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

MolEpidPred: a novel computational tool for the molecular epidemiology of foot-and-mouth disease virus using VP1 nucleotide sequence data

Molecular epidemiology of Foot-and-mouth disease (FMD) is crucial to implement its control strategies including vaccination and containment, which primarily deals with knowing serotype, topotype, and lineage of the virus. The existing approaches including serotyping are biological in nature, which are time-consuming and risky due to live virus handling. Thus, novel computational tools are highly required for large-scale molecular epidemiology of the FMD virus. This study reported a comprehensive computational tool for FMD molecular epidemiology. Ten learning algorithms were initially evaluated on cross-validated and ten independent secondary datasets for serotype prediction using sequence-based features through accuracy, sensitivity and 14 other metrics. Next, best performing algorithms, with higher serotype predictive accuracies, were evaluated for topotype and lineage prediction using cross-validation. These algorithms are implemented in the computational tool. Then, performance of the developed approach was assessed on five independent secondary datasets, never seen before, and primary experimental data. Our cross-validated and independent evaluation of learning algorithms for serotype prediction revealed that support vector machine, random forest, XGBoost, and AdaBoost algorithms outperformed others. Then, these four algorithms were evaluated for topotype and lineage prediction, which achieved accuracy ≥96% and precision ≥95% on cross-validated data. These algorithms are implemented in the web-server (https://nifmd-bbf.icar.gov.in/MolEpidPred), which allows rapid molecular epidemiology of FMD virus. The independent validation of the MolEpidPred observed accuracies ≥98%, ≥90%, and ≥ 80% for serotype, topotype, and lineage prediction, respectively. On wet-lab data, the MolEpidPred tool provided results in fewer seconds and achieved accuracies of 100%, 100%, and 96% for serotype, topotype, and lineage prediction, respectively, when benchmarked with phylogenetic analysis. MolEpidPred tool provides an innovative platform for large-scale molecular epidemiology of FMD virus, which is crucial for tracking FMD virus infection and implementing control program.

A stochastic modeling study of quarantine strategies against foot-and-mouth disease risks through cattle trades across the Thailand-Myanmar border

Foot-and-mouth disease (FMD) is an important endemic disease in livestock in Southeast Asia. Transboundary movement of animals may result in the transnational disease spread. A major cattle market is located at the Thailand-Myanmar border, where most cattle imported from Myanmar are traded. In this study, we built a stochastic susceptible-exposed-infectious-recovered (SEIR) model to investigate the effectiveness of a private animal quarantine service center in preventing FMDV from entering the major cattle market. We computed with different parameters and found that, with 50 % vaccine effectiveness, the risk of releasing infected cattle to the market per batch was generally low during the quarantine period of 21 and 28 days, with the risk ranging from 0.071 to 0.078 and 0.032 to 0.036, respectively. Despite the best scenario, the zero-risk state is difficult to attain. The sensitivity analysis highlights that the percentage of immune animals before entering the quarantine centers and the vaccine effectiveness are important factors. In conclusion, the 21-day quarantine period mitigates the risk of FMDV introduction into the cattle market. This control measure should be rigorously maintained to sustainably prevent FMDV outbreaks through transboundary animal movements, especially among countries in FMD-endemic regions.

Epidemiological and genetic characteristics of foot-and-mouth disease virus in China from 2010 to 2022

Foot-and-mouth disease virus (FMDV) is a highly contagious picornavirus that can infect cloven-hoofed animals of significant agricultural importance. In China, foot-and-mouth disease (FMD) epidemics occur annually, resulting in localized outbreaks or sporadic epidemics that cause significant economic losses. This study summarized 123 cases of FMD reported in China between 2010 and 2022, using data from the official website of the Chinese Center for Animal Disease Control and Prevention. The epidemic situation and genetic characteristics of FMDV in China were studied through phylogenetic analysis, amino acid variation analysis of antigenic epitopes, and genetic recombination analysis. The findings provide important references for predicting the FMDV epidemic situation in China, developing vaccines, and effectively preventing and controlling FMD.

Epidemiological and Genetic Analysis of Foot-and-Mouth Disease Virus O/ME-SA/Ind-2001 in China between 2017 and 2021

The O/ME-SA/Ind-2001 lineage of foot-and-mouth disease virus (FMDV) was introduced into China in 2017, which subsequently caused 19 outbreaks of foot-and-mouth disease (FMD) and emerged in 8 provinces in China between 2017 and 2021. It is the first time for WOAH/national reference laboratory for FMD (LVRI) to comprehensively summarize these 19 outbreaks of O/ME-SA/Ind-2001 for consecutive 5 years. Our study selected and conducted whole viral genome sequencing for 9 representative isolates and the VP1 sequences of the FMDV-positive samples collected between 2017 and 2021. Analyses of these gene sequences showed that all the field strains belonged to O/ME-SA/Ind-2001e. Phylogenetic analysis indicated that these viruses were closely related to those circulating in neighboring countries, and there were at least 3 different FMD viral clades (named cluster 1, cluster 2, and cluster 3) circulating during this period. Also, a gradually decreasing nucleotide identity was observed in newly emerging viruses year by year compared with the first isolate identified in 2017. These results suggest extensive movements and constant and rapid evolvement of the O/ME-SA/Ind-2001e sublineage. Besides, the neutralizing antigenic sites in the structural proteins for these O/ME-SA/Ind-2001e viruses were analyzed to predict the vaccine matching between these strains and the commercial vaccine strain O/BY/CHA/2010. The results showed that the VP1 epitope 135-144, highly associated with neutralizing antibody induction, was variable among these strains. The mutations in this region reflected a potential risk of challenging the current vaccine protection. Therefore, there is an urgent need to reinforce the importance of improved FMD surveillance and monitor the evolution of O/ME-SA/Ind-2001e, which will provide essential information for the FMD control program in China and Asia.

Disease threats to tigers and their prey

The contraction of the global tiger population over the last 100 years into small, often isolated subpopulations has made them increasingly vulnerable to the impact of disease. Despite this, the health of wild tigers continues to be insufficiently funded and explored. For example, canine distemper virus (CDV), has been associated with localized declines and increased risk of extinction, and yet has received little research attention in most tiger range countries. The emergence of new pathogenic threats has posed fresh challenges, including African swine fever virus (ASFV), which has the potential to devastate wild boar populations, and severe acute respiratory syndrome coronavirus (SARS-CoV2) with implications for tiger conservation that remain unknown. The objective of this review is to synthesize current research on the health of tigers and their prey that impacts the conservation of tigers in the wild. Published sources are interpreted based on three mechanisms through which disease can affect the viability of tiger populations: (1) by reducing the survival of adult tigers, (2) by reducing breeding productivity, and (3) by reducing the carrying capacity of tiger habitat through decreased prey abundance. Examples of CDV, SARS-CoV2, carnivore protoparvovirus 1 and ASFV are used to illustrate these processes and inform discussion of research and mitigation priorities.

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).

Evaluation of Vaccine Strains Developed for Efficient, Broad-Range Protection against Foot-and-Mouth Disease Type O

Foot-and-mouth disease (FMD) type O includes 11 genetic topotypes. The Southeast Asia (SEA), Middle East-South Asia (ME-SA), and Cathay topotypes belong to FMD type O and occur frequently in Asia. Therefore, it is necessary to develop a potent vaccine strain with a broad antigenic coverage in order to provide complete protection against these three topotypes. In this study, an experimental vaccine was produced using chimeric vaccine strains (JC-VP1 or PA2-VP1) that contained VP4, VP2, and VP3 of the ME-SA topotype (O Manisa) and VP1 of the SEA topotype (Mya98 lineage; O/SKR/Jincheon/2014) or ME-SA topotype (PanAsia2 lineage; O/PAK/44). Mice were immunized with the experimental vaccines, and they were fully protected against the three topotypes. The neutralizing antibody titers of PA2-VP1 were significantly higher than those of JC-VP1 in the early vaccination phase in pigs. Here, we confirmed complete protection in pigs vaccinated with JC-VP1 or PA2-VP1, when challenged against the SEA (O/SKR/Jincheon/2014), ME-SA (O/SKR/Boeun/2017) and Cathay (O/Taiwan/97) topotype viruses, with moderately higher protection provided by PA2-VP1 than by JC-VP1.

Evaluation of immunogenicity and cross-reactive responses of vaccines prepared from two chimeric serotype O foot-and-mouth disease viruses in pigs and cattle

Foot-and-mouth disease (FMD) remains a very serious barrier to agricultural development and the international trade of animals and animal products. Recently, serotype O has been the most prevalent FMDV serotype in China, and it has evolved into four different lineages: O/SEA/Mya-98, O/ME-SA/PanAsia, O/ME-SA/Ind-2001 and O/Cathay. PanAsia-2, belonging to the O/ME-SA topotype, is prevalent in neighbouring countries and poses the risk of cross-border spread in China. This study aimed to develop a promising vaccine candidate strain that can not only provide the best protection against all serotype O FMDVs circulating in China but also be used as an emergency vaccine for the prevention and control of transboundary incursion of PanAsia-2. Here, two chimeric FMDVs (rHN/TURVP1 and rHN/NXVP1) featuring substitution of VP1 genes of the O/TUR/5/2009 vaccine strain (PanAsia-2) and O/NXYCh/CHA/2018 epidemic strain (Mya98) were constructed and evaluated. The biological properties of the two chimeric FMDVs were similar to those of the wild-type (wt) virus despite slight differences in plaque sizes observed in BHK-21 cells. The structural protein-specific antibody titres induced by the rHN/TURVP1 and wt virus vaccines in pigs and cows were higher than those induced by the rHN/NXVP1 vaccine at 28–56 dpv. The vaccines prepared from the two chimeric viruses and wt virus all induced the production of protective cross-neutralizing antibodies against the viruses of the Mya-98, PanAsia and Ind-2001 lineages in pigs and cattle at 28 dpv; however, only the animals vaccinated with the rHN/TURVP1 vaccine produced a protective immune response to the field isolate of the Cathay lineage at 28 dpv, whereas the animals receiving the wt virus and the rHN/NXVP1 vaccines did not, although the wt virus and O/GXCX/CHA/2018 both belong to the Cathay topotype. This study will provide very useful information to help develop a potential vaccine candidate for the prevention and control of serotype O FMD in China.

Identification of the O/ME-SA/Ind-2001e Sublineage of Foot-and-Mouth Disease Virus in Cambodia

Foot-and-mouth (FMD) is endemic in Cambodia with numerous outbreaks in cattle, pigs and other susceptible animal species reported every year. Historically, these outbreaks were caused by the FMD virus (FMDV) of serotype O PanAsia and Mya-98 lineages and serotype A Sea-97 lineage. However, the trans-pool movement of FMDV between inter-pool regions or countries throughout FMD endemic regions has raised concerns regarding infection with the new genotype or serotype of FMDV in Cambodia. In this study, 19 sequences of VP1 coding region obtained from 33 clinical samples collected from FMDV-affected cattle farms in Cambodia during January to March 2019 were genetically characterized to identify the genotypes/lineages of FMDV. Phylogenetic analysis of VP1 coding sequences revealed that recent field viruses belonged to O/ME-SA/Ind-2001e (15.8%), O/ME-SA/PanAsia (52.7%), and A/ASIA/Sea-97 (31.5%). Besides, the field viruses of O/ME-SA/Ind-2001e in Cambodia showed 93.5-96.8% identity with the VP1 coding sequences of the same sublineage viruses from pool 1 and 2 surrounding Cambodia. This is the first report of O/ME-SA/Ind-2001e infection in Cambodia, suggesting that the trans-pool movement of the new genotype should be closely monitored for efficient control of FMD.

Foot-and-mouth disease viruses of the O/ME-SA/Ind-2001e sublineage in Pakistan

The presence of foot-and-mouth disease virus (FMDV) of the O/ME-SA/Ind-2001e sublineage within Pakistan was initially detected in two samples collected during 2019. Analysis of further serotype O FMDVs responsible for disease outbreaks in 2019-2020 in the country has now identified the spread of this sublineage to 10 districts within two separate provinces in North-Eastern and North-Western Pakistan. Phylogenetic analysis indicates that these viruses are closely related to those circulating in Bhutan, Nepal and India. The VP1 coding sequences of these viruses from Pakistan belong to three distinct clusters, which may indicate multiple introductions of this virus sublineage, although the routes of introduction are unknown. Vaccine matching studies against O1 Manisa, O 3039 and O TUR/5/2009 support the suitability of existing vaccine strains to control current field outbreaks, but further studies are warranted to monitor the spread and evolution of the O/ME-SA/Ind-2001e sublineage in the region. (145 words).

Emergency FMD Serotype O Vaccines Protect Cattle against Heterologous Challenge with a Variant Foot-and-Mouth Disease Virus from the O/ME-SA/Ind2001 Lineage

Vaccination is one of the best approaches to control and eradicate foot-and-mouth disease (FMD). To achieve this goal, vaccines with inactivated FMD virus antigen in suitable adjuvants are being used in addition to other control measures. However, only a limited number of vaccine strains are commercially available, which often have a restricted spectrum of activity against the different FMD virus strains in circulation. As a result, when new strains emerge, it is important to measure the efficacy of the current vaccine strains against these new variants. This is important for countries where FMD is endemic but also for countries that hold an FMD vaccine bank, to ensure they are prepared for emergency vaccination. The emergence and spread of the O/ME-SA/Ind-2001 lineage of viruses posed a serious threat to countries with OIE-endorsed FMD control plans who had not reported FMD for many years. In vitro vaccine-matching results showed a poor match (r₁-value < 0.3) with the more widely used vaccine strain O₁ Manisa and less protection in a challenge test. This paper describes the use of the O3039 vaccine strain as an alternative, either alone or in combination with the O₁ Manisa vaccine strain with virulent challenge by a O/ME-SA/Ind-2001d sub-lineage virus from Algeria (O/ALG/3/2014). The experiment included challenge at 7 days post-vaccination (to study protection and emergency use) and 21 days post-vaccination (as in standard potency studies). The results indicated that the O3039 vaccine strain alone, as well as the combination with O₁ Manisa, is effective against this strain of the O/ME-SA/Ind/2001d lineage, offering protection from clinical disease even after 7 days post-vaccination with a reduction in viraemia and virus excretion.

Molecular Basis of Antigenic Drift in Serotype O Foot-and-Mouth Disease Viruses (2013-2018) from Southeast Asia

Foot and mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals with serious economic consequences. FMD is endemic in Southeast Asia (SEA) and East Asia (EA) with the circulation of multiple serotypes, posing a threat to Australia and other FMD-free countries. Although vaccination is one of the most important control measures to prevent FMD outbreaks, the available vaccines may not be able to provide enough cross-protection against the FMD viruses (FMDVs) circulating in these countries due to the incursion of new lineages and sub-lineages as experienced in South Korea during 2010, a FMD-free country, when a new lineage of serotype O FMDV (Mya-98) spread to the country, resulting in devastating economic consequences. In this study, a total of 62 serotype O (2013-2018) viruses selected from SEA and EA countries were antigenically characterized by virus neutralization tests using three existing (O/HKN/6/83, O/IND/R2/75 and O/PanAsia-2) and one putative (O/MYA/2009) vaccine strains and full capsid sequencing. The Capsid sequence analysis revealed three topotypes, Cathay, SEA and Middle East-South Asia (ME-SA) of FMDVs circulating in the region. The vaccines used in this study showed a good match with the SEA and ME-SA viruses. However, none of the recently circulating Cathay topotype viruses were protected by any of the vaccine strains, including the existing Cathay topotype vaccine (O/HKN/6/83), indicating an antigenic drift and, also the urgency to monitor this topotype in the region and develop a new vaccine strain if necessary, although currently the presence of this topotype is mainly restricted to China, Hong Kong, Taiwan and Vietnam. Further, the capsid sequences of these viruses were analyzed that identified several capsid amino acid substitutions involving neutralizing antigenic sites 1, 2 and 5, which either individually or together could underpin the observed antigenic drift.

Livestock movement patterns in the main livestock production provinces of Lao PDR

Foot-and-mouth disease (FMD) is a highly infectious transboundary disease that is endemic and affects the livelihood of smallholder farmers in Lao People's Democratic Republic (PDR). Knowledge about livestock movement patterns is important for preventing the spread of FMD between villages. This study describes the livestock movement patterns in Champasak, Savannakhet and Xiangkhouang provinces of Lao PDR. Face-to-face interviews were conducted with randomly selected villagers (n = 195) and traders (n = 169) in 115 villages between February and March 2019. Livestock owners commonly purchased (mainly breeding) animals from other smallholders (81%) and sold (mainly slaughter) animals to traders (76%) or other smallholders (16%), typically within the same district and province. The median inter-village trade distance was 20-30 km, with an average frequency of 4 trades per village per month. Traders purchased animals from smallholders (71%) and middlemen (25%) located within their district. It was common for many traders (74%) to retain animals at their property before selling, typically a median of 4 beef cattle per trader. Local trades within the district were far more common (72%) than distant trades. The movements of grazing/fattening large ruminants between villages were reported in 30% of the villages in all three provinces and occurred mostly within the same district or province in short distance (6 km). Social Network Analysis has identified animal movement hubs in the three provinces which could be targeted for FMD control and surveillance. Movements of animals for further use (fattening/ reproduction), long-distance movements and frequent local movements described in this area have important implications for FMD circulation. The findings from the study will inform FMD spread simulation models for Lao PDR. The knowledge gained from these data will also help the Lao PDR authorities understand the patterns of animal movements associated with disease spread.

Genetic characterization of foot-and-mouth disease virus serotype O isolates collected during 2014-2018 revealed dominance of O/ME-SA/Ind2001e and the emergence of a novel lineage in India

Foot-and-mouth disease (FMD) is endemic in India with a preponderance of outbreaks caused by FMD virus (FMDV) serotype O. Out of the 11 global topotypes of serotype O, only ME-SA topotype has been reported in the country so far. Lineage O/ME-SA/Ind2001 and O/ME-SA/PanAsia are documented as the most dominant ones in terms of the number of outbreaks caused by them. To understand the distribution of topotype/lineages in India and their antigenic behaviour during the year 2014-2018, a total of 286 FMDV serotype O viral isolates were sequence determined at the VP1 region, and 109 isolates were characterized antigenically. All the isolates grouped in the ME-SA topotype, being distributed in lineage O/ME-SA/Ind2001 (within sub-lineages O/ME-SA/Ind2001d and O/ME-SA/Ind2001e), and a new group designated here as O/ME-SA/2018 cluster. The sub-lineage O/ME-SA/Ind2001e reported for the first time in India during the year 2015, replaced sub-lineage O/ME-SA/Ind2001d gradually, which was dominating since 2008. During the years 2014-2018, the sub-lineage O/ME-SA/Ind2001e was found to be the most predominant one whose mean evolutionary rate was observed to be faster than that of the sub-lineage O/ME-SA/Ind2001d. The codon sites 45 and 85 of VP1 were found to be under diversifying selection in a large proportion of trees. The common ancestor predicted for sub-lineages O/ME-SA/Ind2001e and O/ME-SA/2018 dates back to 2012 and 2016, respectively. The sustenance and spread of the new O/ME-SA/2018 cluster need to be assessed by continued surveillance. The Indian vaccine strain O/INDR2/1975 was found to provide adequate antigenic coverage to the emerging and prevalent serotype O lineages. The trait association tests showed frequent virus exchange among different states, which could be an important confounder in the region-specific assessment of effectiveness of FMD control programme.

High seroprevalence of Foot and Mouth Disease in Laos: Call for nationwide vaccination campaigns and disease surveillance

Foot and mouth disease (FMD) virus remains enzootic in Lao People's Democratic Republic (Lao PDR) due to insufficient control measures, including low vaccination coverage. We assessed virus epidemiology and evaluated knowledge, attitude and practice of Lao farmers and animal health stakeholders towards FMD to support politics in devising evidence-based control measures. Sera were collected from 972 domestic ruminants in three provinces of Lao PDR: Vientiane Capital, Vientiane and Xiengkhouang provinces. Seroprevalence of antibodies directed against non-structural proteins of FMD virus was assessed using a commercial ELISA. Positive sera were further characterized by detecting antibodies directed against the structural proteins of FMD serotypes O, A and Asia 1. Information about farm management, biosecurity practices, livestock trade, and past FMD outbreaks was obtained. Overall 35% (340/972) of the ruminants had antibodies against FMD virus with a similar seroprevalence in each province. Seroprevalence depended significantly on the ruminant species (p < .001): 61% of buffaloes, but only 41% of cattle and 15% of goats were seropositive. While antibodies against FMD serotype Asia 1 were absent, 87% (297/340) of the seropositive animals had antibodies against FMD serotype O and 32% (110/340) against FMD serotype A. Many seropositive animals (31%) had antibodies against both serotypes O and A. The majority of the farmers could name the symptoms of FMD and the susceptible animal species. Although many had likely observed FMD outbreaks in their herd and were aware of FMD vaccines, only few vaccinated their animals. This study confirms that FMD remains enzootic in at least three provinces of Lao PDR where vaccination coverage is low. It also shows the relevance of nationwide active and passive disease surveillance, as well as of vaccination campaigns using bivalent FMD vaccines and targeting all susceptible animal species.

Vaccine strain of O/ME-SA/Ind-2001e of foot-and-mouth disease virus provides high immunogenicity and broad antigenic coverage

Foot-and-mouth disease (FMD) is an economically devastating animal disease. There are seven serotypes, A, O, C, Asia 1, Southern African Territories 1, 2, and 3 (SAT1, SAT2, and SAT3), among which serotype O shows the greatest distribution worldwide. Specifically, the O/ME-SA/Ind-2001 lineage, which was reported in India in 2001, has since emerged worldwide, with the O/ME-SA/Ind-2001d and O/ME-SA/Ind-2001e sublineages recently emerging in North Africa, Middle East Asia, Southeast Asia, and East Asia. The antigenic relationship (r1) value for the O1 Manisa and O/Mya-98 lineage inactivated vaccine against various O/ME-SA/Ind-2001 lineages of FMDV isolates, were matching (r1 > 0.3) or non-matching (r1 < 0.3), indicating that the vaccine based on the O/ME-SA/Ind-2001 lineage FMDV, is valuable. In this study, we developed a new vaccine strain, O/SKR/Boeun/2017 isolate, belonging to the O/ME-SA/Ind-2001e sublineage as an outbreak of this sublineage occurred in 2017 in the Boeun county of the Republic of Korea (O/SKR/Boeun/2017). This experimental vaccine exhibited high immunogenicity in pigs and cattle and was antigenically matched with representative FMDV lineages (ME-SA, O/ME-SA/PanAsia, O/SEA/Mya-98, and O/Cathay) in Asia, as demonstrated by two-dimensional virus neutralization tests (2D-VNT). In addition, a 100% survival rate in C56BL/6 mice vaccinated with 1/15 of a pig dose was observed following challenge with FMDV O/VIT/2013 (O/ME-SA/PanAsia) at 10 days post-vaccination. Further, we analyzed the major antigenic sites of the O/SKR/Boeun/2017 vaccine strain as well as other viruses, by 2D-VNT. These results suggest that the O/ME-SA/Ind-2001e sublineage is a promising vaccine strain candidate in Asia, and other countries, for protection against the emerging FMDV.

Major swine viral diseases: an Asian perspective after the African swine fever introduction

Asia is a major pig producer of the world, and at present, African swine fever virus (ASFV) continues to significantly impact the Asian pig industry. Since more than 50% of the world’s pig population is in Asia, ASFV outbreaks in Asia will affect the global pig industry. Prior to the introduction of ASF, several outbreaks of major swine viruses occurred in Asia over the last two decades, including porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and foot and mouth disease virus (FMDV). The rapid spreading of those viruses throughout Asia involve many factors such as the various pig production systems and supply chains ranging from back-yard to intensive industrial farms, animal movement and animal product trading within and among countries, and consumer behaviors. ASF has notoriously been known as a human-driven disease. Travelers and international trading are the major ASFV-carriers for the transboundary transmission and introduction to naïve countries. Globalization puts the entire pig industry at risk for ASF and other infectious diseases arising from Asian countries. Disease control strategies for the various pig production systems in Asia are challenging. In order to ensure future food security in the region and to prevent the deleterious consequences of ASF and other major viral disease outbreaks, disease control strategies and production systems must be improved and modernized.

Genome Sequences of Foot-and-Mouth Disease Virus O/ME-SA/Ind-2001e Strains Isolated in Pakistan

The genome sequences of two foot-and-mouth disease type O viruses isolated from outbreaks of disease in cattle in Pakistan in 2019 are described. They were identified as belonging to serotype O, Middle East-South Asia topotype, Ind-2001 lineage, and e sublineage and represent the first identification of this lineage in Pakistan.

The genome sequences of two foot-and-mouth disease type O viruses isolated from outbreaks of disease in cattle in Pakistan in 2019 are described. They were identified as belonging to serotype O, Middle East-South Asia topotype, Ind-2001 lineage, and e sublineage and represent the first identification of this lineage in Pakistan.

A history of FMD research and control programmes in Southeast Asia: lessons from the past informing the future

Foot and mouth disease (FMD) is a major animal health problem within Southeast Asia (SEA). Although Indonesia and more recently the Philippines have achieved freedom from FMD, the disease remains endemic on continental SEA. Control of FMD within SEA would increase access to markets in more developed economies and reduce lost productivity in smallholder and emerging commercial farmer settings. However, despite many years of vaccination by individual countries, numerous factors have prevented the successful control of FMD within the region, including unregulated ‘informal’ transboundary movement of livestock and their products, difficulties implementing vaccination programmes, emergence of new virus topotypes and lineages, low-level technical capacity and biosecurity at national levels, limited farmer knowledge on FMD disease recognition, failure of timely outbreak reporting and response, and limitations in national and international FMD control programmes. This paper examines the published research of FMD in the SEA region, reviewing the history, virology, epidemiology and control programmes and identifies future opportunities for FMD research aimed at the eventual eradication of FMD from the region.

Evaluation of novel inactivated vaccines for the SAT 1, SAT 2 and SAT 3 serotypes of foot-and-mouth disease in pigs

Background

The foot-and-mouth disease (FMD) virus is classified into seven serotypes, of which the South African types have South African Territories (SAT)1, SAT2, and SAT3 that are prevalent in Africa. Especially SAT2 have spread to Arabian Peninsula and the Palestinian Autonomous Territories. Of these viruses, the incidence of SAT2 is the highest. It is important to prepare for the spread of the virus to other continents, even though most FMD viruses are bovine-derived. In particular, due to the high breeding density of pigs in Asia, more attention is usually paid to the immunity and protection of pigs than cattle. For this reason, this study investigated the immunity and protection of pigs against the SAT viruses.

Methods

Specific vaccines were developed for SAT1, SAT2, and SAT3 serotypes. These vaccine viruses were designed to be distinguished from the wild-type strain. An immunogenicity test was conducted using these vaccines in both cattle (n = 5/group) and pigs (n = 20/group).

Results

High virus-neutralizing titer of antibodies (> 1:100) was induced in only 2 weeks after the immunization of cattle with the individual vaccine for SAT1, SAT2 or SAT3, and a clear immune response was induced after the second immunization in pigs. When the vaccinated pigs (n = 4–5/group) were challenged by the homologous wild-type virus strain 4 weeks after immunization, all the pigs were protected from the challenge.

Conclusions

This study confirmed that these vaccines can be used against SAT1, SAT2, and SAT3 viruses in cattle and pigs. The vaccine strains developed in this study are expected to be used as vaccines that can protect against FMD in the event of a future FMD outbreak in pigs in consideration of the situation in Asia.

First detection of foot-and-mouth disease virus O/ME-SA/ Ind2001e sublineage in Jordan

Foot-and-mouth disease (FMD) is a highly contagious vesicular disease that is caused by the FMD virus (FMDV). This disease affects both wild and domestic cloven-hoofed animals, and the latter of which includes cattle, swine, sheep and goats. FMD is endemic to Jordan and has a severe impact on the productivity of domestic livestock. In January 2017, FMD outbreaks were detected in different animal species across Jordan, resulting in high mortality rates among young lamb and goat populations as well as causing classic FMD symptoms in cattle. In this study, clinical specimens were collected from animals affected by FMD. The results obtained from sequencing the VP1 gene place the studied FMDV isolate within the FMDV O/ME-SA/ Ind2001e sublineage. Phylogenetic analysis of VP1 suggests that the O/JOR/1/2017 isolate is very similar to that of viruses isolated from Saudi Arabia in 2016. The possible introduction of this strain to Jordan might occur through transboundary animal movement or other transmission routes from Saudi Arabia, a neighbouring country.

Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples

Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.

Bovine Ephemeral Fever in Asia: Recent Status and Research Gaps

Bovine ephemeral fever is an arthropod-borne viral disease affecting mainly domestic cattle and water buffalo. The etiological agent of this disease is bovine ephemeral fever virus, a member of the genus Ephemerovirus within the family Rhabdoviridae. Bovine ephemeral fever causes economic losses by a sudden drop in milk production in dairy cattle and loss of condition in beef cattle. Although mortality resulting from this disease is usually lower than 1%, it can reach 20% or even higher. Bovine ephemeral fever is distributed across many countries in Asia, Australia, the Middle East, and Africa. Prevention and control of the disease mainly relies on regular vaccination. The impact of bovine ephemeral fever on the cattle industry may be underestimated, and the introduction of bovine ephemeral fever into European countries is possible, similar to the spread of bluetongue virus and Schmallenberg virus. Research on bovine ephemeral fever remains limited and priority of investigation should be given to defining the biological vectors of this disease and identifying virulence determinants.

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

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

Genome Sequences of Foot-and-Mouth Disease Viruses of Serotype O Lineages Mya-98 and Ind-2001d Isolated from Cattle and Buffalo in Myanmar

We report whole-genome sequences and partial genome sequences of eight foot-and-mouth disease viruses obtained from outbreak samples in Myanmar in 2016 and 2017. These viruses are classified into O/ME-SA/Ind-2001d and O/SEA/Mya-98 lineages.

We report whole-genome sequences and partial genome sequences of eight foot-and-mouth disease viruses obtained from outbreak samples in Myanmar in 2016 and 2017. These viruses are classified into O/ME-SA/Ind-2001d and O/SEA/Mya-98 lineages.

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.

Chimeric vaccine strain of type O foot-and-mouth disease elicits a strong immune response in pigs against ME-SA and SEA topotypes

Foot-and-mouth disease (FMD) is an acute infectious disease occurring in cloven-hoofed animals. There are many variations of the virus, making it difficult to protect against the various strains with one virus vaccine. The immunogenicity has generally been evaluated in pigs using neutralizing antibodies to determine the protection level against foot-and-mouth disease virus type O. Therefore, the vaccine from the chimeric vaccine strain of ME-SA (VP4, VP2, and VP3) and SEA (VP1) topotypes developed in this study is expected to be able to protect with high neutralizing antibody titers against most of the eight FMD viruses of the four different topotypes (ME-SA, SEA, Cathay, and EURO-SA) of type O in pigs. This is a new technique for powerful vaccine development, with multiple preventive roles against various epidemic FMD strains.

Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: the impact of recombination within the emerging O/ME-SA/Ind-2001 lineage

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.

Risk factors for emergence of exotic foot-and-mouth disease O/ME-SA/Ind-2001d on smallholder farms in the Greater Mekong Subregion

Foot-and-mouth disease (FMD) is a significant endemic transboundary animal disease in Lao People's Democratic Republic (Lao PDR) and throughout the Greater Mekong Subregion (GMS). The disease has been shown to perpetuate the cycle of smallholder poverty through reduced animal production, plus limitations on market access for trading in livestock and their products. Despite significant national and multilateral efforts to control FMD over the past two decades, endemic FMD viruses (FMDVs) continue to circulate in Lao PDR. Further, the threat from new and emerging FMDVs is increasing as transboundary movements in the region intensify in response to increasing regional demand for meat. Although the economic impacts of FMD on smallholder farmers in Lao PDR are significant, studies investigating household-level risk factors for FMD are lacking. Following an outbreak of a novel FMDV (O/ME-SA/Ind2001d) in Lao PDR in 2015, a questionnaire and serological study were conducted in Naxaythong District to identify household-level risk factors associated with this outbreak, as well as endemic circulating viruses in the outbreak area. Data were analysed using a multivariable generalised estimating equation (GEE) model with a logit link function and associations were calculated as odds ratios (OR) with 95% confidence intervals (CI_95%). After adjusting for other variables, the practice of quarantining new livestock for a minimum of two weeks prior to introduction to a herd was found to be a significant protective factor during the 2015 outbreak (OR 0.225, CI_95% [0.06, 0.88], p-value 0.003). In addition, households owning one or more animals with titres to the non-structural proteins of FMDV, indicating prior infection, had 5.5 times the odds (CI_95% [6.16, 49.11], p-value <0.001) of sharing communal grazing land with neighbouring villages. These findings indicate that implementing basic on-farm biosecurity and improved husbandry measures to minimise FMDV circulation at the household level are important and reinforce the need to enhance the education of smallholder farmers in infectious disease control.

Implementing large Foot and Mouth Disease vaccination programmes for smallholder farmers: lessons from Lao PDR

This study assessed smallholder finances and their attitudes towards the Foot and Mouth Disease (FMD) vaccination programme, when 1 620 000 vaccine doses were provided for strategic administration in large ruminants in FMD 'high-risk' areas in Laos between 2012 and 2016. Farmers (n = 168) in the provinces of Xayyabouli (XYL), Xiengkhoung (XK) and Huaphan (HP), were interviewed. Over 91% of the farmers responded that their livestock were vaccinated for FMD, with over 86% ranking FMD vaccination as a good or very good intervention. No FMD cases were reported from the vaccinated provinces after May 2013. Examination of the total income per household in XYL, XK and HP indicated earnings of US$5060(±650), US$4260(±294) and US$1691(±676), respectively (P = 0.001), with 23%, 28% and 68% of the total incomes from annual sales of large ruminant, respectively. Of the farmers in XYL, XK and HP, 83%, 93% and 70% (P = 0.009) said their annual income increased compared with 2012, and 47%, 64% and 41%, respectively (P = 0.005), indicated this increase was from additional large ruminant sales. The study indicated that this large FMD vaccination programme was well regarded by participating farmers and may have provided satisfactory suppression of the disease in Laos, despite not achieving the preferred vaccination coverage. Continuation of the vaccination programme in FMD high-risk areas is suggested as desirable.

Genome Sequence of Foot-and-Mouth Disease Virus of Serotype O Lineage Ind-2001d Isolated from Cattle in Mongolia in 2015

We report the whole-genome sequence of the foot-and-mouth disease virus (FMDV) O/MOG/BU/2-7/2015 isolated in Mongolia in 2015. This virus is closely related to isolates identified in Southeast Asia in 2015 and is classified under the O/ME-SA/Ind-2001d lineage. This is the first detection of an FMDV of this lineage in Mongolia.