An Integrative Analysis of Foot-and-Mouth Disease Virus Carriers in Vietnam Achieved Through Targeted Surveillance and Molecular Epidemiology

Insights into the Molecular Epidemiology of Foot-and-Mouth Disease Virus in Russia, Kazakhstan, and Mongolia in Terms of O/ME-SA/Ind-2001e Sublineage Expansion

Foot-and-mouth disease (FMD) has long been recognized as a highly contagious, transboundary disease of livestock incurring substantial losses and burdens to animal production and trade across Africa, the Middle East, and Asia. Due to the recent emergence of the O/ME-SA/Ind-2001 lineage globally contributing to the expansion of FMD, molecular epidemiological investigations help in tracing the evolution of foot-and-mouth disease virus (FMDV) across endemic and newly affected regions. In this work, our phylogenetic analysis reveals that the recent FMDV incursions in Russia, Mongolia, and Kazakhstan in 2021–2022 were due to the virus belonging to the O/ME-SA/Ind-2001e sublineage, belonging to the cluster from Cambodian FMDV isolates. The studied isolates varied by 1.0–4.0% at the VP1 nucleotide level. Vaccine matching tests indicated that the vaccination policy in the subregion should be tailored according to the peculiarities of the ongoing epidemiologic situation. The current vaccination should change from such vaccine strains as O1 Manisa (ME–SA), O no 2102/Zabaikalsky/2010 (O/ME-SA/Mya-98) (r1 = 0.05–0.28) to strains that most closely antigenically match the dominant lineage O No. 2212/Primorsky/2014 (O O/ME-SA//Mya-98) and O No. 2311/Zabaikalsky/2016 (O ME-SA/Ind-2001) (r1 = 0.66–1.0).

Phylogeography as a Proxy for Population Connectivity for Spatial Modeling of Foot-and-Mouth Disease Outbreaks in Vietnam

Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independence amongst case counts across spatial units. Structured spatial effects capture correlations in case counts amongst neighboring provinces arising from shared risk factors or population connectivity. For highly mobile populations, spatial adjacency is an imperfect measure of connectivity due to long-distance movement, but we often lack data on host movements. Phylogeographic models inferring routes of viral dissemination across a region could serve as a proxy for patterns of population connectivity. The objective of this study was to investigate whether the effects of population connectivity in space-time regressions of case counts were better captured by spatial adjacency or by inferences from phylogeographic analyses. To compare these two approaches, we used foot-and-mouth disease virus (FMDV) outbreak data from across Vietnam as an example. We identified that accounting for virus movement through phylogeographic analysis serves as a better proxy for population connectivity than spatial adjacency in spatial-temporal risk models. This approach may contribute to design surveillance activities in countries lacking movement data.

Epidemiologic and economic considerations regarding persistently infected cattle during vaccinate-to-live strategies for control of foot-and-mouth disease in FMD-free regions

Development of a foot-and-mouth disease (FMD) carrier state following FMD virus (FMDV) infection is a well-established phenomenon in cattle. However, the proportion of cattle likely to become carriers and the duration of the carrier state at a herd or population-level are incompletely understood. The objective of this study was to examine the epidemiologic and economic impacts of vaccination-to-live strategy in a disease-free region or country. We developed and simulated scenarios of FMD spread and control in the US livestock population, which included depopulation for a limited period, followed by a vaccinate-to-live strategy with strong biosecurity and movement restrictions. Six scenarios of FMD spread and control were simulated in the InterSpread Plus (ISP) modeling tool. Data on the number of infected and depopulated cattle (by operation types) from ISP model runs were used to estimate the monthly number of infected but not depopulated (potential carrier) cattle after the infection. Using available literature data on the FMD carrier state, we estimated the monthly proportion of carrier cattle (from infected but not depopulated cattle) over time following infection. Among the simulated scenarios, the median (25th, 75th percentile) number of infected cattle ranged from 43,217 (42,819, 55,274) head to 148,907 (75,819, 205,350) head, and the epidemic duration ranged from 20 (11, 30) to 76 (38, 136) days. In general, larger outbreaks occurred when depopulation was carried out through longer periods, and the onset of the vaccination was late (p > 0.05). The estimated proportion of surviving cattle, which were infected and not depopulated and had the potential to become persistently infected ranged from 14 to 35% of total infected cattle. Production losses in beef and dairy sectors were higher when outbreaks started in multiple states simultaneously, but production losses were small compared to trade losses and consumer avoidance losses. These results can be used to inform the consideration of a vaccinate-to-live strategy for FMD outbreaks and the development of appropriate post-outbreak management strategies. Furthermore, this output will enable a more detailed examination of the epidemiologic and economic implications of allowing convalescent cattle to survive and remain in production chains after FMD outbreaks in FMD-free regions.

Ecological and evolutionary dynamics of multi-strain RNA viruses

Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host-pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses.

Impact of mass vaccination on the spatiotemporal dynamics of FMD outbreaks in India, 2008-2016

Foot-and-mouth disease (FMD) is endemic in India, where circulation of serotypes O, A and Asia1 is frequent. Here, we provide an epidemiological assessment of the ongoing mass vaccination programs in regard to post-vaccination monitoring and outbreak occurrence. The objective of this study was assessing the contribution of mass vaccination campaigns in reducing the risk of FMD in India from 2008 to 2016 by evaluating sero-monitoring data and modelling the spatiotemporal dynamics of reported outbreaks. Through analyzing antibody titre data from >1 million animals sampled as part of pre- and post-vaccination monitoring, we show that the percent of animals with inferred immunological protection (based on ELISA) was highly variable across states but generally increased through time. In addition, the number of outbreaks in a state was negatively correlated with the percent of animals with inferred protection. We then analyzed the distribution of reported FMD outbreaks across states using a Bayesian space-time model. This approach provides better acuity to disentangle the effect of mass vaccination programs on outbreak occurrence, while accounting for other factors that contribute to spatiotemporal variability in outbreak counts, notably proximity to international borders and inherent spatiotemporal correlations in incidence. This model demonstrated a ∼50% reduction in the risk of outbreaks in states that were part of the vaccination program. In addition, after controlling for spatial autocorrelation in the data, states that had international borders experienced heightened risk of FMD outbreaks. These findings help inform risk-based control strategies for India as the country progresses towards reducing reported clinical disease.

Use of Slaughterhouses as Sentinel Points for Genomic Surveillance of Foot-and-Mouth Disease Virus in Southern Vietnam

The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate the sampling of clinically healthy livestock at slaughterhouses as a strategy for genomic FMDV surveillance. Serum samples (n = 11,875) and oropharyngeal fluid (OPF) samples (n = 5045) were collected from clinically healthy cattle and buffalo on farms in eight provinces in southern and northern Vietnam (2015-2019) to characterize viral diversity. Outbreak sequences were collected between 2009 and 2019. In two slaughterhouses in southern Vietnam, 1200 serum and OPF samples were collected from clinically healthy cattle and buffalo (2017 to 2019) as a pilot study on the use of slaughterhouses as sentinel points in surveillance. FMDV VP1 sequences were analyzed using discriminant principal component analysis and time-scaled phylodynamic trees. Six of seven serotype-O and -A clusters circulating in southern Vietnam between 2017-2019 were detected at least once in slaughterhouses, sometimes pre-dating outbreak sequences associated with the same cluster by 4-6 months. Routine sampling at slaughterhouses may provide a timely and efficient strategy for genomic surveillance to identify circulating and emerging FMDV strains.

Detection of Foot-and-Mouth Disease Virus in the Absence of Clinical Disease in Cattle and Buffalo in South East Asia

Foot-and-mouth disease virus (FMDV) is widespread throughout much of the world, including parts of South East Asia. Surveillance is often limited in endemic areas, relying predominantly on passive outbreak reporting. As part of the World Organisation for Animal Health (OIE)'s South East Asia and China Foot-and-Mouth Disease Project (SEACFMD), field sampling was performed to help understand evidence of widespread virus exposure observed in previous studies. Serum and dry mucosal swabs were collected to evaluate the presence of FMDV RNA on the nasal, oral, and dorsal nasopharyngeal mucosal surfaces of 262 healthy cattle (n = 84 in Laos; n = 125 in Myanmar) and buffalo (n = 48 in Laos; n = 5 in Myanmar) immediately following slaughter in three slaughterhouses. Swabs and serum were tested by the OIE/FAO World Reference Laboratory for foot-and-mouth disease (WRLFMD) using pan-serotypic real-time reverse transcription-PCR (rRT-PCR) and serum was evaluated using the FMD PrioCHECK non-structural protein (NSP) ELISA. In total, 7.3% of animals had detectable FMDV RNA in one or more of the three sites including 5.3% of nasopharyngeal swabs, 2.3% of oral swabs, and 1.5% of nasal swabs. No FMDV RNA was detected in serum. Overall, 37.8% of animals were positive for NSP antibodies, indicating likely past natural exposure to FMDV. Results were comparable for Laos and Myanmar, and for both cattle and buffalo, and were not significantly different between age groups. Detectable FMDV RNA present on the oral and nasal mucosa of clinically-healthy large ruminants in Laos and Myanmar demonstrates the importance of sampling asymptomatic animals as part of surveillance, and may indicate that subclinical infection plays a role in the epidemiology of FMD in these countries.

Extinction Dynamics of the Foot-and-Mouth Disease Virus Carrier State Under Natural Conditions

Foot-and-mouth disease (FMD) is one of the most economically important livestock diseases worldwide. Following the clinical phase of FMD, a large proportion of ruminants remain persistently infected for extended periods. Although extinction of this carrier state occurs continuously at the animal and population levels, studies vary widely in their estimates of the duration of persistent infection. There is a need for robust statistical models to capture the dynamics of persistent infection for the sake of guiding FMD control and trade policies. The goal of the current study was to develop and assess statistical models to describe the extinction of FMD virus (FMDV) persistent infection using data from primary longitudinal studies of naturally infected cattle and Asian buffalo in Vietnam and India. Specifically, accelerated failure time (AFT) models and generalized linear mixed models (GLMM) were developed to predict the probability of persistent infection in seropositive animals and identified carriers at the individual animal level at sequential time points after outbreaks. The primary studies were analyzed by country and combined using an individual-participant data meta-analysis approach. The models estimated similar trends in the duration of persistent infection for the study/species groups included in the analyses, however the significance of the trends differed between the models. The overall probabilities of persistent infection were similar as predicted by the AFT and GLMM models: 6 months: 99% (AFT) /80% (GLMM), 12 months: 51% (AFT) /32% (GLMM), 18 months: 6% (AFT) /5% (GLMM), 24 months: 0.8% (AFT) /0.6% (GLMM). These models utilizing diverse and robust data sets predict higher probabilities of persistence than previously published, suggesting greater endurance of carriers subsequent to an outbreak. This study demonstrates the utility of statistical models to investigate the dynamics of persistent infection and the importance of large datasets, which can be achieved by combining data from several smaller studies in meta-analyses. Results of this study enhance current knowledge of the FMDV carrier state and may inform policy decisions regarding FMDV persistent infection.

The Carrier Conundrum; A Review of Recent Advances and Persistent Gaps Regarding the Carrier State of Foot-and-Mouth Disease Virus

The existence of a prolonged, subclinical phase of foot-and-mouth disease virus (FMDV) infection in cattle was first recognized in the 1950s. Since then, the FMDV carrier state has been a subject of controversy amongst scientists and policymakers. A fundamental conundrum remains in the discordance between the detection of infectious FMDV in carriers and the apparent lack of contagiousness to in-contact animals. Although substantial progress has been made in elucidating the causal mechanisms of persistent FMDV infection, there are still critical knowledge gaps that need to be addressed in order to elucidate, predict, prevent, and model the risks associated with the carrier state. This is further complicated by the occurrence of a distinct form of neoteric subclinical infection, which is indistinguishable from the carrier state in field scenarios, but may have substantially different epidemiological properties. This review summarizes the current state of knowledge of the FMDV carrier state and identifies specific areas of research in need of further attention. Findings from experimental investigations of FMDV pathogenesis are discussed in relation to experience gained from field studies of foot-and-mouth disease.

Temporal patterns and space-time cluster analysis of foot-and-mouth disease (FMD) cases from 2007 to 2017 in Vietnam

In Vietnam, Foot‐and‐mouth disease (FMD) is endemic, but no nationwide studies have been conducted to assess the monthly variations and space‐time clusters of FMD. The main objective was to identify the temporal patterns and space‐time clusters of FMD from 2007 to 2017 using national surveillance data in Vietnam. A total of 163,733 cases were reported from 2007 to 2017. Among them, the proportion of buffaloes (43.31% of total reported cases; 70,909 cases) was highest followed by cattle (30.11%; 49,306 cases), pigs (26.67%; 43,662 cases) and sheep/goats (0.41%; 675 cases). The serotype O was widely distributed across the country while serotype A was observed in Northeast, Central and Southern part of Vietnam while Asia 1 has been not identified since 2007. For monthly variations, most cases were observed during the dry season (from November to March) except Central Highlands. Under the spatial window was set at 50%, a total of seven clusters were identified. The primary cluster was observed from Dec 2009 to Dec 2010 in the northwest (radius: 101.67 km), showing a ratio of 3.75. The secondary cluster was detected in the northeast region (radius: 76.54 km) with a ratio of 3.53 in Feb 2017. The 3rd cluster was the largest with a radius of 176.69 km and located in the southern part of Vietnam. Interestingly, the most temporal clusters included between December and March during the study period. Our findings provide better insight into the temporal patterns and distribution of clusters of FMD in Vietnam. This study provides useful information to policymakers on the hotspot areas and timing of outbreaks. It also identifies when and where national surveillance and control programmes could be implemented more efficiently for the prevention and control of FMD.

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.

Transmission of Foot-and-Mouth Disease from Persistently Infected Carrier Cattle to Naive Cattle via Transfer of Oropharyngeal Fluid

Control and eradication of foot-and-mouth disease (FMD) are impeded by the existence of a persistent, subclinical phase of infection in ruminants; animals with this status are referred to as carriers. However, the epidemiological significance of these FMD virus (FMDV) carriers is uncertain. In the current investigation, the contagion associated with FMDV carrier cattle was investigated by exposure of susceptible cattle and pigs to oropharyngeal fluid (OPF) samples or tissues harvested from persistently infected cattle. Naive cattle were inoculated through intranasopharyngeal deposition of unprocessed OPF samples that had been collected from FMDV carriers at 30 days postinfection. These inoculated cattle developed clinical FMD, and the severity of disease they developed was similar to that of animals that had been infected with a high-titer inoculum. In contrast, pigs exposed via intraoropharyngeal inoculation of the same OPF samples or via ingestion of nasopharyngeal tissues harvested from the same cohort of persistently infected cattle did not develop FMD. These findings indicate that there is demonstrable contagion associated with FMDV carrier cattle despite the lack of evidence for transmission by direct contact. The findings presented herein provide novel information that should be considered for FMD risk mitigation strategies.IMPORTANCE Foot-and-mouth disease (FMD) is a viral disease of livestock with substantial impact on agricultural production and subsistence farming on a global scale. Control of FMD is impeded by the existence of a prolonged asymptomatic carrier phase during which infected cattle shed low quantities of infectious virus in oropharyngeal fluid (OPF) for months to years after infection. The epidemiological significance of FMD virus (FMDV) carriers is unresolved. However, the existence of the FMDV carrier state has substantial impact on international trade in animal products. The current investigation demonstrated that transfer of OPF from persistently infected FMDV carrier cattle to naive cattle led to fulminant clinical FMD. It was thus demonstrated that, although the risk for disease transmission under natural conditions is considered to be low, there is detectable contagion associated with FMDV carrier cattle. This finding is important for optimization of FMD risk mitigation strategies.

Lack of Transmission of Foot-and-Mouth Disease Virus From Persistently Infected Cattle to Naïve Cattle Under Field Conditions in Vietnam

Foot-and-mouth disease (FMD), caused by FMD virus (FMDV; Aphthovirus, Picornaviridae), is a highly contagious and economically important disease of cloven-hoofed domestic livestock and wildlife species worldwide. Subsequent to the clinical phase of FMD, a large proportion of FMDV-infected ruminants become persistently infected carriers, defined by detection of FMDV in oropharyngeal fluid (OPF) samples 28 days or more post-infection. The goal of this prospective study was to characterize the FMD carrier state in cattle subsequent to natural infection under typical husbandry practices in Vietnam. Ten persistently infected cattle on eight farms in the Long An province in southern Vietnam were monitored by monthly screening of serum and oropharyngeal fluid samples for 12 months. To assess transmission from FMDV carriers, 16 naïve cattle were intentionally brought into direct contact with the persistently infected animals for 6 months, and were monitored by clinical and laboratory methods. The restricted mean duration of the FMD carrier state was 27.7 months, and the rate of decrease of the proportion of carrier animals was 0.03 per month. There was no evidence of transmission to naïve animals throughout the study period. Additionally, there was no detection of FMDV infection or seroconversion in three calves born to carrier animals during the study. The force of infection for carrier-to-contact transmission was 0 per month, with upper 95% confidence limit of 0.064 per month. Phylogenetic analysis of viral protein 1 (VP1) coding sequences obtained from carriers indicated that all viruses recovered in this study belonged to the O/ME-SA/PanAsia lineage, and grouped phylogenetically with temporally and geographically related viruses. Analysis of within-host evolution of FMDV, based upon full-length open reading frame sequences recovered from consecutive samples from one animal, indicated that most of the non-synonymous changes occurred in L_pro, VP2, and VP3 protein coding regions. This study suggests that the duration of FMDV persistent infection in cattle may be longer than previously recognized, but the risk of transmission is low. Additional novel insights are provided into within-host viral evolution under natural conditions in an endemic setting.

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.

Evidence of subclinical foot-and-mouth disease virus infection in young calves born from clinically recovered cow under natural condition

Foot-and-mouth disease (FMD) is a highly contagious and economically important, transboundary viral disease of cloven-hoofed animals. It is known that an asymptomatic, persistent FMD virus (FMDV) infection may occur subsequent to acute or subclinical FMDV infection in adult ruminants. However, virus persistence in young calves has not been studied. In the current investigation, FMDV infection parameters were examined for calves born to FMD-clinically recovered cows (CRC), asymptomatic cows from infected herds (ASC) and cows from with no history of FMD (NHF). The study was conducted in natural condition after FMD outbreaks in two dairy herds in India. No calves described herein had any clinical signs of FMD. Six out of 12 calves born to CRC had detectable FMDV RNA in oesophageal-pharyngeal fluid consistent with asymptomatic FMDV infection. Three of the 12 calves of CRC group had seroreactivity against FMDV non-structural proteins. One calf had detectable FMDV RNA at two consecutive samplings at 2 months apart. However, infectious FMDV was not isolated from any calf in the study. None of the calves in the ASC or NHF groups had any evidence of FMDV infection. Overall, these data are consistent with earlier report on calves having been infected in utero. Further investigation of FMDV persistence in calves under controlled conditions may lead to greater understanding of the viral pathogenesis.

Emergence of an exotic strain of serotype O foot-and-mouth disease virus O/ME-SA/Ind-2001d in South-East Asia in 2015

The O/Middle East-South Asia (ME-SA)/Ind-2001 lineage of foot-and-mouth disease virus (FMDV) is endemic in the Indian subcontinent and has been reported in the Middle East and North Africa, but it had not been detected in South-East Asia (SEA) before 2015. This study reports the recent incursions of this viral lineage into SEA, which caused outbreaks in Vientiane Capital of Lao People's Democratic Republic (PDR) in April 2015, in Dak Nong, Dak Lak and Ninh Thuan Provinces of Vietnam from May to October 2015, and in Rakhine State of Myanmar in October 2015. Disease investigations were conducted during the outbreaks and followed up after laboratory results confirmed the involvement of FMDV O/ME-SA/Ind-2001 sublineage d (O/ME-SA/Ind-2001d). Affected host species included cattle, buffalo and pig, and all the outbreaks resolved within 2 months. Animals with clinical signs were separated, and affected premises were disinfected. However, strict movement restrictions were not enforced, and emergency vaccinations were only implemented in Vientiane Capital of Lao PDR and Dak Nong and Ninh Thuan Provinces of Vietnam. Clinical samples were collected from each outbreak and examined by nucleotide sequencing of the FMDV viral protein 1 coding region. Sequence analysis revealed that the O/ME-SA/Ind-2001d isolates from Lao PDR and Vietnam were closely related to each other and similar to viruses previously circulating in India in 2013. Viruses collected from Myanmar were divergent from viruses of the same sublineage recovered from Lao PDR and Vietnam but were closely related to viruses present in Bangladesh in 2015. These findings imply that at least two independent introductions of O/ME-SA/Ind-2001d into SEA have occurred. Our study highlights the transboundary nature of foot-and-mouth disease (FMD) and reinforces the importance of improved FMD surveillance and promotion of safer cross-border trade in SEA to control the risk of introduction and spread of exotic FMDV strains.

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.

Genome Sequences of Seven Foot-and-Mouth Disease Virus Isolates Collected from Serial Samples from One Persistently Infected Carrier Cow in Vietnam

Several foot-and-mouth disease virus (FMDV) carrier cattle were identified in Vietnam by the recovery of infectious virus from oropharyngeal fluid. This report contains the first near-complete genome sequences of seven viruses from sequential samples from one carrier animal collected over the course of 1 year. The characterization of within-host viral evolution has implications for FMDV control strategies.

A Q Method Approach to Evaluating Farmers' Perceptions of Foot-and-Mouth Disease Vaccination in Vietnam

This study aims to explore the farmers’ perceptions of foot-and-mouth disease (FMD) vaccination using a reflexive research method called Q methodology. A structured sample was composed of 46 farmers selected according to gender, farming experience, level of education, and production type. Statements relevant to the farmers’ perceptions of and attitudes toward FMD vaccination, related to confidence, logistics, costs, and impacts of vaccination were developed. Results were analyzed by principal component analysis and factor analysis. The influence of demographics and characterized variables on the respondent’s contribution to each factor was also tested. Regarding the different beliefs and behavior toward FMD vaccination, the common perceptions held by Vietnamese cattle and pig farmers were divided into three discourses named Confidence (24 subjects), Belief (12 subjects), and Challenge (6 subjects). The identified discourses represented 57.3% of the variances. Consensus points were found, such as the feeling of being more secure after FMD vaccination campaigns; the fact that farmers take vaccination decisions themselves without being influenced by other stakeholders; the opinion that FMD vaccination is cheaper than the costs of treating a sick animal; and that vaccines provided by governmental authorities are of high quality. Part of the studied population did not consider vaccination to be the first choice strategy in prevention. This raises the question of how to improve the active participation of farmers in the FMD vaccine strategy. Taking into consideration farmers’ perceptions can help to implement feasible vaccination strategies at the local level.

First detection of foot-and-mouth disease virus O/Ind-2001d in Vietnam

In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam in May, 2015 in Đắk Nông province. Three subsequent outbreaks caused by genetically related viruses occurred between May–October, 2015 after which the virus was not detected in clinical outbreaks for at least 15 subsequent months. The observed outbreaks affected (in chronological order): cattle in Đắk Nông province, pigs in Đắk Lắk province and Đắk Nông province, and cattle in Ninh Thuận province. The clinical syndromes associated with these outbreaks were consistent with typical FMD in the affected species. Overall attack rate on affected premises was 0.85 in pigs and 0.93 in cattle over the course of the outbreak. Amongst 378 pigs at risk on affected premises, 85 pigs died during the outbreaks; there were no deaths among cattle. The manner in which FMDV/O/ME-SA/Ind-2001d was introduced into Vietnam remains undetermined; however, movement of live cattle is the suspected route. This incursion has substantial implications for epidemiology and control of FMD in Southeast Asia.

Phylodynamics of foot-and-mouth disease virus O/PanAsia in Vietnam 2010-2014

Foot-and-mouth disease virus (FMDV) is endemic in Vietnam, a country that plays an important role in livestock trade within Southeast Asia. The large populations of FMDV-susceptible species in Vietnam are important components of food production and of the national livelihood. In this study, we investigated the phylogeny of FMDV O/PanAsia in Vietnam, reconstructing the virus' ancestral host species (pig, cattle or buffalo), clinical stage (subclinical carrier or clinically affected) and geographical location. Phylogenetic divergence time estimation and character state reconstruction analyses suggest that movement of viruses between species differ. While inferred transmissions from cattle to buffalo and pigs and from pigs to cattle are well supported, transmission from buffalo to other species, and from pigs to buffalo may be less frequent. Geographical movements of FMDV O/PanAsia virus appears to occur in all directions within the country, with the South Central Coast and the Northeast regions playing a more important role in FMDV O/PanAsia spread. Genetic selection of variants with changes at specific sites within FMDV VP1 coding region was different depending on host groups analyzed. The overall ratio of non-synonymous to synonymous nucleotide changes was greater in pigs compared to cattle and buffalo, whereas a higher number of individual amino acid sites under positive selection were detected in persistently infected, subclinical animals compared to viruses collected from clinically diseased animals. These results provide novel insights to understand FMDV evolution and its association with viral spread within endemic countries. These findings may support animal health organizations in their endeavor to design animal disease control strategies in response to outbreaks.

Prevalence and risk factors for foot and mouth disease infection in cattle in Israel

Foot and mouth disease (FMD) is a highly contagious viral disease with major economic consequences. In Israel, FMD epidemics recur almost every year and mostly affect cattle. The highest number of outbreaks occurs among beef cattle farms, followed by feedlot farms and dairy farms. We performed several cross-sectional serological studies in Israel during 2006-2014, aimed to reveal if the virus is endemic among cattle and to determine the sero-prevalence of antibodies directed against non-structural proteins (NSP) of FMD virus. Additionally we aimed to determine the risk factors for such sero-positivity. A risk based sampling was performed and the presence of anti-NSP antibodies was estimated using the PrioCHECK(®) ELISA kit. Beef cattle showed the highest sero-prevalence (13.2%, CI95%=10.8-15.8%). Higher FMD sero-prevalence in beef cattle sampled in 2014 was associated with previous FMD outbreaks in the farm and with age (adult cows versus calves (p<0.05)). Sero-prevalence in feedlot calves was significantly lower with only one sero-positive calf out of 256 (0.4%, CI95%=0-2.2%). Sero-prevalence among dairy cattle was 2.7% (CI95%=2-3.6%) with location of up to 3km from FMD outbreaks in multiple farms and location of up to 5km from the nearest border standing out as significant (p<0.05) risk factors for sero-positivity. The extremely low sero-prevalence of FMD in feedlot cattle and the significant association of infection in beef cattle with previous outbreaks suggest absence of virus circulation between these two populations during the study period, although previous data show that during outbreaks such transmission can occur. Low sero-prevalence in dairy cattle located in areas adjacent to previous FMD outbreaks may be attributed to intense routine vaccination and stringent control measures that were applied during outbreaks such as emergency vaccination and strict quarantine. Early detection of FMD outbreaks among grazing beef herds as well as the implementation of control measures among these farms are therefore the methods of choice to prevent future outbreaks in Israel.