoproteins are putative targets in therapy due to its role in HCV viral recognition to enter into hepatic cells. Chen et al. have isolated DNA aptamer against E2 glycoprotein. The selected aptamers have higher affinity to genotype 1a, 1b and 2a than others, and strongly prevented HCV viral infection in Huh7 5.1 cells [81] . Afterwards, Yang et al. described the potential antiviral action of DNA aptamers selected against E1E2 protein by HCV infection suppression in HuH7.5 cells without innate immune response action [117] . In the case of core, an essential protein for HCV viral assembly, Shi et al. have applied for therapy the above-mentioned aptamers in diagnostics. In Huh7.5 cells, the aptamers against HCV core protein repressed viral production as a result of defective assembly of virus particle without stimulation of innate immune response [82] .

Aptamers to Influenza Virus in Diagnostics

The antibodies are the most common probe used to detect either the viral particles or host antibodies developed during the infection. However, although in most cases antibodies are able to distinguish between influenza A and B, only a few antibodies that differentiate subtypes of Influenza A or B have been reported. Alternative probes for subtyping are the aptamers. Thus, aptamers to hemagglutinin (HA) have been successfully and broadly used for the development on sensors for influenza detection. HA is expressed in high amounts in the viral surface and is required for binding and fusion with the host cell. Currently, more than 40 DNA and RNA aptamers to HA have been described since 2004, selected to recombinant hemagglutinins (H1, H3, H5, H9 and Ha from virus B) and to whole viruses (H5N1) (reviewed in [138] ). Misono and Kumar selected an RNA aptamer against to HA of A/Panama/ 2007/1999 (H3N2) using SPR-based SELEX [139] . Gopinath et al. generated two RNA aptamers against intact influenza virus A/Panama/2007/1999 and HA of B/Johannesburg/05/1999. These RNA aptamers are able to discriminate among both A and B influenza viruses [140, 141] .

Aptamers to Influenza Virus as Antiviral Agents

Other aptamers targeting NS1 or the PA polymerase subunit 1 have also been studied. NS1 is a nonstructural protein of small size, between amino acids 230 and 238 and with a molecular weight of 26 kDa. In view of its interaction with both RNAs and viral and cellular proteins, NS1 has been implicated in many of the alterations that occur during influenza virus infection. Moreover, NS1 has anti-interferon (IFN) properties leading to the inhibition of the host's innate immunity [162] . Thus, the importance of NS1 in viral infection makes it an attractive therapeutic target. Woo et al. selected a DNA aptamer specific to NS1 that induced IFN-β production by inhibiting NS1 function. In addition, the selected aptamer was able to inhibit the viral replication without affecting cell viability [163] .

Aptamers to Dengue Virus (DENV)

From a technological point of view, aptamers have been used for efficient isolation of endogenously assembled viral RNA-protein complexes. Hence, Dong et al. developed an affinity purification strategy based on an RNA affinity tag that allows large-scale preparation of native viral RNA-binding proteins (RBPs) using the streptavidin-binding aptamer S1 sequence that was inserted into the 3 end of dengue virus (DENV) 5 -3 UTR RNA, and the DENV RNA UTR fused to the S1 RNA aptamer was expressed in living mammalian cells. This allowed endogenous viral ribonucleoprotein (RNP) assembly and isolation of RNPs from whole cell extract, through binding the S1 aptamer to streptavidin magnetic beads. This strategy led to identify several novel host DENV RBPs by liquid chromatography with tandem mass spectrometry (LC-MS/MS), including RPS8, which were further implicated in DENV replication [185] .

Aptamers to Ebola Virus (EV)

Viral protein 35 (VP35) is a multifunctional dsRNA binding protein that plays important roles in viral replication, innate immune evasion and pathogenesis. These multifunctional proteins offer opportunities to develop molecules that target distinct functional regions. With this purpose, Binning et al. used a combination of structural and functional data to determine regions of Ebola virus (EBOV) VP35 (eVP35) to target aptamer selection. Two distinct classes of aptamers were characterized based on their interaction properties to eVP35. These results revealed that the aptamers bind to distinct regions of eVP35 with high affinity (10-50 nM) and specificity. In addition, the authors showed that these aptamers compete with dsRNA for binding to eVP35 and disturb the eVP35-nucleoprotein (NP) interaction. Consistent with the ability to antagonize eVP35-NP interaction, select aptamers can inhibit the function of the EBOV polymerase complex reconstituted by expression of select viral proteins [186] .

Aptamers to HIV as Antiviral Agents

At present, the treatment HIV-1/AIDS is by a combination of several antiretroviral drugs (cART), which can slow the progress of the disease and reduce the risk of death and disease complication, but it is not curative. Moreover, many patients do not tolerate cART because it has severe side effects, and it is too expensive for patients in developing countries. In this regard, aptamers have been considered an alternative or adjuvant to the chemical antiviral agents in cART to overcome these limitations. To date, highly specific, nucleic acid-based aptamers that target various parts of HIV-1 genomes, HIV-1 proteins (including HIV-1 protease (PR), reverse transcriptase (RT), nucleocapsid, gp120, and Gag) and cellular proteins (nucleolin, CD4 or CCR5) have been isolated and shown to effectively suppress viral replication to apply in HIV therapy [5, [25] [26] [27] (Figure 2 ). diamond field-effect transistor (FET) technique [24] . These "apta-biosensors" have high sensibility and specificity but the devices are complex and expensive.

Use of Aptamers for Delivery of Therapeutic Molecules

Aptamers can also serve as elements that selectively recognize and bind to defined cell types or tissues. By attaching drug molecules, the aptamers can be used to deliver cargo molecules to or into specific cells or tissues of interest [64] . In order to reach efficient RNAi activity, aptamer-siRNA conjugates must be successfully internalized and released into the cytoplasm where they can meet the RNAi machinery [65] . To improve the Dicer entry and processing of the siRNA, one pair of complementary guanosine and cytosine (GC)-rich "sticky bridge" sequences can be chemically appended to the 3 end of the aptamer and one of the siRNA strands, respectively. Both the aptamer and siRNA portions are chemically synthesized and subsequently annealed via "sticky bridge" [66] .

Perspectives

In the field of viral diseases, the number of drugs for treating these infections is very small and most of the available therapeutics are not very effective [194] . In addition, current diagnostic tools for viral infections are expensive and time consuming. These important diagnostic and therapeutic limitations have favored the development of aptamer-based systems, mainly because these show several interesting advantages in relation to antibodies. Thus, aptamers can recognize and/or inhibit target activity through specific and strong interactions superior to other biologics and small molecule therapeutics, with lower toxicity and immunogenicity profiles. In this sense, during the last years, aptamer technology is being used in a wide range of diagnostic and therapeutic applications associated with viral pathologies [195, 196] . It is significant that aptamers selected as specific anti-viral molecules are effective in infected cells, however, none of the selected antiviral aptamers entered into clinical trials. In conclusion, it is necessary to continue research studies and successfully develop clinical trials to establish the use of aptamers as antivirals.
Nanoparticles have been considered for a wide range of applications, both in soluble and insoluble forms. An advantage of soluble forms of nanoparticles is that they can encapsulate antibiotics/drugs and then release them when they reach the cellular environment, making them highly applicable for drug delivery systems. Studies on aptamer-based enhanced drug delivery have been reported for prostate cancer and lymphoblastic leukemia cells [201] . With this purpose, for HIV therapy, nanoparticles successfully loaded with the antiretroviral (ARV) drugs efficiently inhibited HIV-1 infection [202, 203] . These results showed the benefit of the nanoparticles' application to delivery of antiviral drugs to improve its bioavailability.
In conclusion, the use of aptamers in the development of diagnostic platforms or as therapeutic drugs is a promising alternative for the treatment of viral diseases.
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Abstract

Nipah (Nee-pa) viral disease is a zoonotic infection caused by Nipah virus (NiV), a paramyxovirus belonging to the genus Henipavirus of the family Paramyxoviridae. It is a biosafety level-4 pathogen, which is transmitted by specific types of fruit bats, mainly Pteropus spp. which are natural reservoir host. The disease was reported for the first time from the Kampung Sungai Nipah village of Malaysia in 1998. Human-to-human transmission also occurs. Outbreaks have been reported also from other countries in South and Southeast Asia. Phylogenetic analysis affirmed the circulation of two major clades of NiV as based on currently available complete N and G gene sequences. NiV isolates from Malaysia and Cambodia clustered together in NiV-MY clade, whereas isolates from Bangladesh and India clusterered within NiV-BD clade. NiV isolates from Thailand harboured mixed population of sequences. In humans, the virus is responsible for causing rapidly progressing severe illness which might be characterized by severe respiratory illness and/or deadly encephalitis. In pigs below six months of age, respiratory illness along with nervous symptoms may develop. Different types of enzyme-linked immunosorbent assays along with molecular methods based on polymerase chain reaction have been developed for diagnostic purposes. Due to the expensive nature of the antibody drugs, identification of broad-spectrum antivirals is essential along with focusing on small interfering RNAs (siRNAs). High pathogenicity of NiV in humans, and lack of vaccines or therapeutics to counter this disease have attracted attention of researchers worldwide for developing effective NiV vaccine and treatment regimens.