Meta-analysis of Genetic Diversity of the VP1 Gene Among the Circulating O, A, and SAT2 Serotypes and Vaccine Strains of FMD Virus in Egypt

Introduction

Three strains of the FMD virus (A, O, and SAT 2) were recognised as causes of the FMD circulating in Egypt. The aims of this study were to trace the FMDV isolates from outbreaks in Egypt to understand their epidemiology and evolution and to understand the situation of the vaccine strains compared with the circulating serotypes.

Material and Methods

A meta-analysis was carried out by using the data available for FMD outbreaks in Egypt from GenBank and the World Reference Laboratory for Foot-and-Mouth Disease (WRLFMD); a comparison was done with both data sets for the three serotypes. MEGA-X was used for the evolution analysis, through constructions of phylogenetic trees for all sequences recorded in GenBank for each serotype in different Egyptian outbreaks in different years and also within the same year. Additionally, nucleotide substitution rate, molecular clock, and mean evolutionary rates were estimated for the three serotypes to understand and compare their evolution.

Results

Absence of some records of certain serotype outbreaks from the WRLFMD database was noted as were subsequent missing appropriate vaccine programmes. Genetic variation was recorded among the virus isolates within the same years and also the vaccine strain was associated with up to 26 amino acid substitutions. The evolution rate of the SAT2 strain was the highest of the circulating strains. SAT2 had high amino acid substitution per year at an important immunogenic site (130–170), serotype A had less, and serotype O the least.

Conclusion

The need for different strategies for vaccine serotype selection is indicated.

Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales

Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes-Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.

The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa

Foot-and-mouth disease (FMD) is a major livestock disease with direct clinical impacts as well as indirect trade implications. Control through vaccination and stamping-out has successfully reduced or eradicated the disease from Europe and large parts of South America. However, sub-Saharan Africa remains endemically affected with 5/7 serotypes currently known to be circulating across the continent. This has significant implications both locally for livestock production and poverty reduction but also globally as it represents a major reservoir of viruses, which could spark new epidemics in disease free countries or vaccination zones. This paper describes the phylodynamics of serotypes A and SAT2 in Africa including recent isolates from Cameroon in Central Africa. We estimated the most recent common ancestor for serotype A was an East African virus from the 1930s (median 1937; HPD 1922-1950) compared to SAT2 which has a much older common ancestor from the early 1700s (median 1709; HPD 1502-1814). Detailed analysis of the different clades shows clearly that different clades are evolving and diffusing across the landscape at different rates with both serotypes having a particularly recent clade that is evolving and spreading more rapidly than other clades within their serotype. However, the lack of detailed sequence data available for Africa seriously limits our understanding of FMD epidemiology across the continent. A comprehensive view of the evolutionary history and dynamics of FMD viruses is essential to understand many basic epidemiological aspects of FMD in Africa such as the scale of persistence and the role of wildlife and thus the opportunities and scale at which vaccination and other controls could be applied. Finally we ask endemic countries to join the OIE/FAO supported regional networks and take advantage of new cheap technologies being rolled out to collect isolates and submit them to the World Reference Laboratory.

Inoculation of newborn mice with non-coding regions of foot-and-mouth disease virus RNA can induce a rapid, solid and wide-range protection against viral infection

We have recently described the ability of in vitro-transcribed RNAs, mimicking structural domains in the 5' and 3' non-coding regions (NCRs) of the foot-and-mouth disease virus (FMDV) genome, to trigger the innate immune response in porcine cultured cells and mice. In this work, the antiviral effect exerted in vivo by these small synthetic non-infectious RNA molecules was analyzed extensively. The susceptibility of transfected newborn Swiss mice to FMDV challenge was tested using a wide range of viral doses. The level of protection depended on the specific RNA inoculated and was dose-dependent. The RNA giving the best protection was the internal ribosome entry site (IRES), followed by the transcripts corresponding to the S fragment. The time course of resistance to FMDV of the RNA-transfected mice was studied. Our results show the efficacy of these RNAs to prevent viral infection as well as to contain ongoing FMDV infection in certain time intervals. Protection proved to be independent of the serotype of FMDV used for challenge. These results support the potential use of the FMDV NCR transcripts as both prophylactic and therapeutic molecules for new FMDV control strategies.

Phylogenomics and molecular evolution of foot-and-mouth disease virus

This report describes the use of Bayesian methods to analyze polyprotein coding region sequences (n = 217) obtained from GenBank to define the genome-wide phylogeny of foot and mouth disease virus (FMDV). The results strongly supported the monophyly of five FMDV serotypes, O, A, Asia 1, C, and SAT 3, while sequences for the two remaining FMDV serotypes, SAT 1 and SAT 2 did not separate into entirely distinct clades. The phylogenomic tree revealed three sister-group relationships, serotype O + Asia 1, A + C, and SAT 1 + 3 + 2, with a new branching pattern: {[(O, Asia 1), (A, C)], (SAT 1, 2, 3)}. Within each serotype, there was no apparent periodic, geographic, or host species influence on the evolution of global FMDVs. Analysis of the polyprotein coding region of these sequences provided evidence for the influence of purifying selection on the evolution of FMDV. Using a Bayesian coalescent approach, the evolutionary rate of FMDV isolates that circulated during the years 1932-2007 was estimated to be 1.46 × 10(-3) substitutions/site/year, and the most recent common ancestor of the virus existed approximately 481 years ago. Bayesian skyline plot revealed a population expansion in the early 20(th) century that was followed by a rapid decline in population size from the late 20(th) century to the present day. These findings provide new insights into the mechanisms that impact on the evolution of this important livestock pathogen.

Differentiation of foot-and-mouth disease-infected pigs from vaccinated pigs using antibody-detecting sandwich ELISA

The presence of serum antibodies for nonstructural proteins of the foot-and-mouth disease virus (FMDV) can differentiate FMDV-infected animals from vaccinated animals. In this study, a sandwich ELISA was developed for rapid detection of the foot-and-mouth disease (FMD) antibodies; it was based on an Escherichia coli-expressed, highly conserved region of the 3ABC nonstructural protein of the FMDV O/TW/99 strain and a monoclonal antibody derived from the expressed protein. The diagnostic sensitivity of the assay was 98.4%, and the diagnostic specificity was 100% for naïve and vaccinated pigs; the detection ability of the assay was comparable those of the PrioCHECK and UBI kits. There was 97.5, 93.4 and 66.6% agreement between the results obtained from our ELISA and those obtained from the PrioCHECK, UBI and CHEKIT kits, respectively. The kappa statistics were 0.95, 0.87 and 0.37, respectively. Moreover, antibodies for nonstructural proteins of the serotypes A, C, Asia 1, SAT 1, SAT 2 and SAT 3 were also detected in bovine sera. Furthermore, the absence of cross-reactions generated by different antibody titers against the swine vesicular disease virus and vesicular stomatitis virus (VSV) was also highlighted in this assay's specificity.

Molecular epidemiology of foot-and-mouth disease virus serotypes A and O with emphasis on Korean isolates: temporal and spatial dynamics

We determined complete 1D gene sequences for one serotype A and seven additional serotype O Korean foot-and-mouth disease viruses (FMDV) and then analyzed them together with published sequences for 180 type A and 300 type O isolates from throughout the world using a Bayesian coalescent approach. Here, Korean serotype A virus was linked with those from Laos. Korean serotype O viruses were divided into three clades and were closely related to isolates from Japan, Thailand, the UK, France, Ireland, South Africa, and Singapore, as well as Laos. There was no apparent correlation between time, country, or host species and the evolution of global FMDVs. Additionally, our results showed that purifying selection acts on the overall 1D sequences and there was no evidence of recombination among the FMDV sequences. The evolutionary rates were 5.77 × 10(-3) substitutions/site/year for serotype A and 4.81 × 10(-3) substitutions/site/year for serotype O. Serotype A viruses diverged approximately 110 years ago, while serotype O isolates segregated approximately 127 years before the present. In both serotype isolates, the effective number of infections remained constant until the late 1990 s, after which the virus population size underwent a rapid, sharp decline until the present.

Heterogeneity and genetic variations of serotypes O and Asia 1 foot-and-mouth disease viruses isolated in Vietnam

Six field foot-and-mouth disease viruses (FMDVs), including four serotype O and two serotype Asia 1 strains, were collected from endemic outbreaks in 2005, 2006, and 2007 from four different provinces in Vietnam. The viruses were isolated and genetically characterized for their complete genomic sequences. The genetic analysis based on the complete genomic coding sequences revealed that the four serotype O FMDVs were related to each other, sharing 95.2% nucleotide (nt) identity and 97.5-97.6% amino acid (aa) identity. Genetic analysis and a phylogenetic tree, based on the VP1 gene of FMDV, showed that the four present Vietnamese serotype O strains have a high level of identity with other serotype O representatives of the Mya-98 lineage of the Southeast Asian (SEA) topotype. The four viruses were all clustered into the Mya-98 lineage of the SEA topotype, sharing 92.3-95.6% nt and 93.4-96.7% aa identity. This finding of the Mya-98 lineage was different from previous reports that the Vietnamese serotype O strains belonged to the Cam-94 lineage of the SEA topotype and two other topotypes, Middle East-South Asia (ME-SA) and Cathay. For the two serotype Asia 1 FMDVs, the genetic analysis based on the complete genomic coding sequences as well as on the VP1 gene revealed that they belonged to two genogroups, IV and V. Of note, the As1/VN/QT03/2007 strain of genogroup V, isolated in 2007, was very closely related to the pandemic Asia 1 strain which caused FMD outbreaks in China (Asia1/WHN/CHA/06, FJ906802) and Mongolia (Asia1/MOG/05, EF614458) in 2005, sharing 99.0-99.3% nt and 99.5-100% aa identity. In contrast, the second strain As1/VN/LC04/2005 of genogroup IV, isolated in 2005, was closely related to all referenced Vietnamese serotype Asia 1 strains found in the GenBank databases, sharing 86.4-100% nt and 90.9-100% aa identity with each. This study is the first description of the full-length genomic sequence of Vietnamese FMDV serotypes O and Asia 1 and may provide the evidence of the concurrent circulation of different serotypes and subtypes of FMDV in recent years in Vietnam.

Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

Most viruses are maintained by complex processes of evolution that enable them to survive but also complicate efforts to achieve their control. In this paper, we study patterns of evolution in foot-and-mouth disease (FMD) serotype C virus isolates from Kenya, one of the few places in the world where serotype C has been endemic and is suspected to remain. The nucleotide sequences encoding the capsid protein VP1 from eight isolates collected between 1967 and 2004 were analysed for patterns of sequence divergence and evolution. Very low nucleotide diversity (π=0·0025) and remarkably little change (only five segregating sites and three amino-acid changes) were observed in these isolates collected over a period of almost 40 years. We interpret these results as being suggestive of re-introductions of the vaccine strain into the field. The implications of these results for the maintenance of serotype C FMD virus and the use of vaccination as a control measure in Kenya are discussed.

Identifying coevolutionary patterns in human leukocyte antigen (HLA) molecules

The antigenic peptide, major histocompatibility complex molecule (MHC; also called human leukocyte antigen, HLA), coreceptor CD8, or CD4 and T-cell receptor (TCR) function as a complex to initiate effectors' mechanisms of the immune system. The tight functional and physical interaction among these molecules may have involved strong coevolution links among domains within and between proteins. Despite the importance of unraveling such dependencies to understand the arms race of host-pathogen interaction, no previous studies have aimed at achieving such an objective. Here, we perform an exhaustive coevolution analysis and show that indeed such dependencies are strongly shaping the evolution and probably the function of these molecules. We identify intramolecular coevolution in HLA class I and II at domains important for their immune activity. Most of the amino acid sites identified to be coevolving in HLAI have been also detected to undergo positive Darwinian selection highlighting therefore their adaptive value. We also identify coevolution among antigen-binding pockets (P1-P9) and among these and TCR-binding sites. Conversely to HLAI, coevolution is weaker in HLAII. Our results support that such coevolutionary patterns are due to selective pressures of host-pathogen coevolution and cooperative binding of TCRs, antigenic peptides, and CD8/CD4 to HLAI and HLAII.

Modulation of inter-vaccination interval to avoid antigenic competition in multivalent footrot (Dichelobacter nodosus) vaccines in sheep

Virulent footrot is a significant disease of sheep in most sheep farming countries; a strain/serogroup of the anaerobic bacterium Dichelobacter nodosus is the essential transmitting agent. Commercial multivalent footrot vaccines containing nine fimbrial serogroups (A through I) of D. nodosus produce relatively low and short term antibody responses due to antigenic competition, in contrast to higher and longer responses provided by monovalent or bivalent vaccines. The latter were important components of successful eradication programs for endemic footrot caused by either one or two serogroups of D. nodosus in Nepal, Bhutan, and several flocks in Australia. However, the presence of up to six serogroups in some Australian flocks and the use of an annual bivalent vaccination regime to progressively eradicate serogroups would require a long term program. In this study we report the results of a sequential vaccination trial testing different time intervals between different bivalent vaccinations. Intervals of 12, 9, 6, 3 and 0 months were tested. The 1st vaccination was with recombinant fimbrial antigens for serogroups A and B while the 2nd vaccination was with D and E. There were no significant differences between the antibody responses for time intervals of 3, 6, 9 and 12 months whereas there was a reduced response when sheep were vaccinated with two bivalent vaccines (four antigens) concurrently, indicating antigenic competition. Therefore an inter-vaccination interval of 3 months can be applied between two different bivalent vaccines without detrimental impact on the humoral immune responses to the various fimbrial antigens of D. nodosus. These results could have wider applications in vaccination against diseases caused by multivalent or multistrain microbes.