Molecular characterization of serotype Asia-1 foot-and-mouth disease viruses in Pakistan and Afghanistan; emergence of a new genetic Group and evidence for a novel recombinant virus

Complete coding region sequence analyses and antigenic characterization of emerging lineage G-IX of foot- and-mouth disease virus serotype Asia1

Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.

Foot-and-mouth disease virus dynamics in border areas of Pakistan with Afghanistan

BACKGROUND

Foot and mouth disease (FMD) is a highly contagious disease that impacts cloven-hoofed animals globally. The illegal trade of livestock between the border regions of Pakistan and Afghanistan can contribute to the spread of this disease. This study focuses on investigating the outbreaks of FMD that occurred in this area from June 2020 to May 2021.

METHODS

RESULTS: A total of 233 epithelial tissue samples were collected, and 77% were found positive for FMDV through an antigen-detection by ELISA and molecular conformation through RT-PCR. The study found three serotypes of FMDV dominating in the border area of Pakistan with Afghanistan: O, A, and Asia-1. The outbreak activity was peaked between August/September followed by July/October 2020. Phylogenetic analysis conducted using the VP1 region sequence showed that serotype O isolates belonged to the Middle East-South Asia (ME-SA) topotype, PanAsia-2 lineage, and ANT-10 sub-lineage, while serotype Asia-1 isolates belonged to a novel lineage BD-18.The highest prevalence of serotype O of FMDV was found in cattle and buffalo of 1-2 year age group, while the highest outbreak ratio of serotype O was recorded in goats of 0-1 year age group and sheep of > 2 year age group. The serotype O was more prevalent in male than female sheep. The type A was more prevalent in females of sheep and goats than their corresponding males. The serotype Asia-1 was more prevalent in females of cattle and sheep than their corresponding males. The outbreak epidemiology of FMD varied significantly between various regions, months of study, animal species, age groups, and gender.

CONCLUSIONS

The study found that FMD outbreaks in the border area of Pakistan and Afghanistan were diverse and complicated, and that different types of FMDV were circulating. The study recommended effective actions to stop FMD transmission in this area.

Foot-and-mouth disease virus strains isolated in Vietnam during 2010-2019: genetic characterization and antigenic relatedness to the Euro SA vaccine

Foot-and-mouth disease is a highly contagious disease that affects cloven-hoofed animals. It has an important socio-economic impact on the livestock industry because it produces a drastic decrease of productivity. The disease has been successfully eradicated from some regions, including North America and Western Europe, but it is still endemic in developing countries. Agriculture plays an important role in the national economy of Vietnam, to which animal production contributes a great proportion. The concurrent circulation of foot-and-mouth disease virus (FMDV) serotypes O, A, and Asia 1 has been detected in recent years, but serotype O remains the most prevalent and is responsible for the highest numbers of outbreaks. Appropriate vaccine strain selection is an important element in the control of FMD and is necessary for the application of vaccination programs in FMD-affected regions. Here, we present updated information about the genetic and antigenic characteristics of circulating strains, collected from endemic outbreaks involving types O and A, between 2010 and 2019. Neutralizing assays showed a good in vitro match between type O strains and the monovalent O1 Campos vaccine strain. High r1 values were obtained (above 0.7) when testing a swine serum pool collected 21 days after vaccination, but the O/VTN/2/2019 strain was an exception. An EPP estimation resulted in a median neutralizing titre of about 1.65 log10, indicating that good protection could be achieved. For type A Asia SEA 97 lineage strains, acceptable individual neutralizing titres were obtained with estimated EPP values over 80% for different combinations of vaccine strains. Taking into account that the r1 value is one tool of a battery of tests that should be considered for estimating the cross-protection of a field strain against a vaccine strain, an in vivo challenge experiment was also performed, yielding a PD50 value of 8.0. The results indicate that South American strains could be potentially used for controlling outbreaks involving these lineages. This study demonstrates the importance of considering strain characteristics when choosing vaccine strains and controls.

Viral Protein 1 (VP1) Sequence-Based Genetic Diversity of SAT 2 FMDV Circulating in Ethiopia from 1990 to 2015

Introduction

Pathogen molecular epidemiology determines the origin of specific outbreaks locality of foot-and-mouth disease virus serotype South African Territories-2 sequence-based analysis of highly variable Viral Protein 1 (VP1), which helps to identify the evolution of this virus through time and space. The objective of this study was to compare the differences between SAT-2 VP1 sequences of FMDV circulated in Ethiopia from 1990 to 2015 at the genetic level.

Methods

The nucleotide and amino acid sequences were analyzed using Basic Local Alignment Search Tools (BLAST), Multiple sequence alignment and sequence editing and Phylogenetic tree reconstruction. The nucleotide and amino acid sequences alignment, distance matrix, and phylogenetic tree constructions were done using the MEGA 6.0 software package.

Result and Discussion

In this analysis, we found 76% nucleotide identities and amino acid similarities among the sequences. The overall group mean distance at nucleotide level was 19% with a mean intra-population diversity of 2%. The lowest sequence variation was observed among sequences obtained from the years 2007/09/10, 2014/15, and 1990/91 which was less than 5% among them. This analysis revealed that in the last 25 years, four different topotypes of the FMDV SAT-2 were circulating in Ethiopia. The Arg-Gly-Asp (RGD) amino acid (AA) motif at AA position 144-146 within the G-H loop of the VP1 protein of FMDV is conserved, but up- and downstream hyper-variable AA sequences are identified. In this study, it was observed that four topotypes (IV, XIV, XIII, and VII) were circulating in Ethiopia for 25 years. Further, compared with sequences from neighboring countries (Sudan, Kenya) confirmed the presence of these topotypes.

Conclusion

Pertinent to this genetic diversity control strategies in Ethiopia should be based on having regular antigenic and genetic vaccine matching tests with the circulating strain within a defined period, space, transboundary nature of the disease and applying biosecurity measures.

Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement

The Horn of Africa is a large area of arid and semi-arid land, holding about 10% of the global and 40% of the entire African livestock population. The region's livestock production system is mainly extensive and pastoralist. It faces countless problems, such as a shortage of pastures and watering points, poor access to veterinary services, and multiple endemic diseases like foot-and-mouth disease (FMD). Foot-and-mouth disease is one of the most economically important livestock diseases worldwide and is endemic in most developing countries. Within Africa, five of the seven serotypes of the FMD virus (FMDV) are described, but serotype C is not circulating anymore, a burden unseen anywhere in the world. The enormous genetic diversity of FMDV is favored by an error-prone RNA-dependent RNA polymerase, intra-typic and inter-typic recombination, as well as the quasi-species nature of the virus. This paper describes the epidemiological dynamics of foot-and-mouth disease in the Horn of Africa with regard to the serotypes and topotypes distribution of FMDV, the livestock production systems practiced, animal movement, the role of wildlife, and the epidemiological complexity of FMD. Within this review, outbreak investigation data and serological studies confirm the endemicity of the disease in the Horn of Africa. Multiple topotypes of FMDV are described in the literature as circulating in the region, with further evolution of virus diversity predicted. A large susceptible livestock population and the presence of wild ungulates are described as complicating the epidemiology of the disease. Further, the husbandry practices and legal and illegal trading of livestock and their products, coupled with poor biosecurity practices, are also reported to impact the spread of FMDV within and between countries in the region. The porosity of borders for pastoralist herders fuels the unregulated transboundary livestock trade. There are no systematic control strategies in the region except for sporadic vaccination with locally produced vaccines, while literature indicates that effective control measures should also consider virus diversity, livestock movements/biosecurity, transboundary trade, and the reduction of contact with wild, susceptible ungulates.

Genome Sequences of Foot-and-Mouth Disease Virus Serotype A and O Strains Obtained from Subclinically Infected Asian Buffalo (Bubalus bubalis) in Pakistan

We report the nearly full genome sequences of 14 isolates of serotype A foot-and-mouth disease virus and 5 isolates of serotype O, which were obtained from subclinically infected Asian buffalo in Pakistan in 2011 to 2012. Sequences from subclinically infected animals are rare and complement the more commonly available sequences from clinical cases.

Foot-and-Mouth Disease Virus Serotypes O and A from Outbreaks in Pakistan 2011–2012

We report the near full genome sequences of 18 isolates of foot-and-mouth disease virus serotype O and 6 isolates of serotype A obtained from outbreaks in Pakistan between 2011 and 2012. The scarcity of full-length FMDV sequences from this region enhances the importance of these genomes for understanding regional molecular epidemiology.

Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan

Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.

Foot-and-Mouth Disease Virus Interserotypic Recombination in Superinfected Carrier Cattle

Viral recombination contributes to the emergence of novel strains with the potential for altered host range, transmissibility, virulence, and immune evasion. For foot-and-mouth disease virus (FMDV), cell culture experiments and phylogenetic analyses of field samples have demonstrated the occurrence of recombination. However, the frequency of recombination and associated virus–host interactions within an infected host have not been determined. We have previously reported the detection of interserotypic recombinant FMDVs in oropharyngeal fluid (OPF) samples of 42% (5/12) of heterologously superinfected FMDV carrier cattle. The present investigation consists of a detailed analysis of the virus populations in these samples including identification and characterization of additional interserotypic minority recombinants. In every animal in which recombination was detected, recombinant viruses were identified in the OPF at the earliest sampling point after superinfection. Some recombinants remained dominant until the end of the experiment, whereas others were outcompeted by parental strains. Genomic analysis of detected recombinants suggests host immune pressure as a major driver of recombinant emergence as all recombinants had capsid-coding regions derived from the superinfecting virus to which the animals did not have detectable antibodies at the time of infection. In vitro analysis of a plaque-purified recombinant virus demonstrated a growth rate comparable to its parental precursors, and measurement of its specific infectivity suggested that the recombinant virus incurred no penalty in packaging its new chimeric genome. These findings have important implications for the potential role of persistently infected carriers in FMDV ecology and the emergence of novel strains.

Deciphering Molecular Dynamics of Foot and Mouth Disease Virus (FMDV): A Looming Threat to Pakistan’s Dairy Industry

Milk is seen as a chief source of protein and other biologically available nutrients for human beings. Pakistan, the fourth largest milk-producing country, is badly affected by the contagious transboundary apthoviral disease of ungulate animals; the foot and mouth disease (FMD) virus. FMD is endemic in Pakistan and has caused significant economic loss to the dairy industry in the form of a profound decrease in milk production and increased morbidity and deaths of dairy animals. Inclusively, the case fatality ratio of FMD was 15.11%. Of the seven FMDV serotypes, (O, A, C, Asia 1, SAT 1, SAT2, and SAT 3), three serotypes (O, A, and Asia-1) are endemic in Pakistan. Rapid and highly sensitive diagnostic tools are required for efficient control of this disease. Presently, FMD in the laboratory is diagnosed via ELISA and molecular approaches, i.e., RT-PCR. Serotype-specific RT-PCR analysis not only confirms ELISA serotyping results but can also be used for the screening of ELISA negative samples. Genotypically, FMDV serotype O has a topotype (Middle East–South Asia (ME–SA) and lineage PanAsia-2) that is reported frequently from different areas of Pakistan. Confirmed cases of serotype A and Asia-1 are also reported. The information gathered can be used for understanding the molecular epidemiology of FMD in Pakistan. Further studies on the molecular dynamics of FMD could be useful for ensuring the timely diagnosis of this deadly pathogen, which would ultimately be beneficial for the mass vaccination programs of FMD in Pakistan.

Demonstration of Co-Infection and Trans-Encapsidation of Viral RNA In Vitro Using Epitope-Tagged Foot-and-Mouth Disease Viruses

Foot-and-mouth disease, caused by foot-and-mouth disease virus (FMDV), is an economically devastating disease affecting several important livestock species. FMDV is antigenically diverse and exists as seven serotypes comprised of many strains which are poorly cross-neutralised by antibodies induced by infection or vaccination. Co-infection and recombination are important drivers of antigenic diversity, especially in regions where several serotypes co-circulate at high prevalence, and therefore experimental systems to study these events in vitro would be beneficial. Here we have utilised recombinant FMDVs containing an HA or a FLAG epitope tag within the VP1 capsid protein to investigate the products of co-infection in vitro. Co-infection with viruses from the same and from different serotypes was demonstrated by immunofluorescence microscopy and flow cytometry using anti-tag antibodies. FLAG-tagged VP1 and HA-tagged VP1 could be co-immunoprecipitated from co-infected cells, suggesting that newly synthesised capsids may contain VP1 proteins from both co-infecting viruses. Furthermore, we provide the first demonstration of trans-encapsidation of an FMDV genome into capsids comprised of proteins encoded by a co-infecting heterologous virus. This system provides a useful tool for investigating co-infection dynamics in vitro, particularly between closely related strains, and has the advantage that it does not depend upon the availability of strain-specific FMDV antibodies.

Simultaneous and Staggered Foot-and-Mouth Disease Virus Coinfection of Cattle

Foot-and-mouth disease (FMD) field studies have suggested the occurrence of simultaneous infection of individual hosts by multiple virus strains; however, the pathogenesis of foot-and-mouth disease virus (FMDV) coinfections is largely unknown. In the current study, cattle were experimentally exposed to two FMDV strains of different serotypes (O and A). One cohort was simultaneously infected with both viruses, while additional cohorts were initially infected with FMDV A and subsequently superinfected with FMDV O after 21 or 35 days. Coinfections were confirmed during acute infection, with both viruses concurrently detected in blood, lesions, and secretions. Staggered exposures resulted in overlapping infections as convalescent animals with persistent subclinical FMDV infection were superinfected with a heterologous virus. Staggering virus exposure by 21 days conferred clinical protection in six of eight cattle, which were subclinically infected following the heterologous virus exposure. This effect was transient, as all animals superinfected at 35 days post-initial infection developed fulminant FMD. The majority of cattle maintained persistent infection with one of the two viruses while clearing the other. Analysis of viral genomes confirmed interserotypic recombination events within 10 days in the upper respiratory tract of five superinfected animals from which the dominant genomes contained the capsid coding regions of the O virus and nonstructural coding regions of the A virus. In contrast, there were no dominant recombinant genomes detected in samples from simultaneously coinfected cattle. These findings inculpate persistently infected carriers as potential FMDV mixing vessels in which novel strains may rapidly emerge through superinfection and recombination. IMPORTANCE Foot-and-mouth disease (FMD) is a viral infection of livestock of critical socioeconomic importance. Field studies from areas of endemic FMD suggest that animals can be simultaneously infected by more than one distinct variant of FMD virus (FMDV), potentially resulting in emergence of novel viral strains through recombination. However, there has been limited investigation of the mechanisms of in vivo FMDV coinfections under controlled experimental conditions. Our findings confirmed that cattle could be simultaneously infected by two distinct serotypes of FMDV, with different outcomes associated with the timing of exposure to the two different viruses. Additionally, dominant interserotypic recombinant FMDVs were discovered in multiple samples from the upper respiratory tracts of five superinfected animals, emphasizing the potential importance of persistently infected FMDV carriers as sources of novel FMDV strains.

Evaluation of Sandwich Enzyme-Linked Immunosorbent Assay and Reverse Transcription Polymerase Chain Reaction for the Diagnosis of Foot-and-Mouth Disease

BACKGROUND

Foot-and-mouth disease (FMD) is an infectious and highly contagious disease of cloven-hoofed domestic and wild animals, causing heavy economic losses to the livestock industry. Rapid and reliable diagnosis of the disease is essential for the implementation of effective control measures. This study compared sandwich enzyme-linked immunosorbent assay (S-ELISA) and conventional reverse transcription polymerase chain reaction (RT-PCR) for the diagnosis of FMD.

METHODS

A total of 60 epithelial samples from suspected cases of FMD were tested using both S-ELISA and RT-PCR assays. The level of agreement between the assays was assessed by calculating the Kappa value.

RESULTS

S-ELISA detected 38 (63%) samples positive for FMD virus (FMDV). Being predominant, serotype O was detected in 22 (57.9%) of the total samples tested positive, whereas 9 (23.7%) and 7 (18.4%) samples were found positive for serotypes A and Asia-1, respectively. RT-PCR detected viral genome in 51 (85%) of the samples using pan-FMDV primers set, 1F/1R. Thirty-six samples were found positive and 7 negative by both the tests. The level of agreement between the tests was assessed by calculating the Kappa value, which was found to be fair (Kappa value = 0.303 and 95% CI = 0.089; 0.517) and significant (p = 0.009). However, 2 samples, which were found positive on S-ELISA tested negative on RT-PCR. This may be attributed to the presence of nucleotide mismatch(es) in the primer-binding sites that may have resulted in failure of amplification of the viral genome. The serotype-specific RT-PCR assays not only confirmed serotyping results of S-ELISA but were also able to establish serotype in 9 S-ELISA-negative but pan-FMDV RT-PCR-positive samples.

CONCLUSIONS

The RT-PCR assay contributes significantly to establishing a quick, sensitive, and definitive diagnosis of FMD in resource-constrained countries. Samples giving negative results in S-ELISA should be tested in RT-PCR for the disease detection and virus typing.

Characterization of Foot and Mouth Disease Virus Serotype SAT-2 in Swamp Water Buffaloes (Bubalus bubalis) under the Egyptian Smallholder Production System

Simple Summary

Continuous mutations of the foot and mouth disease virus (FMDV) result in the emergence of new topotypes and lineages of FMDV, which contribute to an occasional vaccination failure. Thus, molecular characterization of the circulating FMDV strains associated with a recent outbreak in Egyptian water buffaloes is essential for the control strategies. The results revealed that the circulating virus was SAT-2 serotype, closely related to the lineage of lib12, topotype VII, with a similarity of 98.9%. The new incursions reported in this study explain the considerable high morbidity of FMDV outbreaks in Egypt in early 2019.

Abstract

Spontaneous mutations are a common characteristic of the foot and mouth disease virus (FMDV), leading to wide antigenic variations resulting in the emergence of new topotypes and lineages of FMDV, which contributes to occasional vaccination failures. The objectives of the present study were to genetically characterize FMDV isolated from water buffaloes and study the biochemical and histopathological indicators of infected animals. Fifty-four water buffaloes of both sexes and different ages suffered from acute symptoms of FMD were clinically examined and randomly selected for inclusion in this study. Oral desquamated epithelial and oropharyngeal fluid samples have been tested for FMDV by reverse transcriptase PCR (RT-PCR). Tissue and serum samples were also collected from the diseased buffaloes and subjected to histopathological and biochemical analysis. Our findings showed that all examined samples were confirmed to be positive to FMDV serotype SAT-2 and were adjusted to be responsible for the recent disease outbreak in this study. Phylogenetic analysis revealed that the circulating viruses were of the SAT-2 serotype, closely related to the lineage of lib12, topotype VII, with 98.9% identity. The new lineage of SAT-2 showed a high virulence resulting in the deaths of water buffaloes due to heart failure, confirmed by high serum levels of inflammatory and cardiac markers, including haptoglobin, ceruloplasmin, cardiac troponin I and creatine phosphokinase-MB, indicating an unfavorable FMD-infection prognosis. In conclusion, we document the presence of new incursions circulating in water buffalo populations in Egypt in early 2019, explaining the high morbidity rate of FMD outbreak in early 2019. Furthermore, the newly identified serotype SAT-2 lib12 lineage, topotype VII, showed an aggressive pattern in water buffaloes of the smallholder production system.

Immunogenic profiling and designing of a novel vaccine from capsid proteins of FMDV serotype Asia-1 through reverse vaccinology

Foot-and-mouth disease is one of the devastating transboundary animal diseases causing heavy losses to the livestock industry. Different vaccines based on the inactivated FMD virus are used against this disease, but lack of immunological memory and the need for high biocontainment are the major drawbacks of these vaccines. A novel vaccine comprising recombinant antigenic regions is effective, as they lack viruses for production. Considering the fact, capsid proteins vp4, vp2, vp3, and vp1 with 3C protease of FMDV serotype Asia-1 were analyzed through reverse vaccinology approaches in this study. The sequence and structural analysis of the proteins is carried out through various bioinformatic tools and the sequence analysis has figured out the acidic nature and thermal stability of the proteins, likewise, the phylogenetic analysis helped us to trace the FMDV isolates, elucidating that selected proteins belong to the strain (Group VII), which is currently circulating in Pakistan. Next, the B-cell and MHC Class-I epitopes are identified from the antigenic proteins by immunoinformatic tools. The highly conserved, antigenic, and non-allergenic epitopes are used to design the vaccine. Accordingly, the codon adaptation and in silico cloning of the corresponding genes is performed. Thus, the bacterial expression vector could be used for efficient expression and large-scale production of the vaccine.

New possibilities for egg white lysozyme: heat-denatured lysozyme partially inactivates select foot-and-mouth disease virus strains

Foot-and-mouth disease (FMD) is one of the most contagious diseases of cloven-hoofed animals. Disinfectants are used to inactivate FMD virus (FMDV) in Japan. Reports that heat-denatured lysozyme inactivates bacteria as well as viruses, such as norovirus and hepatitis A virus, led us to determine its effects on FMDV. We show here that heat-denatured lysozyme partially inhibited the infectivity of FMDV O/JPN/2010-1/14C but of FMDVs A/TAI/46-1/2015 and Asia1/Shamir (ISR/3/89). Further, heat-denatured lysozyme variably reduced RNA loads of FMDVs O/JPN/2010-1/14C, O/MOG/2/Ca/BU/2017, O/Taiwan/1997, Asia1/Shamir (ISR/3/89), Asia1/TUR/49/2011, SAT1/KEN/117/2009, SAT2/SAU/6/2000 and SAT3/ZIM/3/83 but could not those of O/JPN/2000, A/TAI/46-1/2015, A₂₂/IRQ/24/64, A₁₅/TAI/1/60 and C/PHI/7/84. These findings indicate that heat-denatured lysozyme may serve as a new disinfectant against FMDV.

In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection

Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1-SAT3). Studies suggest that VP2 is relatively conserved among three surface-exposed capsid proteins (VP1-VP3) of FMDV, but the level of conservation has not yet been reported. Here we analyzed the comparative evolutionary divergence of VP2 and VP1 to determine the level of conservation in VP2 at different hierarchical levels of three FMDV serotypes (O, A, and Asia1) currently circulating in Asia through an in-depth computational analysis of 14 compiled datasets and designed a consensus VP2 protein that can be used for the development of a serotype-independent FMDV detection tool. The phylogenetic analysis clearly represented a significant level of conservation in VP2 over VP1 at each subgroup level. The protein variability analysis and mutational study showed the presence of 67.4% invariant amino acids in VP2, with the N-terminal end being highly conserved. Nine inter-serotypically conserved fragments located on VP2 have been identified, among which four sites showed promising antigenicity value and surface exposure. The designed 130 amino acid long consensus VP2 protein possessed six surface-exposed B cell epitopes, which suggests the possible potentiality of the protein for the development of a serotype-independent FMDV detection tool in Asia. Conclusively, this is the first study to report the comparative evolutionary divergence between VP2 and VP1, along with proposing the possible potentiality of a designed protein candidate in serotype-independent FMDV detection.

Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

In spite of annual mass vaccination programs with polyvalent inactivated vaccines, the incidence and economic impact of foot-and-mouth disease (FMD) in Egypt is high. Viruses of the A, O and SAT 2 serotypes are endemic and repeated incursions of new lineages from other countries lead to an unstable situation that makes the selection of appropriate vaccine antigens very difficult. In this study, whole genome sequencing of a 2016 serotype A isolate from Egypt revealed a recombination event with an African serotype O virus. Based on available vaccine matching data, none of the vaccines currently used in Egypt are expected to sufficiently protect against this virus or other viruses of this lineage (A/AFRICA/G-IV) circulating there since 2012. In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.

Emergence of foot-and-mouth disease virus serotype Asia1 group IX in India

Foot-and-mouth disease virus (FMDV) serotype Asia1 is prevalent in India and is responsible for a minor proportion of FMD outbreaks. Globally, serotype Asia1 is grouped into nine different groups (GI-IX) based on genetic analysis. In India, only Asia1/G-III and Asia1/G-VIII have been documented so far. Phylogenetic analysis of recent serotype Asia1 isolates from India revealed the emergence of Asia1/G-IX. The Asia1/G-IX lineage shares recent common ancestry with Asia1/G-VIII dating to 2016. The root state posterior probabilities of Asia1/G-VIII are inclusive and there may have been either an incursion of the virus from Bangladesh, where it was first identified, or in situ evolution of the virus within India, which is an intriguing possibility.

Antigenic properties of a novel vaccine strain for type Asia1 foot-and-mouth disease in pigs

Newly developed vaccine strains to prevent foot-and-mouth disease caused by the emerging serotype Asia1 virus were evaluated. To protect against the group (G)-VIII strain, which occurred recently, we produced an infectious cDNA clone of Asia1 Shamir cDNA (Asia1 Shamir-R). In addition, by adding a site 1 epitope of VP1 of the G-VIII lineage virus to this virus, we produced a new virus (Sham GVIII- EPI), and another virus(Sham GVIII-VP1) was replaced with that of G-VIII lineage in the VP1 region of Shamir. Test vaccines were produced using these three types of vaccine virus, and their immunogenicity and protection capabilities were evaluated in mice. Immunized mice were challenged with the Asia1 Shamir or G-VIII virus, and the results show that all the vaccines have similar protective effects. As they showed similar antigenicity, we chose the Shamir-R vaccine. Pigs maintained relatively high neutralizing antibody levels against homologous viruses of the Shamir and G-VII or G-VIII lineage three to four weeks after immunization. However, they formed relatively low levels of antibodies to G-IV and G-V viruses. In conclusion, we produced a vaccine candidate capable of protection against the G-VIII virus in the vaccine experiment for the type Asia1 serotype vaccine. This Shamir-R vaccine virus was found to protect against the viruses of the Asia1 genotype G-VII and G-VIII lineages, which occurred recently in Asia.

Towards improvements in foot-and-mouth disease vaccine performance

Foot-and-mouth disease (FMD) remains one of the most economically important infectious diseases of production animals. Six (out of 7 that have been identified) different serotypes of the FMD virus continue to circulate in different parts of the world. Within each serotype there is also extensive diversity as the virus constantly changes. Vaccines need to be “matched” to the outbreak strain, not just to the serotype, to confer protection. Vaccination has been used successfully to assist in the eradication of the disease from Europe but is no longer employed there unless outbreaks occur. Thus the animal population in Europe, as in North America, is fully susceptible to the virus if it is accidentally (or deliberately) introduced. Almost 3 billion doses of the vaccine are made each year to control the disease elsewhere. Current vaccines are produced from chemically inactivated virus that has to be grown, on a large scale, under high containment conditions. The vaccine efficiently prevents disease but the duration of immunity is rather limited (about 6 months) and vaccination does not provide sterile immunity or block the development of carriers. Furthermore, the vaccine is quite unstable and a cold chain needs to be maintained to preserve the efficacy of the vaccine. This can be a challenge in the parts of the world where the disease is endemic. There is a significant interest in developing improved vaccines and significant progress in this direction has been made using a variety of approaches. However, no alternative vaccines are yet available commercially. Improved disease control globally is clearly beneficial to all countries as it reduces the risk of virus incursions into disease free areas.

The first full genome characterization of an Iranian foot and mouth disease virus

High transmissibility of FMDV and drop in productivity following infection, make FMD an important economically disease of livestock. According to the endemic nature of the disease in Iran, vaccines have been routinely applied, but not able to prevent frequent outbreaks. Circulation of different FMDV types in Iran along with unrestricted animal movements complicates epidemiological situations. The relatively short length of VP1 does not provide high resolution molecular epidemiological data, therefore FMDV full genome sequencing has been employed. Outbreaks of FMD occurred in Qom province, Iran during 2017. A 8190 nucleotide-long FMDV complete genome was sequenced. Phylogenetic analysis clustered the virus into Asia 1 serotype. Complete genome analysis revealed a high level of homology of the virus to Asia 1 viruses previously detected in Turkey, India, Israel, and Pakistan. The data suggest that Asia 1/Shimi/2017 probably originated from India, have circulating in Iran since the last couple of years and reached Turkey in 2013. The results highlight the role of Iran in westward spreading of FMDV among South-central Asia, hinting the urgent need for an effective vaccine against Asia 1 type FMDV and also applying restriction rules on animal movements.

Evidence for multiple recombination events within foot-and-mouth disease viruses circulating in West Eurasia

Phylogenetic studies on foot-and-mouth disease viruses (FMDVs) circulating in the West Eurasian region have largely focused on the genomic sequences encoding the structural proteins that determine the serotype. The present study has compared near-complete genome sequences of FMDVs representative of the viruses that circulate in this region. The near-complete genome sequences (ca. 7,600 nt) were generated from multiple overlapping RT-PCR products. These amplicons were from FMDVs belonging to serotypes O, A and Asia-1, including members of the O-PanAsia-II and the A-Iran05 lineages, and of Group-II and Group-VII (Sindh-08) within serotype Asia-1, which are currently predominant and widespread in West Eurasia. These new sequences were analysed together with other sequences obtained from GenBank. Comparison of different regions of the FMDVs genomes revealed evidence for multiple, inter-serotypic, recombination events between FMDVs belonging to the serotypes O, A and Asia-1. It is concluded from the present study that dramatic changes in virus sequences can occur in the field through recombination between different FMDV genomes. These analyses provide information about the ancestry of the serotype O, A and Asia-1 FMDVs that are currently circulating within the West Eurasian region.

Development and evaluation of silver amplification immunochromatography kit for foot-and-mouth disease virus antigen detection

A silver amplification immunochromatography (SAI) kit for the detection of all seven serotypes of foot-and-mouth disease virus (FMDV)-FMDV-Ag SAI-was developed using the monoclonal antibody 1H5 recognizing the highly conserved N terminus region of VP2. The FMDV-Ag SAI can be used under conditions of high biosecurity containment as it does not require any apparatus. The FMDV-Ag SAI exhibited 10-100 times higher sensitivity against the five serotypes (O, A, Asia1, C, and SAT1) and similar sensitivity against SAT2 and SAT3, compared with the Svanodip® FMDV-Ag kit immunochromatography kit. The Svanodip kit showed inhibitory results with several saliva samples but not with the FMDV-Ag SAI kit. In a validation study using clinical samples (n = 132; vesicular epithelium = 92, vesicular lesion swabs = 20, saliva = 20) in Mongolia, the sensitivity of FMDV-Ag SAI in comparison with real-time reverse transcription-polymerase chain reaction revealed the following data: vesicular epithelium, 85.4% (76/89); vesicular lesion swab, 46.7% (7/17); and saliva, 36.8% (7/19). No cross-reactivity with the non-FMDV vesicular-forming viruses and taxonomically related viruses of the Picornaviridae family occurred. The FMDV-Ag SAI is a highly sensitive diagnostic tool that enables pen-side diagnosis without requiring the use of any equipment.

Emergence of novel lineage of foot-and-mouth disease virus serotype Asia1 BD-18 (G-IX) in Bangladesh

Foot-and-mouth disease virus (FMDV) is a highly evolutionary divergent pathogen causing great economic havoc in many countries. Among its seven existing serotypes, Asia1 is the least divergent with a single topotype both genetically and antigenically. It is reported sporadically in Indian subcontinent and was classified under lineage G-VIII. In 2018, serotype Asia1 re-emerged in Bangladesh after 2013, along with circulation of a novel serotype Asia1 BD-18 (G-IX) lineage. VP1 phylogeny and sequence variation clearly demonstrated the novel strains which was estimated to have at least >5% nucleotide divergence with distinct clade formation. Also, the Bayesian phylogeographic inferences traced back to the origin time of lineage G-IX in early 2017 and a possible origin in Bangladesh. Mutational analysis considering established eight lineages revealed that the virus strains belonged to lineage G-IX contained a unique mutation at 44 position in the B-C loop region of VP1. Inappropriate vaccination and inefficient outbreak surveillance possibly contributed to the current episode of emergence. Therefore, active surveillance and continued vigilance are essential to assess and timely detect the occurrence, extent and distribution of this novel Asia1 strains in Bangladesh and the neighbouring countries.

Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India

The role of foot-and-mouth disease virus (FMDV) persistently infected ruminants in initiating new outbreaks remains controversial, and the perceived threat posed by such animals hinders international trade in FMD-endemic countries. In this study we report longitudinal analyses of genetic and antigenic variations of FMDV serotype O/ME-SA/Ind2001d sublineage during naturally occurring, persistent infection in cattle and buffalo at an organised dairy farm in India. The proportion of animals from which FMDV RNA was recovered was not significantly different between convalescent (post-clinical) and sub-clinically infected animals or between cattle and buffalo across the sampling period. However, infectious virus was isolated from a higher proportion of buffalo samples and for a longer duration compared to cattle. Analysis of the P1 sequences from recovered viruses indicated fixation of mutations at the rate of 1.816 x 10-2substitution/site/year (s/s/y) (95% CI 1.362-2.31 x 10-2 s/s/y). However, the majority of point mutations were transitional substitutions. Within individual animals, the mean dN/dS (ω) value for the P1 region varied from 0.076 to 0.357, suggesting the selection pressure acting on viral genomes differed substantially across individual animals. Statistical parsimony analysis indicated that all of the virus isolates from carrier animals originated from the outbreak virus. The antigenic relationship value as determined by 2D-VNT assay revealed fluctuation of antigenic variants within and between carrier animals during the carrier state which suggested that some carrier viruses had diverged substantially from the protection provided by the vaccine strain. This study contributes to understanding the extent of within-host and within-herd evolution that occurs during the carrier state of FMDV.

The epidemiology of foot-and-mouth disease outbreaks and its history in Iraq

Background and Aims:

Foot-and-mouth disease (FMD) is reported in Iraq since 1937 and occurs as a devastating seasonal epidemic. This study intended to explore the epidemiology of FMD in Iraq during 2011-2016, through assessment of outbreak reports among cow, buffalo, and small ruminants (sheep and goat) in 15 Iraqi governorates except for Kurdistan region.

Materials and Methods:

The reported data regarding FMD cases were collected from veterinary hospitals in 15 Iraqi governorates and were analyzed.

Results:

The results revealed annual FMD outbreaks in cow, buffalo, and small ruminants in Iraqi governorates with variability in the numbers of the infected and dead animals. The total number of infected animals increased in 2016 compared to 2015 due to the illegal importation of FMD-infected cows at the end of 2015. The prevalence rates of FMD were 68.7%, 46.6%, and 30.3% in cattle, buffalo, and small ruminants, respectively, in 2016, while this was 18.4%, 19.9%, and 17.3%, respectively, in 2015.

Conclusion:

This study approved the reemergence and endemic nature of FMD in Iraqi livestock. Prompt procedures and a new future strategy need to be implemented to control the increasing incidences of FMD in Iraq.

Co-infection with different serotypes of FMDV in vaccinated cattle in Southern Egypt

During 2015-2016 period, an outbreak of foot-and-mouth disease virus (FMDV) was observed in cattle in four governorates of the upper of Egypt. The infection was extended to the vaccinated cattle. A total of 54 mouth swabs and serum samples were collected from vaccinated cattle for serological and virological investigation. The typical clinical signs of FMDV infection were observed in all cattle under investigation. All samples were positive for FMDV using molecular methods, while the serological method showed 85% positive of tested samples. Typing of FMDV-positive samples using serotype-specific primers showed that 51.8% of samples were serotype O, 9.2% were serotype A, and 18.5% were SAT 2. Surprisingly, co-infections of serotypes A/SAT 2 (12.9%) and O/SAT 2 (7.4%) were also detected. By geographical location, the 3 serotypes A, O, and SAT2 were detected in all four governorates. The phylogenetic assessment of the detected viruses showed that two distinct groups of FMDV serotype O of East Africa-3 (EA-3) topotype were most closely related to circulating viruses in Sudan, as well as FMDV strains belonging to the topotype VII of serotype SAT 2. The detected SAT 2 strains clustered in separate clades in topotype VII, indicating new incursions. The VP1 signatures and protein sequences of some characterized viruses were analyzed. Multiple mutations were detected in VP1. Therefore, to enhance the control of FMD in Egypt, we recommend establishing an active surveillance system to characterize newly emerging virus strains/serotypes and subsequently updating vaccine strains.

Foot-and-mouth disease outbreaks due to an exotic serotype Asia 1 virus in Myanmar in 2017

In January 2017, two villages located in Rakhine State of Myanmar reported clinical signs in cattle suggestive of foot-and-mouth disease virus (FMDV) infection. Laboratory analysis identified the outbreak virus as FMDV serotype Asia 1, which represented the first detection of this serotype in Myanmar since 2005 and in the region of South-East Asia (SEA) since 2007. Genetic analysis revealed that the outbreak virus was different from historical viruses from Myanmar and was more closely related to viruses circulating in Bangladesh and India during 2012-2013, indicating that a novel viral introduction had occurred. The precise origin of the outbreaks was not clear, but frequent informal livestock trade with South Asia was reported. Responses to the outbreaks involved disinfection, quarantine and animal movement restrictions; no further outbreaks were detected under the present passive surveillance system. Detection of serotype Asia 1 highlights the complex and dynamic nature of FMDV in SEA. Active surveillance is needed to assess the extent and distribution of this exotic Asia 1 strain and continued vigilance to timely detect the occurrence of emerging and re-emerging FMDV strains is essential.

The full-length genome characterization, genetic diversity and evolutionary analyses of Senecavirus A isolated in Thailand in 2016

Senecavirus A (SVA) is a novel picornavirus that causes porcine idiopathic vesicular disease characterized by lameness, coronary band hyperemia, and vesicles on the snout and coronary bands. An increase in the detection rate of SVA in several countries suggests that the disease has become a widespread problem. Herein, we report the detection of SVA in Thailand and the characterization of full-length genomic sequences of six Thai SVA isolates. Phylogenetic, genetic, recombination, and evolutionary analyses were performed. The full-length genome, excluding the poly (A) tail of the Thai SVA isolates, was 7282 nucleotides long, with the genomic organization resembling other previously reported SVA isolates. Phylogenetic and genetic analyses based on full-length genome demonstrated that the Thai SVA isolates were grouped in a novel cluster, separated from SVA isolates from other countries. Although the Thai SVA isolates were closely related to 11-55910-3, the first SVA isolate from Canada, with 97.9-98.2%, but they are different. Evolutionary and recombinant analyses suggested that the Thai SVA isolates shared a common ancestor with the 11-55910-3 isolate. The positive selection in the VP4 and 3D genes suggests that the virus was not externally introduced, but rather continuously evolved in the population prior to the first detection. Addition, the presence of SVA could have been ignored due to the presence of other pathogens causing similar clinical diseases. This study warrants further investigations into molecular epidemiology and genetic evolution of the SVA in Thailand.

Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome

Recombination is one of the determinants of genetic diversity in the foot-and-mouth disease virus (FMDV). FMDV sequences have a mosaic structure caused by extensive intra- and inter-serotype recombination, with the exception of the capsid-encoding region. While these genome-wide patterns of broad-scale recombination are well studied, not much is known about the patterns of recombination that may exist within infected hosts. In addition, detection of recombination among viruses evolving at the within-host level is challenging due to the similarity of the sequences and the limitations in differentiating recombination from point mutations. Here, we present the first analysis of recombination events between closely related FMDV sequences occurring within buffalo hosts. The detection of these events was made possible by the occurrence of co-infection of two viral swarms with about 1% nucleotide divergence. We found more than 15 recombination events, unequally distributed across eight samples from different animals. The distribution of these events along the FMDV genome was neither uniform nor related to the phylogenetic distribution of recombination breakpoints, suggesting a mismatch between within-host evolutionary pressures and long-term selection for infectivity and transmissibility.

A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

Molecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) is responsible for one of the most economically important infectious diseases of livestock. The virus spreads very easily and continues to affect many countries (mainly in Africa and Asia). The risks associated with the introduction of FMDV result in major barriers to trade in animals and their products. Seven antigenically distinct forms of the virus are known, called serotypes, but serotype C has not been detected anywhere for many years and may now be extinct. The serotypes have been further divided into topotypes (except for serotype Asia-1 viruses, which comprise a single topotype), genotypes, lineages and sub-lineages, which are usually restricted to specific geographical regions. However, sometimes, trans-regional spread of some strains occurs. Due to the error-prone replication of the RNA genome, the virus continuously evolves and new strains frequently arise (e.g. with modified antigenicity). Using nucleotide sequencing technologies, this rapid evolution of the viral genome can be followed. This allows the tracing of virus transmission pathways within an outbreak of disease if (near) full-length genome sequences can be generated. Furthermore, the movement of distinct virus lineages, from one country to another can be analyzed. Some important examples of the spread of new strains of FMD virus are described.

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-and-mouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo. Using next-generation sequencing (NGS) we obtained 21 near complete FMDV genome sequences from 12 sub-clinically infected buffalo over a period of one year. Four animals yielded only one virus isolate and one yielded two isolates of different serotype suggesting a serial infection. Seven persistently infected animals yielded more than one virus of the same serotype showing a long-term intra-host viral genetic divergence at the consensus level of less than 2.5%. Quasi-species analysis showed few nucleotide variants and non-synonymous substitutions of progeny virus despite intra-host persistence of up to 152 days. Phylogenetic analyses of serotype Asia-1 VP1 sequences clustered all viruses from persistent animals with Group VII viruses circulating in Pakistan in 2011, but distinct from those circulating on 2008–2009. Furthermore, signature amino acid (aa) substitutions were found in the antigenically relevant VP1 of persistent viruses compared with viruses from 2008–2009. Intra-host purifying selective pressure was observed, with few codons in structural proteins undergoing positive selection. However, FMD persistent viruses did not show a clear pattern of antigenic selection. Our findings provide insight into the evolutionary dynamics of FMDV populations within naturally occurring subclinical and persistent infections that may have implications to vaccination strategies in the region.

Dynamics of widespread foot-and-mouth disease virus serotypes A, O and Asia-1 in southern Asia: A Bayesian phylogenetic perspective

Foot-and-mouth disease (FMD) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV) have emerged. Here, we performed an integrative phylogenetic analysis of all FMDV serotypes (A, O and Asia-1) circulating in southern Asia, including viral sequences collected until 2013. Our results describe the occurrence of FMD caused by different serotypes and lineages, focusing in the cycles where a specific lineage predominates within a region for a protracted period and then are rapidly or progressively replaced by an emergent or re-emergent strain that is introduced from an adjacent region. Transmission between the two main regions in southern Asia (the Indian subcontinent and the region comprised by Afghanistan, Iran and Pakistan) has been limited. Results of time divergence estimation of lineages that currently circulate in this region indicate that the most recent common ancestor of endemic lineages are: 1992 [1989-1995] for lineage O/PanAsia; 1997 [1995-1999] for PanAsia2; 2001 [1998-2004] for O/Ind2001; 2001 [2000-2002] for A/Iran-05; 1990 [1988-1991] for A/G-18 (G-VII); 2003 [2000-2006] for Asia-1 Sindh08 and 2002 [1999-2004] for Asia-1 G-VIII. We estimated the mean of the overall substitution rate of the VP1 coding region (substitution/site/year) for serotype O (5.95 × 10^-3 ), serotype A (1.19 × 10^-2 ) and serotype Asia-1 (3.08 × 10^-3 ). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV.

Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008-2012

We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.

Evolutionary phylodynamics of foot-and-mouth disease virus serotypes O and A circulating in Vietnam

BACKGROUND

Foot-and-mouth disease virus (FMDV) is one of the highest risk factors that affects the animal industry of the country. The virus causes production loss and high ratio mortality in young cloven-hoofed animals in Vietnam. The VP1 coding gene of 80 FMDV samples (66 samples of the serotype O and 14 samples of the serotype A) collected from endemic outbreaks during 2006-2014 were analyzed to investigate their phylogeny and genetic relationship with other available FMDVs globally.

RESULTS

Phylogenetic analysis indicated that the serotype O strains were clustered into two distinct viral topotypes (the SEA and ME-SA), while the serotype A strains were all clustered into the genotype IX. Among the study strains, the amino acid sequence identities were shared at a level of 90.1-100, 92.9-100, and 92.8-100% for the topotypes SEA, ME-SA, and genotype IX, respectively. Substitutions leading to changes in the amino acid sequence, which are critical for the VP1 antigenic sites were also identified. Our results showed that the studied strains are most closely related to the recent FMDV isolates from Southeast Asian countries (Myanmar, Thailand, Cambodia, Malaysia, and Laos), but are distinct from the earlier FMDV isolates within the genotypes.

CONCLUSIONS

This study provides important evidence of recent movement of FMDVs serotype O and A into Vietnam within the last decade and their genetic accumulation to be closely related to strains causing FMD in surrounding countries.

Phylogeographic analysis of the 2000-2002 foot-and-mouth disease epidemic in Argentina

Foot-and-mouth disease (FMD) is a highly transmissible disease of hooved livestock. Although FMD has been eradicated from many countries, economic and social consequences of FMD reintroductions are devastating. After achieving disease eradication, Argentina was affected by a major epidemic in 2000-2002, and within few months, FMD virus spread throughout most of the country and affected >2500 herds. Available records and viral strains allowed us to assess the origins, spread and progression of this FMD epidemic, which remained uncertain. We used whole genome viral sequences and a continuous phylogeographic diffusion approach, which revealed that the viruses that caused the outbreaks spread fast in different directions from a central area in Argentina. The analysis also suggests that the virus that caused the outbreaks in the year 2000 was different from those found during the 2001 epidemic. To estimate if the approximate overall genetic diversity of the virus was related to disease transmission, we reconstructed the viral demographic variation in time using Bayesian Skygrid approach and compared it with the epidemic curve and the within-herd transmission rate and showed that the genetic temporal diversity of the virus was associated with the increasing number of outbreaks in the exponential phase of the epidemic. Results here provide new evidence of how the disease entered and spread throughout the country. We further demonstrate that genetic data collected during a FMD epidemic can be informative indicators of the progression of an ongoing epidemic.

Serotype Diversity of Foot-and-Mouth-Disease Virus in Livestock without History of Vaccination in the Far North Region of Cameroon

Little information is available about the natural cycle of foot-and-mouth disease (FMD) in the absence of control measures such as vaccination. Cameroon presents a unique opportunity for epidemiological studies because FMD vaccination is not practiced. We carried out a prospective study including serological, antigenic and genetic aspects of FMD virus (FMDV) infections among different livestock production systems in the Far North of Cameroon to gain insight into the natural ecology of the virus. We found serological evidence of FMDV infection in over 75% of the animals sampled with no significant differences of prevalence observed among the sampled groups (i.e. market, sedentary, transboundary trade and mobile). We also found antibodies reactive to five of the seven FMDV serotypes (A, O, SAT1, SAT2 and SAT3) among the animals sampled. Finally, we were able to genetically characterize viruses obtained from clinical and subclinical FMD infections in Cameroon. Serotype O viruses grouped into two topotypes (West and East Africa). SAT2 viruses grouped with viruses from Central and Northern Africa, notably within the sublineage causing the large epidemic in Northern Africa in 2012, suggesting a common origin for these viruses. This research will guide future interventions for the control of FMD such as improved diagnostics, guidance for vaccine formulation and epidemiological understanding in support of the progressive control of FMD in Cameroon.

Development and Characterization of Probe-Based Real Time Quantitative RT-PCR Assays for Detection and Serotyping of Foot-And-Mouth Disease Viruses Circulating in West Eurasia

Rapid and accurate diagnosis of foot-and-mouth disease (FMD) and virus serotyping are of paramount importance for control of this disease in endemic areas where vaccination is practiced. Ideally this virus characterization should be achieved without the need for virus amplification in cell culture. Due to the heterogeneity of FMD viruses (FMDVs) in different parts of the world, region specific diagnostic tests are required. In this study, hydrolysable probe-based real time reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays were developed for specific detection and serotyping of the FMDVs currently circulating in West Eurasia. These assays were evaluated, in parallel with pan-FMDV diagnostic assays and earlier serotype-specific assays, using field samples originating from Pakistan and Afghanistan containing FMD viruses belonging to different sublineages of O-PanAsia, A-Iran05 and Asia-1 (Group-II and Group-VII (Sindh-08)). In addition, field samples from Iran and Bulgaria, containing FMDVs belonging to the O-PanAsia^ANT-10 sublineage were also tested. Each of the three primer/probe sets was designed to be specific for just one of the serotypes O, A and Asia-1 of FMDV and detected the RNA from the target viruses with cycle threshold (C_T) values comparable with those obtained with the serotype-independent pan-FMDV diagnostic assays. No cross-reactivity was observed in these assays between the heterotypic viruses circulating in the region. The assays reported here have higher diagnostic sensitivity (100% each for serotypes O and Asia-1, and 92% [95% CI = 81.4–100%] for serotype A positive samples) and specificity (100% each for serotypes O, A and Asia-1 positive samples) for the viruses currently circulating in West Eurasia compared to the serotyping assays reported earlier. Comparisons of the sequences of the primers and probes used in these assays and the corresponding regions of the circulating viruses provided explanations for the poor recognition of some of the viruses by the earlier assays. These new assays should help in the early detection and typing of serotype O, A and Asia-1 FMDVs circulating in West Eurasia to enable improved disease control.

Development and Evaluation of a Rapid Antigen Detection and Serotyping Lateral Flow Antigen Detection System for Foot-and-Mouth Disease Virus

We developed a lateral flow strip using monoclonal antibodies (MAbs) which allows for rapid antigen detection and serotyping of foot-and-mouth disease virus (FMDV). This FMDV serotyping strip was able to detect all 7 serotypes and distinguish serotypes O, A, C and Asia1. Its sensitivities ranged from 10³ to 10⁴ of a 50% tissue culture infectious dose of each FMDV stain; this is equal to those of the commercial product Svanodip (Boehringer Ingelheim Svanova, Uppsala, Sweden), which can detect all seven serotypes of FMDV, but does not distinguish them. Our evaluation of the FMDV serotyping strip using a total of 118 clinical samples (vesicular fluids, vesicular epithelial emulsions and oral and/or nasal swabs) showed highly sensitive antigen detection and accuracy in serotyping in accordance with ELISA or RT-PCR. To the best of our knowledge, this is the first report on any FMDV serotyping strip that provides both rapid antigen detection and serotyping of FMDV at the same time on one strip without extra devices. This method will be useful in both FMD-free countries and FMD-infected countries, especially where laboratory diagnosis cannot be carried out.

Evolutionary analysis of structural protein gene VP1 of foot-and-mouth disease virus serotype Asia 1

Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I–VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10⁻³ substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown.