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 Virus Serotype O Exhibits Phenomenal Genetic Lineage Diversity in India during 2018-2022

In India, widespread foot-and-mouth disease (FMD) outbreaks occurred in 2021. The objective of this study was to identify genetic lineages and evaluate the antigenic relationships of FMD virus (FMDV) isolates gathered from outbreaks reported between 2019 and 2022. Our study shows that the lineages O/ME-SA/Ind2001e and the O/ME-SA/Cluster-2018 were both responsible for the FMD outbreaks on an epidemic scale during 2021. This observation is in contrast to earlier findings that suggested epidemic-scale FMD outbreaks in India are often connected to a single genetic lineage. Additionally, we report here the identification of the O/ME-SA/PanAsia-2/ANT10 sub-lineage in India for the first time, which was connected to two intermittent outbreaks in Jammu and Kashmir. The current study demonstrates that the O/ME-SA/ind2001e lineage has a strong presence outside of the Indian subcontinent. Furthermore, the O/ME-SA/Cluster-2018 was observed to have a wider geographic distribution than previously, and like the O/ME-SA/Ind2001d and O/ME-SA/Ind2001e lineages in the past, it may eventually spread outside of its geographic niche. For O/ME-SA/Ind2001e and O/ME-SA/Cluster-2018, the predicted substitution rate for the VP1 region was 6.737 × 10^-3 and 8.257 × 10^-3 nt substitutions per site per year, respectively. The time of the most recent common ancestor of the O/ME-SA/Ind2001e and O/ME-SA/Cluster-2018 strains suggests that the viruses possibly emerged during 2003-2011 and 2009-2017, respectively. Recent sightings of the O/ME-SA/PanAsia2/ANT10 virus in India and the O/ME-SA/Ind2001e virus in Pakistan point to possible cross-border transit of the viruses. The results of a two-dimensional viral neutralization test revealed that all of the field isolates were antigenically matched to the currently used Indian vaccine strain O INDR2/1975. These results suggest that the serotype O vaccine strain can protect against outbreaks brought on by all three circulating lineages.

Foot-and-mouth disease status in India during the second decade of the twenty-first century (2011-2020)

Foot-and-mouth disease (FMD) is a major disease of livestock in India and causes huge economic losses. The formal FMD control program started in 2003–04 in selected districts and was gradually expanded. The present study provides a descriptive review of the FMD outbreaks, prevalent serotypes, and genetic and antigenic features of the FMD virus (FMDV) that circulated in the country between 2011 and 2020. FMD outbreaks were regularly reported in cloven-hoofed domestic livestock and wildlife, with three serotypes including O, A, and Asia1. During the study period, a total of 2226 FMD outbreaks were documented and serotypes confirmed. FMDV serotype O dominated the outbreak scenario, accounting for about 92% of all outbreaks, followed by Asia1 (5% of all outbreaks) and A (3% of all outbreaks). Two major epidemics of FMD on an unprecedented scale during the years 2013 and 2018 by serotype O were recorded. The spatial distribution of FMD was characterized by a larger number of outbreaks in the southern region of the country. In an annual-scale analysis, 2020 was the year with the lowest outbreaks, and 2013 was the year with the highest. The month-scale analysis showed that outbreaks were reported throughout the year, with the highest numbers between October and March. The emergence of three major lineages (O/ME-SA/Ind2001d, O/ME-SA/Ind2001e, and O/ME-SA/Ind2018) of serotype O was observed during the period. In the cases of serotype A and Asia1, the appearance of at least one novel lineage/genetic group, including A/G-18/non-deletion/2019 and Asia1/Group-IX, was documented. While serotype A showed the advent of antigenic variants, serotypes O and Asia1 did not show any antigenic diversity. It was noticed during the course of an outbreak that animal movement contributes significantly to disease transmission. Except for 2018, when numerous FMD outbreaks were recorded, the number of annual outbreaks reported after 2016 has been lower than in the first half of the decade, probably due to mass vaccination and COVID-19 pandemic-linked movement restrictions. Even during outbreaks, disease symptoms in ruminant populations, including cattle, were found to be less severe. Regular six-monthly immunization certainly has a positive impact on the reduction of disease burden and should be followed without fail and delay, along with intensive disease surveillance.

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.

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.

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.

The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

Characterization of the FMDV-serotype-O isolates collected during 1962 and 1997 discloses new topotypes, CEY-1 and WCSA-1, and six new lineages

The genetic diversity of the FMD viruses collected from the outbreaks during the second half of the 20th Century in Sri Lanka was assessed in the present study. We sequenced the VP1 genomic region of the samples collected during FMDV epidemics caused by serotype O in Sri Lanka during 1962 and 1997. For comparison, we sequenced the VP1 of the related viral isolates collected from other Asian countries. We analyzed the VP1 sequences of the viral strains using the UPGMA method with uncorrected pairwise distances. Nucleotide divergence (ND) thresholds of 15%-20% and 5%-<15% were used to differentiate topotypes and lineages, respectively. We calibrated the divergence times and lineage-specific substitution rates using Bayesian-skyline models. Based on the ND estimations and phylogenetic relationships, we identified and named two new topotypes [CEYLON 1 (CEY-1) and WEST, CENTRAL AND SOUTH ASIA 1 (WCSA-1)] and six new lineages (Syr-62, Srl-77, Tur-69, May-78, Tai-87 and Bur-77) of serotype O. We believe that the novel topotypes and lineages named may have disappeared although they have similar substitution rates for epizootic outbreaks. Because the amino acid selection analysis revealed that the two topotypes and six lineages identified were under purifying selection during the outbreaks.

Assessing biases in phylodynamic inferences in the presence of super-spreaders

Phylodynamic analyses using pathogen genetic data have become popular for making epidemiological inferences. However, many methods assume that the underlying host population follows homogenous mixing patterns. Nevertheless, in real disease outbreaks, a small number of individuals infect a disproportionately large number of others (super-spreaders). Our objective was to quantify the degree of bias in estimating the epidemic starting date in the presence of super-spreaders using different sample selection strategies. We simulated 100 epidemics of a hypothetical pathogen (fast evolving foot and mouth disease virus-like) over a real livestock movement network allowing the genetic mutations in pathogen sequence. Genetic sequences were sampled serially over the epidemic, which were then used to estimate the epidemic starting date using Extended Bayesian Coalescent Skyline plot (EBSP) and Birth–death skyline plot (BDSKY) models. Our results showed that the degree of bias varies over different epidemic situations, with substantial overestimations on the epidemic duration occurring in some occasions. While the accuracy and precision of BDSKY were deteriorated when a super-spreader generated a larger proportion of secondary cases, those of EBSP were deteriorated when epidemics were shorter. The accuracies of the inference were similar irrespective of whether the analysis used all sampled sequences or only a subset of them, although the former required substantially longer computational times. When phylodynamic analyses need to be performed under a time constraint to inform policy makers, we suggest multiple phylodynamics models to be used simultaneously for a subset of data to ascertain the robustness of inferences.

Knowledge and behavior of cattle and sheep owners and herders regarding foot-and-mouth disease in Northern Algeria

Background and Aim:

Foot-and-mouth disease (FMD) has been occurring in Algeria since 2014, when an outbreak was announced in Setif, a district in the eastern region of the country. The problem was apparently resolved with the help of vaccination. However, in 2015, 2016, and 2018, FMD recurred. The veterinary authorities and media educated breeders on how to recognize the clinical signs and how to report the disease. This study aimed to evaluate the knowledge and recognition of FMD by farmers and breeders. Moreover, an assessment of the behavior of cattle and sheep owners and herders following FMD cases is examined.

Materials and Methods:

A cross-sectional survey was conducted from June to October 2018 to evaluate the perception of cattle and sheep owners and breeders regarding FMD in the Northern regions of Algeria, using questionnaires.

Results:

One hundred questionnaires were distributed; 71 were collected. Data showed that all the responders claimed to know about the disease, while more than half of the owners/herders claimed that they knew the clinical symptoms of FMD and mentioned fever, hypersalivation, lameness, and vesicles. Fewer than half (42%) (30/71) took some measures to prevent the disease, while more than half (58%) (41/71) did not take any measures in 2018. No one claimed to have reported the disease to authorities in 2018, while more than half had done so in 2014.

Conclusion:

It appears that experienced farmers recognized the clinical signs of FMD, while an academic background was not conclusively necessary for the identification of the clinical signs of the disease. Concerning the assessment of risk-associated behavior in the event of FMD occurrence, the responses of the breeders were not significantly different from those of risk-associated behaviors in the event of an epidemic. Farmers and breeders expressed similarity in terms of communicating the appearance of the disease in their livestock; the majority of them seemed to be aware of the importance of reporting the disease to local authorities, especially in 2014, when the disease first occurred. This behavior is encouraged by refund and technical assistance policies by the veterinary authorities, but in 2018, no disease was reported due to fear of slaughtering and economic loss.

Foot-and-Mouth Disease Virus: Immunobiology, Advances in Vaccines and Vaccination Strategies Addressing Vaccine Failures-An Indian Perspective

A mass vaccination campaign in India seeks to control and eventually eradicate foot-and-mouth disease (FMD). Biosanitary measures along with FMD monitoring are being conducted along with vaccination. The implementation of the FMD control program has drastically reduced the incidence of FMD. However, cases are still reported, even in regions where vaccination is carried out regularly. Control of FMD outbreaks is difficult when the virus remains in circulation in the vaccinated population. Various FMD risk factors have been identified that are responsible for FMD in vaccinated areas. The factors are discussed along with strategies to address these challenges. The current chemically inactivated trivalent vaccine formulation containing strains of serotype O, A, and Asia 1 has limitations including thermolability and induction of only short-term immunity. Advantages and disadvantages of several new-generation alternate vaccine formulations are discussed. It is unfeasible to study every incidence of FMD in vaccinated animals/areas in such a big country as India with its huge livestock population. However, at the same time, it is absolutely necessary to identify the precise reason for vaccination failure. Failure to vaccinate is one reason for the occurrence of FMD in vaccinated areas. FMD epidemiology, emerging and re-emerging virus strains, and serological status over the past 10 years are discussed to understand the impact of vaccination and incidences of vaccination failure in India. Other factors that are important in vaccination failure that we discuss include disrupted herd immunity, health status of animals, FMD carrier status, and FMD prevalence in other species. Recommendations to boost the search of alternate vaccine formulation, strengthen the veterinary infrastructure, bolster the real-time monitoring of FMD, as well as a detailed investigation and documentation of every case of vaccination failure are provided with the goal of refining the control program.

Foot-and-mouth disease virus O/ME-SA/Ind 2001 lineage outbreak in vaccinated Holstein Friesian cattle in Saudi Arabia in 2016

Background: Foot-and-mouth disease virus (FMDV) is a highly contagious viral infection of large ruminants. Despite the massive application of vaccines against FMDV, several outbreaks are still being reported in Africa and Asia.

Aim: To perform molecular characterization of FMDV in an outbreak among a cattle herd Saudi Arabia in 2016. This herd had been vaccinated with a polyvalent FMDV vaccine.

Methods: To investigate this outbreak, we collected specimens from 77 animals showing typical clinical signs of FMDV. Specimens including sera, nasal swabs, and tissues (tongue, coronary bands, hooves, and hearts) were collected. We tested the collected cattle sera for the presence of FMDV antibodies with commercial ELISA kits. In addition, we tested the swabs for the presence of the most common FMDV strains (O, A, Asia-1 and SAT-2) with RT-PCR using serotype-specific oligonucleotides.

Results: Serology showed that 22% of the tested sera were positive. Molecular testing of the examined swabs confirmed that 24% of the tested animals were positive. Our sequencing analysis confirmed that the circulating strains of FMDV belonged to FMDV serotype O. The phylogenetic tree based on the FMDV-VP-1 gene revealed high nucleotide identity between the circulating strains and the Bangladesh strain (99%). These strains were distinct (shared 89% nucleotide identity) from the FMDV-O strains used for the preparation of the vaccine administered to the animals in this herd. Moreover, they had 7% nucleotide difference between the FMDV-O strains reported in Saudi Arabian in 2013.

Conclusion: More in-depth molecular characterization of these FMDV strains is warranted.

Molecular Epidemiology of Foot-and-Mouth Disease Virus in the Context of Transboundary Animal Movement in the Far North Region of Cameroon

Transboundary movement of animals is an important mechanism for foot-and-mouth disease virus (FMDV) spread in endemic regions, such as Cameroon. Several transboundary animal trade routes cross the Far North Region of Cameroon, and cattle moved on foot along these routes often come in contact with native (sedentary and transhumant) herds. The purpose of this study was to investigate the role of transboundary trade cattle in the epidemiology of FMDV in the Far North Region of Cameroon. A total of 582 oropharyngeal fluid (OPF) samples were collected from asymptomatic transboundary trade cattle at official border check points and 57 vesicle epithelial tissues were collected from clinically affected native cattle in the Far North Region of Cameroon during 2010-2014. Viral protein 1 (VP1) coding sequences were obtained from 6 OPF samples from transboundary cattle (4 serotype O, 2 serotype SAT2) and 19 epithelial tissue samples from native cattle (7 serotype O, 3 serotype SAT2, 9 serotype A). FMDV serotype O viruses belonged to two topotypes (East Africa-3 and West Africa), and phylogenetic analyses suggested a pattern of continuous transmission in the region. Serotype SAT2 viruses belonged to a single topotype (VII), and phylogenetic analysis suggested a pattern of repeated introductions of different SAT2 lineages in the region. Serotype A viruses belonged to topotype AFRICA/G-IV, and the pattern of transmission was unclear. Spearman rank correlation analysis of VP1 coding sequences obtained in this study from transboundary and native cattle showed a positive correlation between genetic distance and time for serotype O (ρ = 0.71, p = 0.003) and between genetic distance and geographic distance for serotype SAT2 (ρ = 0.54, p = 0.1). These data suggest that transboundary trade cattle participate in the transmission of FMDV in the Far North Region of Cameroon, however the dynamics and direction of transmission could not be determined in this study. Results of this study contribute to the understanding of transboundary FMDV epidemiology in Central Africa and will help to inform control programs in Cameroon and in the region.