New observations on antigenic diversification of RNA viruses. Antigenic variation is not dependent on immune selection

SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice

The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution.

Diagnostic and Epitope Mapping Potential of Single-Chain Antibody Fragments Against Foot-and-Mouth Disease Virus Serotypes A, SAT1, and SAT3

Foot-and-mouth disease (FMD) affects cloven-hoofed domestic and wildlife animals and an outbreak can cause severe losses in milk production, reduction in meat production and death amongst young animals. Several parts of Asia, most of Africa, and the Middle East remain endemic, thus emphasis on improved FMD vaccines, diagnostic assays, and control measures are key research areas. FMD virus (FMDV) populations are quasispecies, which pose serious implications in vaccine design and efficacy where an effective vaccine should include multiple independent neutralizing epitopes to elicit an adequate immune response. Further investigation of the residues that comprise the antigenic determinants of the virus will allow the identification of mutations in outbreak strains that potentially lessen the efficacy of a vaccine. Additionally, of utmost importance in endemic regions, is the accurate diagnosis of FMDV infection for the control and eradication of the disease. To this end, a phage display library was explored to identify FMDV epitopes for recombinant vaccines and for the generation of reagents for improved diagnostic FMD enzyme-linked immunosorbent assays (ELISAs). A naïve semi-synthetic chicken single chain variable fragment (scFv) phage display library i.e., the Nkuku ^® library was used for bio-panning against FMD Southern-African Territories (SAT) 1, SAT3, and serotype A viruses. Biopanning yielded one unique scFv against SAT1, two for SAT3, and nine for A22. SAT1 and SAT3 specific scFvs were exploited as capturing and detecting reagents to develop an improved diagnostic ELISA for FMDV. The SAT1 soluble scFv showed potential as a detecting reagent in the liquid phase blocking ELISA (LPBE) as it reacted specifically with a panel of SAT1 viruses, albeit with different ELISA absorbance signals. The SAT1svFv1 had little or no change on its paratope when coated on polystyrene plates whilst the SAT3scFv's paratope may have changed. SAT1 and SAT3 soluble scFvs did not neutralize the SAT1 and SAT3 viruses; however, three of the nine A22 binders i.e., A22scFv1, A22scFv2, and A22scFv8 were able to neutralize A22 virus. Following the generation of virus escape mutants through successive virus passage under scFv pressure, FMDV epitopes were postulated i.e., RGD+3 and +4 positions respectively, proving the epitope mapping potential of scFvs.

Early Phylogenetic Diversification of SARS-CoV-2: Determination of Variants and the Effect on Epidemiology, Immunology, and Diagnostics

The phylogenetic clustering of 95 SARS-CoV-2 sequences from the first 3 months of the pandemic reveals insights into the early evolution of the virus and gives first indications of how the variants are globally distributed. Variants might become a challenge in terms of diagnostics, immunology, and effectiveness of drugs. All available whole genome sequence data from the NCBI database (March 16, 2020) were phylogenetically analyzed, and gene prediction as well as analysis of selected variants were performed. Antigenic regions and the secondary protein structure were predicted for selected variants. While some clusters are presenting the same variant with 100% identical bases, other SARS-CoV-2 lineages show a beginning diversification and phylogenetic clustering due to base substitutions and deletions in the genomes. First molecular epidemiological investigations are possible with the results by adding metadata as travelling history to the presented data. The advantage of variants in source tracing can be a challenge in terms of virulence, immune response, and immunological memory. Variants of viruses often show differences in virulence or antigenicity. This must also be considered in decisions like herd immunity. Diagnostic methods might not work if the variations or deletions are in target regions for the detection of the pathogen. One base substitution was detected in a primer binding site.

Interaction of virus populations with their hosts

Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided into basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.

Antigenic variability of foot-and-mouth disease virus serotype O during serial cytolytic passage

The emergence and disappearance of antigenic variants of foot-and-mouth disease virus (FMDV) during a field outbreak occurs periodically due to the volatile nature of its genome. In the present analysis, change in antigenic behavior of serotype O FMDV during the serial cytolytic passage in the absence of immune pressure was observed. Initially, the isolate showed a poor antigenic match (relationship value <0.3) with the serotype O vaccine strain and upon serial passage increase in relationship value was observed. Comparison of capsid sequence revealed substitution at four positions (VP3:K₅₈ → E and P₁₅₈ → S, VP1:E₈₃ → K and R₁₇₂ → Q) acquired during the serial passage. Examination of passage level and amino acid substitution revealed the critical role of position VP3-58 that was identified earlier as crucial for antigenic site IV, in the observed antigenic variability. The role of position VP3-58 was further confirmed using reverse genetics approach.

SAT2 Foot-and-Mouth Disease Virus Structurally Modified for Increased Thermostability

Foot-and-mouth disease virus (FMDV), particularly strains of the O and SAT serotypes, is notoriously unstable. Consequently, vaccines derived from heat-labile SAT viruses have been linked to the induction of immunity with a poor duration and hence require more frequent vaccinations to ensure protection. In silico calculations predicted residue substitutions that would increase interactions at the interpentamer interface, supporting increased stability. We assessed the stability of the 18 recombinant mutant viruses in regard to their growth kinetics, antigenicity, plaque morphology, genetic stability, and temperature, ionic, and pH stability by using Thermofluor and inactivation assays in order to evaluate potential SAT2 vaccine candidates with improved stability. The most stable mutant for temperature and pH stability was the S2093Y single mutant, while other promising mutants were the E3198A, L2094V, and S2093H single mutants and the F2062Y-H2087M-H3143V triple mutant. Although the S2093Y mutant had the greatest stability, it exhibited smaller plaques, a reduced growth rate, a change in monoclonal antibody footprint, and poor genetic stability properties compared to those of the wild-type virus. However, these factors affecting production can be overcome. The addition of 1 M NaCl was found to further increase the stability of the SAT2 panel of viruses. The S2093Y and S2093H mutants were selected for future use in stabilizing SAT2 vaccines.IMPORTANCE Foot-and-mouth disease virus (FMDV) causes a highly contagious acute vesicular disease in cloven-hoofed livestock and wildlife. The control of the disease by vaccination is essential, especially at livestock-wildlife interfaces. The instability of some serotypes, such as SAT2, affects the quality of vaccines and therefore the duration of immunity. We have shown that we can improve the stability of SAT2 viruses by mutating residues at the capsid interface through predictive modeling. This is an important finding for the potential use of such mutants in improving the stability of SAT2 vaccines in countries where FMD is endemic, which rely heavily on the maintenance of the cold chain, with potential improvement to the duration of immune responses.

Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B

In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10^-4substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections.

Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A

We studied the molecular evolution of the fusion protein (F) gene in the human respiratory syncytial virus subgroup A (HRSV-A). We performed time-scaled phylogenetic analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. We also conducted genetic distance (p-distance), positive/negative selection, and Bayesian skyline plot analyses. Furthermore, we mapped the amino acid substitutions of the protein. The MCMC-constructed tree indicated that the HRSV F gene diverged from the bovine RSV (BRSV) gene approximately 550years ago and had a relatively low substitution rate (7.59×10(-4) substitutions/site/year). Moreover, a common ancestor of HRSV-A and -B diverged approximately 280years ago, which has since formed four distinct clusters. The present HRSV-A strains were assigned six genotypes based on F gene sequences and attachment glycoprotein gene sequences. The present strains exhibited high F gene sequence similarity values and low genetic divergence. No positive selection sites were identified; however, 50 negative selection sites were identified. F protein amino acid substitutions at 17 sites were distributed in the F protein. The effective population size of the gene has remained relatively constant, but the population size of the prevalent genotype (GA2) has increased in the last 10years. These results suggest that the HRSV-AF gene has evolved independently and formed some genotypes.

Interaction of Virus Populations with Their Hosts

Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided in basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.

Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10

We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period.

Cell culture adaptation mutations in foot-and-mouth disease virus serotype A capsid proteins: implications for receptor interactions

In this study we describe the adaptive changes fixed on the capsid of several foot-and-mouth disease virus serotype A strains during propagation in cell monolayers. Viruses passaged extensively in three cell lines (BHK-21, LFBK and IB-RS-2) consistently gained positively charged amino acids in the putative heparin-sulfate-binding pocket (VP2 βE-βF loop, VP1 C-terminus and VP3 β-B knob) surrounding the fivefold symmetry axis (VP1 βF-βG loop) and at other discrete sites on the capsid (VP3 βG-βH loop, VP1 C-terminus, VP2 βC strand and VP1 βG-βH loop). A lysine insertion in the VP1 βF-βG loop of two of the BHK-21-adapted viruses supports the biological advantage of positively charged residues acquired in cell culture. The charge transitions occurred irrespective of cell line, suggesting their possible role in ionic interaction with ubiquitous negatively charged cell-surface molecules such as glycosaminoglycans (GAG). This was supported by the ability of the cell-culture-adapted variants to replicate in the integrin-deficient, GAG-positive CHO-K1 cells and their superior fitness in competition assays compared with the lower passage viruses with WT genotypes. Substitutions fixed in the VP1 βG-βH loop (-3, -2 and +2 'RGD' positions) or in the structural element known to be juxtaposed against that loop (VP1 βB-βC loop) suggest their possible role in modulating the efficiency and specificity of interaction of the 'RGD' motif with αv-integrin receptors. The nature and location of the substitutions described in this study could be applied in the rapid cell culture adaptation of viral strains for vaccine production.

Porcine reproductive and respiratory syndrome virus vaccines: current status and strategies to a universal vaccine

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of PRRS, the most significant infectious disease currently affecting swine industry worldwide. In the United States alone, the economic losses caused by PRRS amount to more than 560 million US dollars every year. Due to immune evasion strategies and the antigenic heterogeneity of the virus, current commercial PRRSV vaccines (killed-virus and modified-live vaccines) are of unsatisfactory efficacy, especially against heterologous infection. Continuous efforts have been devoted to develop better PRRSV vaccines. Experimental PRRSV vaccines, including live attenuated vaccines, recombinant vectors expressing PRRSV viral proteins, DNA vaccines and plant-made subunit vaccines, have been developed. However, the genetic and antigenic heterogeneity of the virus limits the value of almost all of the PRRSV vaccines tested. Developing a universal vaccine that can provide broad protection against circulating PRRSV strains has become a major challenge for current vaccine development. This paper reviews current status of PRRSV vaccine development and discusses strategies to develop a universal PRRSV vaccine.

Autologous HIV-1 clade-B Nef peptides elicit increased frequency, breadth and function of CD8+ T-cells compared to consensus peptides

OBJECTIVE

To determine the function and phenotype of CD8(+) T-cells targeting consensus and autologous sequences of entire HIV-1 Nef protein.

METHODS

Multiparameter flow cytometry-based analysis was used to evaluate the responses of two treatment naïve HIV-infected individuals, during primary and the chronic phases of infection.

RESULTS

A greater breadth and magnitude of CD8 IFN-γ responses to autologous compared to clade-B consensus peptides was observed in both subjects. Cross recognition between autologous and consensus peptides decreased in both subjects during progression from primary to chronic infection. The frequencies of TEMRA and TEM CD8(+) T-cells targeting autologous peptides were higher than those targeting consensus peptides and were more polyfunctional (IFN-γ(+) Gr-B(+) CD107a(+)).

CONCLUSIONS

Our data indicate superior sensitivity and specificity of autologous peptides. The functional and maturational aspects of "real" versus "cross-recognized" responses were also found to differ, highlighting the importance of a sequence-specific approach towards understanding HIV immune response.

Sequence analysis of capsid coding region of foot-and-mouth disease virus type A vaccine strain during serial passages in BHK-21 adherent and suspension cells

Sequence variability within the capsid coding region of the foot-and-mouth disease virus type A vaccine strain during serial in vitro passage was investigated. Specifically, two methods of virus propagation were utilized, a monolayer and suspension culture of BHK-21 cells. At three positions (VP2(131) E-K in both monolayer and suspension passages, VP3(85) H-R in late monolayer passages and VP3(139) K-E in only suspension passages), all mapped to surface exposed loops, amino acid substitutions were apparently fixed without reversion till the end of the passage regime. Interestingly, VP2(131, 121) and VP3(85) which form part of the heparan sulphate binding pocket, showed a tendency to acquire positively charged amino acids in either monolayer or suspension environment probably to better interact with the negatively charged cell surface glycosaminoglycans. At three identified antigenically critical positions (VP2(79), VP3(139) and VP1(154)), amino acids substitutions even in the absence of immune pressure were noticed. Hence both random drift and adaptive mutations attributable to the strong selective pressure exerted by the proposed cell surface alternate receptors could play a role in modifying the capsid sequence of cell culture propagated FMDV vaccine virus, which in turn may alter the desired potency of the vaccine formulations.

Greater numbers of nucleotide substitutions are introduced into the genomic RNA of bovine viral diarrhea virus during acute infections of pregnant cattle than of non-pregnant cattle

Background

Bovine viral diarrhea virus (BVDV) strains circulating in livestock herds show significant sequence variation. Conventional wisdom states that most sequence variation arises during acute infections in response to immune or other environmental pressures. A recent study showed that more nucleotide changes were introduced into the BVDV genomic RNA during the establishment of a single fetal persistent infection than following a series of acute infections of naïve cattle. However, it was not known if nucleotide changes were introduce when the virus crossed the placenta and infected the fetus or during the acute infection of the dam.

Methods

The sequence of the open reading frame (ORF) from viruses isolated from four acutely infected pregnant heifers following exposure to persistently infected (PI) calves was compared to the sequences of the virus from the progenitor PI calf and the virus from the resulting progeny PI calf to determine when genetic change was introduced. This was compared to genetic change found in viruses isolated from a pregnant PI cow and its PI calf, and in three viruses isolated from acutely infected, non-pregnant cattle exposed to PI calves.

Results

Most genetic changes previously identified between the progenitor and progeny PI viruses were in place in the acute phase viruses isolated from the dams six days post-exposure to the progenitor PI calf. Additionally, each progeny PI virus had two to three unique nucleotide substitutions that were introduced in crossing the placenta and infection of the fetus. The nucleotide sequence of two acute phase viruses isolated from steers exposed to PI calves revealed that six and seven nucleotide changes were introduced during the acute infection. The sequence of the BVDV-2 virus isolated from an acute infection of a PI calf (BVDV-1a) co-housed with a BVDV-2 PI calf had ten nucleotides that were different from the progenitor PI virus. Finally, twenty nucleotide changes were identified in the PI virus of a calf born to a PI dam.

Conclusions

These results demonstrate that nucleotide changes are introduced into the BVDV infecting pregnant cattle at rates of 2.3 to 8 fold higher then during the acute infection of non-pregnant animals.

Genetic change in the open reading frame of bovine viral diarrhea virus is introduced more rapidly during the establishment of a single persistent infection than from multiple acute infections

Bovine viral diarrhea viruses (BVDV) are ubiquitous viral pathogens of cattle with a high degree of sequence diversity amongst strains circulating in livestock herds. The driving force behind change in sequence is not well established but the inaccurate replication of the genomic RNA by a viral RNA polymerase without proof-reading capabilities as well as immune pressure on immunodominant proteins are thought to play major roles. Additionally, it is not clear when the majority of changes are introduced, whether during acute infections with exposure to innate and adaptive immune responses or in establishment of persistent infections (PI) in utero. To examine which generates greater sequence diversity, two groups of viruses were compared. The first was six isolates of a single strain of BVDV-2 that were isolated over greater than a year's time. These viruses caused a series of severe acute (SA) BVD outbreaks over a large geographic area. Changes in nucleotide sequence were determined by comparison of the sequence of each strain to the six virus consensus sequence. The second group was composed of six BVDV strains isolated from PI calves whose dams were exposed to PI cattle. Changes were identified by comparison of the sequence of the progenitor PI virus to that of the progeny viruses from the single in vivo 'passage'. The open reading frames (ORF) of the six SA isolates were >99% identical at the nucleotide level with 30% of the changes being nonsynonymous changes. The amount of genetic change increased with time and distance from the original outbreak. Similarly, the PI viruses isolated from single passage PI calves had >99% identity with the progenitor virus. The number of nucleotide changes in these viruses was equal to or greater than that observed in the SA viruses. The majority of the nonsynonymous changes were found in the structural proteins, with 65% of these occurring in the immunodominant E2 protein. Antigenic mapping studies using a monoclonal antibody panel specific for the BVDV E2 protein showed no antigenic differences amongst the six SA viruses, nor between the progenitor and progeny type 1a and type 2 persistent viruses. However, antigenic differences were observed in the two type 1b progeny viruses that possessed the greatest number of amino acid changes. Two antibodies were found to have altered staining patterns. These results suggest that the establishment of a single persistent infection results in more rapid generation of genetic diversity in BVDV strains than a series of acute infections and may contribute to antigenic change in the absence of an immune response.

Mechanisms of viral emergence

A number of virologic and environmental factors are involved in the emergence and re-emergence of viral disease. Viruses do not conservatively occupy a single and permanent ecological niche. Rather, due to their intrinsic capacity for genetic change, and to the evolvability of fitness levels, viruses display a potential to parasitize alternative host species. Mutation, recombination and genome segment reassortment, and combination of these molecular events, produce complex and phenotypically diverse populations of viruses, which constitute the raw material on which selection acts. The majority of emerging viral diseases of humans have a zoonotic origin. Sociologic and ecologic factors produce diverse and changing environments in which viral subpopulations have ample opportunities to be selected from intrinsically heterogeneous viral populations, particularly in the case of RNA viruses. In this manner, new human, animal and plant viruses have emerged periodically and, from all evidence, will continue to emerge. This article reviews some of the mechanisms that have been identified in viral emergence, with a focus on the importance of genetic variation of viruses, and on the general concept of biological complexity.

The quasispecies nature and biological implications of the hepatitis C virus

Many RNA viruses exist as a cloud of closely related sequence variants called a quasispecies, rather than as a population of identical clones. In this article, we explain the quasispecies nature of RNA viral genomes, and briefly review the principles of quasispecies dynamics and the differences with classical population genetics. We then discuss the current methods for quasispecies analysis and conclude with the biological implications of this phenomenon, focusing on the hepatitis C virus.

Genetic variation analysis of porcine reproductive and respiratory syndrome virus isolated in China from 2002 to 2007 based on ORF5

The complete open reading frame 5 (ORF5) sequences of 34 field porcine reproductive and respiratory syndrome virus (PRRSV) isolates from China in 2002-2007 were detected and compared with the different variable Chinese isolates S1, CH-1a, HB-1, HB-2 and JXA1. The results showed that all isolates were of type 2 PRRSV and could be assigned to two clusters. The isolates in cluster sg1 was high similar with the highly pathogenic PRRSV strain JXA1, while sg2 clustered with type 2 PRRSV isolate VR2332. It was interesting that the isolate SH02 which was isolated from Shanghai in 2002 has 98.8% identity with JXA1 emerged in 2006. And the ZJJ07 isolate was found to be a natural recombinant between a Chinese highly pathogenic SY0608 isolate and a VR-2332 derivative NH04 isolate. Analysis of the potential glycosylation sites indicated that they were frequently mutated and formed five putative N-linked glycosylation (NGS) sites patterns based on N30, 33-35, 44 and 51 in those isolates. It indicated that the highly variable PRRSV strain with different NGS patterns spread widely in China. The great genetic diversity could be taken into consideration for the control and prevention of this disease.

Influence of the mutant spectrum in viral evolution: focused selection of antigenic variants in a reconstructed viral quasispecies

RNA viruses replicate as complex mutant distributions termed viral quasispecies. Despite this, studies on virus populations subjected to positive selection have generally been performed and analyzed as if the viral population consisted of a defined genomic nucleotide sequence; such a simplification may not reflect accurately the molecular events underlying the selection process. In the present study, we have reconstructed a foot-and-mouth disease virus quasispecies with multiple, low-frequency, genetically distinguishable mutants that can escape neutralization by a monoclonal antibody. Some of the mutants included an amino acid substitution that affected an integrin recognition motif that overlaps with the antibody-binding site, whereas other mutants included an amino acid substitution that affected antibody binding but not integrin recognition. We have monitored consensus and clonal nucleotide sequences of populations passaged either in the absence or the presence of the neutralizing antibody. In both cases, the populations focused toward a specific mutant that was surrounded by a cloud of mutants with different antigenic and cell recognition specificities. In the absence of antibody selection, an antigenic variant that maintained integrin recognition became dominant, but the mutant cloud included as one of its minority components a variant with altered integrin recognition. Conversely, in the presence of antibody selection, a variant with altered integrin recognition motif became dominant, but it was surrounded by a cloud of antigenic variants that maintained integrin recognition. The results have documented that a mutant spectrum can exert an influence on a viral population subjected to a sustained positive selection pressure and have unveiled a mechanism of antigenic flexibility in viral populations, consisting in the presence in the selected quasispecies of mutants with different antigenic and cell recognition specificities.

Transmission events within outbreaks of gastroenteritis determined through analysis of nucleotide sequences of the P2 domain of genogroup II noroviruses

Tracking the spread of noroviruses during outbreaks of gastroenteritis is hampered by the lack of sequence diversity in those regions of the genome chosen for virus detection and characterization. Sequence analysis of regions of the genes encoding the RNA-dependent RNA polymerase and the S domain of the capsid does not provide sufficient discrimination between genotypically related strains of different outbreaks. However, analysis of sequences derived from the region encoding the P2 domain showed 100% similarity among strains from the same outbreak and <100% similarity among strains of different outbreaks. The prolonged nature of some hospital outbreaks, links between hospitals, and the introduction of multiple strains of a single genotype associated with an outbreak aboard a cruise ship were determined using this method. This provides a powerful tool for tracking outbreak strains and the subsequent analysis and validation of interventions in a background of multiple introductions of virus strains of the same genotype or genetic cluster.

Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability

Severe structural constraints in the hepatitis A virus (HAV) capsid have been suggested as the reason for the lack of emergence of new serotypes in spite of the occurrence of complex distributions of mutants or quasispecies. Analysis of the HAV mutant spectra under immune pressure by the monoclonal antibodies (MAbs) K34C8 (immunodominant site) and H7C27 (glycophorin binding site) has revealed different evolutionary dynamics. Populations composed of complex ensembles of mutants with very low fitness or single dominant mutants with high fitness permit the acquisition of resistance to each of the MAbs, respectively. Deletion mutants were detected as components of the mutant spectra: up to 61 residues, with an average of 19, and up to 83 residues, with an average of 45, in VP3 and VP1 proteins, respectively. A clear negative selection of those replacements affecting the residues encoded by rare codons of the capsid surface has been detected through the present quasispecies analysis, confirming a certain beneficial role of such clusters. Since these clusters are located near or at the epitope regions, the need to maintain such clusters might prevent the emergence of new serotypes.

Inter-seasonal diversity of norovirus genotypes: Emergence and selection of virus variants

This study describes a method used to determine the diversity of NoVs co-circulating in the community that consisted of the analysis of a limited number of strains collected from outbreaks occurring at different times of the NoV season. The diversity of twenty NoV strains collected from outbreaks occurring at the beginning of each NoV season (September) was compared to the diversity found in the middle (December) and at the end of the season (March). The method was validated through the characterisation of greater numbers of strains at times when novel genotypes or variants were detected. A total of 864 strains from outbreaks of gastroenteritis from the 2003/04, 2004/05 and 2005/06 seasons were genotyped, with the majority of outbreaks occurring in the UK. There was a greater diversity of NoV genotypes at the beginning of two of the three seasons, 2003/04 and 2005/06, when compared to strains circulating at the end of the seasons, and GII-4 NoV strains predominated (>90%) at the end of each season. Data from this study also identified the co-circulation and differentiation of three major GII-4 variants (v2, v3, and v4). Detailed analysis of a larger number of strains throughout each season confirmed that variants emerged, became the predominant circulating strain and were ultimately replaced with another variant selected from a pool of variants. By June 2006, GII-4 v4 (Hu/NoV/Rhyl440/2005/UK) emerged as the predominant GII-4 strain, usurping the previous GII-4 v3 strain [Hu/NoV/Hunter284E/040/AU] to become the commonest co-circulating strain, in the UK in 2006.

Consistent change in the B-C loop of VP2 observed in foot-and-mouth disease virus from persistently infected cattle: implications for association with persistence

The mechanisms of foot-and-mouth disease virus (FMDV) persistence are poorly understood. It is thought the existence of viral quasispecies that encompass sub-populations with varying survival competencies and antigenicities may play some role in the maintenance of virus in persistently infected animals. By analyzing nucleotide sequences encoding the viral VP2 protein in oesophageal-pharyngeal fluid (probang) samples from cattle at different stages of infection, the significance of any amino acid changes in relation to persistence was investigated. Twenty-two experimentally infected cattle (including six carriers) from three animal experiments with FMDV type O UKG34/2001 were studied. Comparison of VP2 sequences in these samples with the inoculum sequence revealed a consistent change in the B-C loop in FMDV from persistently infected cattle. Residue 2079 changed from Y to H in five carrier animals and residue 2080 changed from A to Q in one carrier from 14 days post-infection onward. In contrast, there were no changes evident in any of the non-carriers up to 28 days post-infection. The results indicate that a substitution change in the B-C loop of VP2 may be associated with persistent FMDV infection in cattle.

New insights into the genetic diversity of European porcine reproductive and respiratory syndrome virus (PRRSV)

The complete ORF5 sequences of 66 porcine reproductive and respiratory syndrome (PRRS) field virus strains (1991-2001) and three European modified live vaccine strains were determined, as well as ORFs 6 and 7 of 19 selected strains. The variability of the deduced ORF5 amino acid sequences was analysed using statistical process control (SPC), allowing for the objective assessment of variable and conserved regions. Four variable and four conserved regions as well as five hypervariable amino acid positions were defined. The effects of genetic variability on possible structural and functional properties were discussed with emphasis on immunogenic features. Phylogenetic analysis and pairwise comparison of the nucleotide sequences revealed that the genetic distances between the strains has greatly increased over time. The data do not support an evolutionary influence of the geographical location or the time of sample collection, nor of PRRSV vaccination on strain development. In contrast to other authors who tended to concentrate on the samples from either a common geographic origin or a short sampling period, we could not confirm geographically separate PRRSV clusters nor did we find evidence of positive selective pressure as measured by the ratio of synonymous to non-synonymous substitutions in ORF5, 6 or 7. Immunological implications and vaccination strategies are discussed.

Diversity of noroviruses cocirculating in the north of England from 1998 to 2001

A study was undertaken to investigate the diversity of noroviruses (NVs) in fecal samples from patients from 529 outbreaks and 141 sporadic cases of gastroenteritis in the North of England from September 1998 to August 2001. NV strains were detected by electron microscopy and characterized by a combination of the Grimsby virus antigen enzyme-linked immunosorbent assay, reverse transcriptase PCR, the heteroduplex mobility assay, and DNA sequencing. Twenty-one distinct NV strains, including several novel or variant strains not seen previously, were found circulating in the population studied. Genogroup II NVs were responsible for 83% of the outbreaks. Several strains cocirculated at any one time. The Bristol (Grimsby/Lordsdale) and Hawaii (Girlington) genotypes were the most prevalent among the NVs identified, detected in 49 and 20% of the outbreaks, respectively. A limited number of other genogroup II and I strains were cocirculating. The virus populations detected in hospitals and nursing homes were distinct from those found in community-based outbreaks. Outbreaks in hospitals and nursing homes were more likely to be caused by genogroup II strain Grimsby or Girlington (P < 0.0001) than by other genogroup II or I strains.

Foot-and-mouth disease

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals. The disease was initially described in the 16th century and was the first animal pathogen identified as a virus. Recent FMD outbreaks in developed countries and their significant economic impact have increased the concern of governments worldwide. This review describes the reemergence of FMD in developed countries that had been disease free for many years and the effect that this has had on disease control strategies. The etiologic agent, FMD virus (FMDV), a member of the Picornaviridae family, is examined in detail at the genetic, structural, and biochemical levels and in terms of its antigenic diversity. The virus replication cycle, including virus-receptor interactions as well as unique aspects of virus translation and shutoff of host macromolecular synthesis, is discussed. This information has been the basis for the development of improved protocols to rapidly identify disease outbreaks, to differentiate vaccinated from infected animals, and to begin to identify and test novel vaccine candidates. Furthermore, this knowledge, coupled with the ability to manipulate FMDV genomes at the molecular level, has provided the framework for examination of disease pathogenesis and the development of a more complete understanding of the virus and host factors involved.

Negative selection on neutralization epitopes of poliovirus surface proteins: implications for prediction of candidate epitopes for immunization

For development of effective vaccines against viruses, it is of importance to choose appropriate epitopes as the target for immunization. These epitopes should eventually be determined experimentally, but it would be helpful if we could predict candidate epitopes computationally because it accelerates the entire process. To predict candidate epitopes for immunization, it is of great interest to characterize the target epitopes of poliovirus vaccine, which has empirically proven to be the most effective among all vaccines available. Here I show that almost all amino acid sites of poliovirus surface proteins VP1, VP2, and VP3 including neutralization epitopes are negatively selected and no site is under positive selection. These results, together with those obtained in previous studies, indicate that vaccines directed against epitopes, which consist of negatively selected sites protect vaccinees more effectively than those directed against epitopes which contain positively selected sites. These observations suggest that candidate epitopes for immunization are predicted by the molecular evolutionary analysis of viral protein (and its coding nucleotide) sequences, as the epitopes which consist exclusively of negatively selected amino acid sites.

Evidence for quasispecies distributions in the human hepatitis A virus genome

Nucleotide sequence analysis of multiple molecular clones of the hepatitis A virus (HAV), generated by reverse transcription-PCR of two capsid-coding regions, revealed a degree of heterogeneity compatible with a quasispecies structure in three clinical samples. Passage of plaque-purified reference strain HAV pHM175 43c in FRhK-4 cells documented the generation of a mutant distribution of HAV genomes. The mutant spectra showed mutation frequencies in the range of 1 x 10(-3) to 1 x 10(-4) substitutions per nucleotide, with a dominance of transition over transversion mutations. While in the VP3-coding region, nonsynonymous mutations were predominant; in the VP1-coding region they were uncommon. Around 50% of the amino acid replacements involved residues located at or near antigenic sites. Most of the detected mutations occurred at or in the vicinity of rare codons, suggesting a dynamics of mutation-selection, predominantly at and around rare codons. The results indicate that despite antigenic conservation, HAV replicates as a complex distribution of mutants, a feature of viral quasispecies.

Detection of human respiratory syncytial virus sequences in peripheral blood mononuclear cells

Peripheral blood mononuclear cells (PBMC) obtained from patients with lower respiratory infections were examined for the detection of human respiratory syncytial virus (RSV) sequences in the N region using the reverse transcription polymerase chain reaction (RT-PCR). RSV infection was confirmed by at least one method, i.e., virus isolation, enzyme immunoassay for viral antigen, and RT-PCR of nasopharyngeal secretions (NPS) samples. The detection rate for RSV RNA in PBMC obtained from RSV-infected patients was 40% (38/94), compared to 5% (1/20) in controls (P = 0.002). Between the groups positive (38) and negative (56) for RSV RNA in PBMC, there was no significant difference in clinical parameters. Seven patients had eight episodes of reinfection and RSV RNA was detected in 50% (4/8) during consecutive infections. Sequences of their PBMC samples were distinct from those of prototype strains of subgroup A and B. However, they were not always consistent with those of paired NPS samples. The findings suggested that RSV RNA could be detected in PBMC even during reinfection and as might have the possibility of quasispecies dynamics, reflecting the nature of RNA viruses.

Evolution of foot-and-mouth disease virus

Foot-and-mouth disease virus evolution is strongly influenced by high mutation rates and a quasispecies dynamics. Mutant swarms are subjected to positive selection, negative selection and random drift of genomes. Adaptation is the result of selective amplification of subpopulations of genomes. The extent of adaptation to a given environment is quantified by a relative fitness value. Fitness values depend on the virus and its physical and biological environment. Generally, infections involving large population passages result in fitness gain and population bottlenecks lead to fitness loss. Very different types of mutations tend to accumulate in the foot-and-mouth disease virus (FMDV) genome depending on the virus population size during replication. Quasispecies dynamics predict higher probability of success of antiviral strategies based on multivalent vaccines and combination therapy, and this has been supported by clinical and veterinary practice. Quasispecies suggest also new antiviral strategies based on virus entry into error catastrophe, and such procedures are under investigation. Studies with FMDV have contributed to the understanding of quasispecies dynamics and some of its biological implications.

Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus

Recombination is one of the factors that contribute to genetic diversity in foot-and-mouth disease virus (FMDV). Similarity and bootscan analyses have provided evidence of recombination in the capsid-coding (P1) region of the virus. In the present study, of the 14 subtype A22 field isolates that were distributed in three previously described genotypes (IV, VI and VII) based on the 1D (VP1-encoding) gene sequence (Tosh et al., 2002 ), one isolate (IND 170/88) was found to be a hybrid of genotypes VI and VII in the P1 region. VP1, VP4, the 5' region of VP2 and the 3' region of VP3 of this virus were characteristic of genotype VI, whereas the remaining 3' region of VP2 and the 5' region of VP3 were characteristic of genotype VII. No insertion or deletion was observed in the recombinant virus. Recombination in the P1 region may provide an escape mechanism for the virus.

Selection of antigenic variants in maedi-visna virus infection

In order to analyse the pattern of sequence variation in maedi-visna virus (MVV) in persistently infected sheep and to answer the question of whether antigenic variants are selected in a long-term MVV infection, an 87 bp variable region in the env gene of ten antigenic variants and 24 non-variants was sequenced. Nine of the ten antigenic variants had mutations in this region, comprising 24 point mutations and a deletion of 3 bp. Twenty-three of the point mutations (96%) were non-synonymous. There was only a single mutation in this region in the 24 non-variants. A type-specific neutralizing antibody response appeared in all the sheep 2-5 months post-infection, and in most sheep more broadly reacting neutralizing antibodies appeared up to 4 years later. All the antigenic variants were neutralized by the broadly reacting sera. It is noteworthy that the antigenic variants were isolated at a time when only the type-specific antibodies were acting, before the broadly reacting antibodies appeared. The same picture emerged when molecularly cloned virus was used for infection. Three sheep were infected with a molecularly cloned virus, and of six virus isolates, one was an antigenic variant. This variant arose in the absence of broadly reacting antibodies. The results indicate that there is selection for mutants that escape neutralization.

Equine rhinitis B virus: a new serotype

Equine rhinovirus serotype 3 isolate P313/75 was assigned, with an unclassified genus status, to the family PICORNAVIRIDAE: The sequence from the 5' poly(C) tract to the 3' poly(A) tract of P313/75 was determined. The sequence is 8821 bases in length and contains a potential open reading frame for a polyprotein of 2583 amino acids. Sequence comparison and phylogenic analysis suggest that P313/75 is most closely related to the prototype equine rhinitis B virus (ERBV) strain P1436/71, formerly named equine rhinovirus type 2. A high degree of sequence similarity was found in the P2 and P3 regions of the two genomes. However, the deduced amino acid sequences of the P1 region of P313/75 and ERBV strain P1436/71 contained significant differences, which presumably account for the serological segregation of the two viruses. It is suggested that P313/75 can be classified as a new serotype of the genus Erbovirus, tentatively named ERBV2. Seroepidemiological data indicate that ERBV2 infection of horses may be common (24%) in Australia.

Neutralizing antiviral antibody responses

Neutralizing antibodies are evolutionarily important effectors of immunity against viruses. Their evaluation has revealed a number of basic insights into specificity, rules of reactivity (tolerance), and memory—namely, (1) Specificity of neutralizing antibodies is defined by their capacity to distinguish between virus serotypes; (2) B cell reactivity is determined by antigen structure, concentration, and time of availability in secondary lymphoid organs; and (3) B cell memory is provided by elevated protective antibody titers in serum that are depending on antigen stimulation. These perhaps slightly overstated rules are simple, correlate with in vivo evidence as well as clinical observations, and appear to largely demystify many speculations about antibodies and B cell physiology. The chapter also considers successful vaccines and compares them with those infectious diseases where efficient protective vaccines are lacking, it is striking to note that all successful vaccines induce high levels of neutralizing antibodies (nAbs) that are both necessary and sufficient to protect the host from disease. Successful vaccination against infectious diseases such as tuberculosis, leprosy, or HIV would require induction of additional long-lasting T cell responses to control infection.

B-cell epitopes of the envelope glycoprotein of caprine arthritis-encephalitis virus and antibody response in infected goats

Goats infected with caprine arthritis-encephalitis virus (CAEV) develop high titres of antibodies to Env. Not only is no consistent neutralizing response found but anti-Env antibodies have even been associated with disease in infected goats. To identify the continuous antigenic determinants involved in this atypical anti-Env response, we mapped CAEV-CO Env by screening an epitope expression library with infected goat sera. In addition to the four previously described epitopes, seven novel antigenic sites were identified, of which five were located on the surface (SU) and two in the transmembrane (TM) subunits of Env. The SU antibody-binding domains located in the variable regions of the C-terminal part of the molecule (SU3 to SU5) showed the strongest reactivity and induced a rapid seroconversion in six experimentally infected goats. However, the response to these immunodominant epitopes did not appear to be associated with any neutralizing activity. The pattern of serum reactivity of naturally infected goats with these epitopes was restricted, suggesting a type-specific reaction. Interestingly, the reactivity of peptides representing SU5 sequences derived from CAEV field isolates varied with the geographical and/or breeding origin of the animals. This suggests that peptides corresponding to the immunodominant SU epitopes may well be useful in the serotyping of CAEV isolates. Furthermore, the identification of the CAEV Env epitopes will permit us to functionally dissect the antibody response and to address the role of anti-Env antibodies either in the protection from or in the pathogenesis of CAEV infection.

Participation of the Dengue virus in the fibrinolytic process

To date, the phatophysiology of hemorrhagic dengue is still unknown and hypotheses which aim to explain the unfortunate cases of the disease (hemorrhagic fever/shock syndrome) are based on epidemiological data and favor the notion of the participation of heterotypic non-neutralizing antibodies during the course of secondary infection (immunologic status of the host). However, cases of hemorrhagic dengue have been reported during the course of primary infections. We propose that the dengue virus, specifically the envelope glycoprotein can participate directly in the installation of the hemorrhagic phenomenon by means of the binding and activation of plasminogen (PLG) as condition previous to the development of the fibrinolytic process. Based on this hypothesis, we evaluated the biological activity of some viral isolates proceeding from hemorrhagic and from dengue fever cases in an in vitro model of fibrinolysis. Dengue isolates were capable of activating PLG. The plasmin generated specifically degraded the fibrin/fibrinogen molecule. This catalytic process can be prevented by the presence of the specific plasmin inhibitor, alpha-2-antiplasmin, for virus isolates from dengue fever, but not for isolates associated with dengue hemorrhagic disease, favoring the exacerbation of the fibrinolytic activity. This new approach allows us to suggest the importance of viral factors in the dengue hemorrhagic fever.

Carriers of foot-and-mouth disease virus: a review

This review describes current knowledge about persistent foot-and-mouth disease virus (FMDV) infections, the available methods to detect carrier animals, the properties of persisting virus, the immunological mechanisms, and the risk of transmission. In particular, knowledge about the carrier state, the period in which virus can be isolated from animals 28 days or longer post infection, is important, because the risk that animals may carry the virus will influence the diagnostic and preventive measures that need to be taken. Although many years of research have led to much knowledge about foot-and mouth disease and its causative agent, there are still numerous aspects of the virus and the disease that are not yet fully understood. Areas for further research on persistence of FMDV are discussed.

Antigenic variation and genotype of isolates of porcine reproductive and respiratory syndrome virus in Korea

A panel of three anti-glycoprotein 5 (gp5) protein monoclonal antibodies (mAbs) (15, 28 and 246) and three anti-nucleocapsid (N) protein mAbs (SDOW17, VO17 and EP147) was used to investigate, by an indirect fluorescent antibody test, the antigenic variations of 50 Korean isolates of porcine reproductive and respiratory syndrome virus (PRRSV), and compare them with a us ATCC vR2332-derived attenuated vaccine strain and the reference European Lelystad strain of PRRSV. A multiplex PCR assay for the differentiation of European and North American genotypes of PRRSV was used to determine the genotype of the 50 Korean isolates. Forty-six (92 per cent) of the 50 Korean isolates shared the epitopes recognised by the anti-N protein mAb SDOW17. No reactivity to the anti-gp5 and anti-N protein mAbs was observed with the other four isolates. Six distinct patterns could be identified on the basis of their reactivities with the anti-PRRSV mAbs. All 50 isolates were identified as North American genotypes by the differential PCR.

Genetic evolution of GB virus C/hepatitis G virus (GBV-C/HGV) under interferon pressure

The epidemiology and clinical features of chronic GBV-C/HGV infection have largely been explored, but there is little information about the mechanisms enabling GBV-C/HGV to cause persistent infection. Since analysis of the genomic variation of GBV-C/HGV under interferon pressure might provide some insight into this issue, we analyzed the nucleotide sequence variation of the 5'NC and NS3 regions in GBV-C/HGV isolates obtained sequentially from seven patients co-infected with HCV and treated with interferon. A reduction of GBV-C/HGV-RNA serum level below the detection limit of the RT-PCR assay was observed during treatment in all patients, but upon interferon withdrawal, viral RNA remained undetectable in only two patients. Among the five patients who did not clear GBV-C/HGV-RNA, viral strains emerging after treatment were identical to those present at baseline in three cases. In a further case, in whom GBV-C/HGV-RNA re-emerged during therapy (breakthrough episode), several mutations appeared in relapse samples. In the remaining patient, with a mixed infection before therapy, only one of the two GBV-C/HGV strains present at baseline was detected upon treatment withdrawal. These data raise the possibility that positive selection may act over GBV-C/HGV genome during interferon therapy, and contribute to persistence of infection with this virus.

Respiratory syncytial virus genetic and antigenic diversity

Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.

Respiratory syncytial virus genetic and antigenic diversity

Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.

Genomic nucleotide sequence of a foot-and-mouth disease virus clone and its persistent derivatives. Implications for the evolution of viral quasispecies during a persistent infection

The consensus nucleotide sequence of the entire genome of foot-and-mouth disease virus (FMDV) (biological clone C-S8c1) has been completed, and compared with that of two persistent derivatives R99 and R146, rescued after 99 and 146 passages of the carrier BHK-21 cells. Consensus sequences were determined directly from supernatants of persistently infected cells, without intervening cytolytic amplification of the viruses. These genomic sequences have also been compared with that of FMDV R100, a virus that was also rescued from persistently infected cells, but that was subjected to cytolytic amplification prior to sequencing. Mutation frequencies for R99 and R146 relative to C-S8c1 were in the range of 2.8x10(-3) to 7.7x10(-3) substitutions per nucleotide for the 5'-UTR and the L-, P1-, P2- and P3-coding regions. No mutations were fixed in the polymerase (3D)-coding region. Striking contrasts were noted regarding the distribution of mutation types along the persistent genomes, notably the complete absence of transversion mutations within the 5'-UTR, compared with 53% transversions in the L- and P1-coding regions. The sequencing results presented here, combined with previous sequences of FMDV C-S8c1 genomes at the onset of persistence, provide evidence of sequence fluctuations with a non-linear accumulation of mutations during prolonged persistence, a hallmark of quasispecies dynamics.