Direct detection and characterization of foot‐and‐mouth disease virus in East Africa using a field‐ready real‐time PCR platform

Effective control and monitoring of foot‐and‐mouth disease (FMD ) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE ). However, the requirements for prompt and serotype‐specific diagnosis during FMD outbreaks, and the need to establish robust laboratory testing capacity in FMD ‐endemic countries have motivated the development of simple diagnostic platforms to support local decision‐making. Using a portable thermocycler, the T‐COR ™ 8, this study describes the laboratory and field evaluation of a commercially available, lyophilized pan‐serotype‐specific real‐time RT ‐PCR (rRT ‐PCR ) assay and a newly available FMD virus (FMDV) typing assay (East Africa‐specific for serotypes: O, A, Southern African Territories [SAT ] 1 and 2). Analytical sensitivity, diagnostic sensitivity and specificity of the pan‐serotype‐specific lyophilized assay were comparable to that of an OIE ‐recommended laboratory‐based rRT ‐PCR (determined using a panel of 57 FMDV ‐positive samples and six non‐FMDV vesicular disease samples for differential diagnosis). The FMDV ‐typing assay was able to correctly identify the serotype of 33/36 FMDV ‐positive samples (no cross‐reactivity between serotypes was evident). Furthermore, the assays were able to accurately detect and type FMDV RNA in multiple sample types, including epithelial tissue suspensions, serum, oesophageal–pharyngeal (OP ) fluid and oral swabs, both with and without the use of nucleic acid extraction. When deployed in laboratory and field settings in Tanzania, Kenya and Ethiopia, both assays reliably detected and serotyped FMDV RNA in samples (n  = 144) collected from pre‐clinical, clinical and clinically recovered cattle. These data support the use of field‐ready rRT ‐PCR platforms in endemic settings for simple, highly sensitive and rapid detection and/or characterization of FMDV.     

Environmental persistence of foot‐and‐mouth disease virus applied to endemic regions

The consequences of foot‐and‐mouth disease impact regional economies and food security through animal mortality and morbidity, trade restrictions and burdens to veterinary infrastructure. Despite efforts to control the disease, some regions, mostly in warmer climates, persistently report disease outbreaks. Consequently, it is necessary to understand how environmental factors influence transmission, of this economically devastating disease. Extensive research covers basic aetiology and transmission potential of livestock and livestock products for foot‐and‐mouth disease virus (FMDV), with a subset evaluating environmental survival. However, this subset, completed in the early to mid‐20th century in Northern Europe and the United States, is not easily generalized to today's endemic locations. This review uncovered 20 studies, to assess current knowledge and analyse the effects of environmental variables on FMDV survival, using a Cox proportional hazards (Coxph) model. However, the dataset is limited, for example pH was included in three studies and only five studies reported both relative humidity (RH) and temperature. After dropping pH from the analysis, our results suggest that temperature alone does not describe FMDV survival; instead, interactions between RH and temperature have broader impacts across various conditions. For instance, FMDV is expected to survive longer during the wet season (survival at day 50 is ~90% at 16°C and 86% RH) versus the dry season (survival at day 50 approaches 0% at 16°C and 37.5% RH) or comparatively in the UK versus the Southwestern United States. Additionally, survival on vegetation topped 70% on day 75 when conditions exceeded 20°C with high RH (86%), drastically higher than the survival on inanimate surfaces at the same temperature and RH (~0%). This is important in tropical regions, where high temperatures can persist throughout the year, but RH varies. Therefore, parameter estimates, for disease modelling and control in endemic areas, require environmental survival data from a wider range of conditions.     

Rapid and simple detection of foot‐and‐mouth disease virus: Evaluation of a cartridge‐based molecular detection system for use in basic laboratories

Highly contagious transboundary animal diseases such as foot‐and‐mouth disease (FMD ) are major threats to the productivity of farm animals. To limit the impact of outbreaks and to take efficient steps towards a timely control and eradication of the disease, rapid and reliable diagnostic systems are of utmost importance. Confirmatory diagnostic assays are typically performed by experienced operators in specialized laboratories, and access to this capability is often limited in the developing countries with the highest disease burden. Advances in molecular technologies allow implementation of modern and reliable techniques for quick and simple pathogen detection either in basic laboratories or even at the pen‐side. Here, we report on a study to evaluate a fully automated cartridge‐based real‐time RT ‐PCR diagnostic system (Enigma MiniLab^®) for the detection of FMD virus (FMDV ). The modular system integrates both nucleic acid extraction and downstream real‐time RT ‐PCR (rRT ‐PCR ). The analytical sensitivity of this assay was determined using serially diluted culture grown FMDV , and the performance of the assay was evaluated using a selected range of FMDV positive and negative clinical samples of bovine, porcine and ovine origin. The robustness of the assay was evaluated in an international inter‐laboratory proficiency test and by deployment into an African laboratory. It was demonstrated that the system is easy to use and can detect FMDV with high sensitivity and specificity, roughly on par with standard laboratory methods. This cartridge‐based automated real‐time RT ‐PCR system for the detection of FMDV represents a reliable and easy to use diagnostic tool for the early and rapid disease detection of acutely infected animals even in remote areas. This type of system could be easily deployed for routine surveillance within endemic regions such as Africa or could alternatively be used in the developed world.     

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

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

Molecular Characterisation of Foot‐and‐Mouth Disease Viruses from Pakistan, 2005–2008

Foot‐and‐mouth disease (FMD), an economically important disease of cloven‐hoofed animals, is endemic in Pakistan where three virus serotypes are present (O, A and Asia 1). Fifty‐eight clinical samples collected between 2005 and 2008 from animals with suspected FMD in various locations in Pakistan were subjected to virus isolation on primary cell culture, antigen ELISA and real‐time RT‐PCR (rRT‐PCR). Viruses were isolated from 32 of these samples and identified as FMDV type O (n = 31) or type A (n = 1). Foot‐and‐mouth disease virus (FMDV) genome was detected in a further 11 samples by real‐time RT‐PCR. Phylogenetic analyses of the VP1 nucleotide sequences showed that all of the type O viruses belonged to the MIDDLE EAST–SOUTH ASIA topotype with the majority belonging to the PanAsia‐2 lineage; a single example of the older PanAsia lineage was identified. The single FMDV type A virus belonged to the ASIA topotype, but did not cluster with known strains that are currently circulating (such as Iran‐05) and was not closely related to other type A viruses from the region. These findings demonstrate the widespread distribution of O‐PanAsia‐2 in Pakistan and the presence of undisclosed novel type A lineages in the region.     

Outbreak investigations and molecular characterization of foot‐and‐mouth disease viruses circulating in south‐west Niger

In Niger, the epidemiological situation regarding foot‐and‐mouth disease is unclear as many outbreaks are unreported. This study aimed (i) to identify Foot‐and‐mouth disease virus (FMDV ) strains currently circulating in cattle herds, and (ii) to identify risk factors associated with Foot‐and‐mouth disease (FMD )‐seropositive animals in clinical outbreaks. Epithelial tissues (n  = 25) and sera (n  = 227) were collected from cattle in eight districts of the south‐western part of Niger. Testing of clinical material revealed the presence of FMDV serotype O that was characterized within the O/WEST AFRICA topotype. The antigenic relationship between one of the FMDV isolates from Niger (O/NGR /4/2015) and three reference vaccine strains was determined by the two‐dimensional virus neutralization test (2dmVNT ), revealing a close antigenic match between the field isolate from Niger and three FMDV serotype O vaccine strains. Serological analyses using a non‐structural protein (NSP ) test provided evidence for previous FMDV infection in 70% (158/227) of the sera tested. Multivariate logistic regression analysis revealed that only the herd composition (presence of both cattle and small ruminants) was significantly associated with FMDV seropositivity as defined by NSP ‐positive results (p ‐value = .006). Of these positive sera, subsequent testing by liquid‐phase blocking ELISA (LPBE ) showed that 86% (136/158) were positive for one (or more) of four FMDV serotypes (A, O, Southern African Territories (SAT ) 1 and SAT 2). This study provides epidemiological information about FMD in the south‐western part of Niger and highlights the complex transboundary nature of FMD in Africa. These findings may help to develop effective control and preventive strategies for FMD in Niger as well, as other countries in West Africa.     

Spatiotemporal analysis of foot‐and‐mouth disease outbreaks in the Republic of Kazakhstan, 1955 – 2013

Foot‐and‐mouth disease (FMD ) poses a significant obstacle to international trade and economic development, and for that reason, FMD prevention, control and eradication are major goals guiding animal health policy in most countries. The purpose of this study was to conduct a retrospective spatiotemporal analysis of FMD outbreaks among livestock in the Republic of Kazakhstan (RK ) from 1955 to 2013. During that time, several FMD control strategies were implemented in RK , which culminated with the World Organization for Animal Health (OIE ) recognition of RK as a country that is FMD ‐free with partial vaccination (2015). Here, we describe and analyse the changes in spatial and temporal dynamics of FMD under different control strategies that were utilized as the country progressively moved towards eradication of the disease. A total number of 5,260 FMD outbreaks of serotype O and A (including the A₂₂ lineage) were recorded in the cattle, pig and small ruminant populations of RK during that period. We found that outbreaks occurred in spatiotemporal clusters only prior to 1970, which is before ring vaccination around outbreaks was first employed. This finding suggests that ring vaccination substantially reduced local spread and prevented large FMD epidemics in the country. Disease incidence steadily decreased after the implementation of ring vaccination and culling of infected animals, with spatiotemporal clusters only occurring as a result of an introduction of an antigenically distinct variant of serotype A. From 1955 to 1984, FMD outbreaks demonstrated two seasonal peaks of incidence in the spring and fall. In contrast, only the peak in spring was observed between 1984 and 2013. Quantitative knowledge on how different policy and alternative control strategies contributed to RK achieving FMD ‐free status could improve prospects for continued control in RK and inform control strategies in other FMD ‐endemic regions.     

Genetic Characterization of Serotypes A and Asia‐1 Foot‐and‐mouth Disease Viruses in Balochistan,Pakistan, in 2011

This study reports characterization of foot‐and‐mouth disease virus (FMDV) in samples collected from Balochistan, Pakistan. FMDV was detected by pan‐FMDV real‐time RT‐PCR in 31 samples (epithelial and oral swabs) collected in 2011 from clinical suspect cases. Of these, 29 samples were serotyped by serotype‐specific real‐time RT‐PCR assays and were confirmed by sequencing the VP1 coding region. Sixteen samples were found positive for serotype A and eight for serotype Asia‐1, whereas five samples were found positive for both serotypes A and Asia‐1. Two serotype A positive samples were found positive for two different strains of serotype A FMDV each. Phylogenetic analyses of serotype A FMDVs showed circulation of at least three different sublineages within the A‐Iran05 lineage. These included two earlier reported sublineages, A‐Iran05^HER−10 and A‐Iran05^FAR−11, and a new sublineage, designated here as A‐Iran05^BAL−11. This shows that viruses belonging to the A‐Iran05 lineage are continuously evolving in the region. Viruses belonging to the A‐Iran05^FAR−11 sublineage showed close identity with the viruses circulating in 2009 in Pakistan and Afghanistan. However, viruses belonging to the A‐Iran05^HER−10 detected in Balochistan, Pakistan, showed close identity with the viruses circulating in Kyrgyzstan, Iran and Kazakhstan in 2011 and 2012, showing that viruses responsible for outbreak in these countries have a common origin. Serotype Asia‐1 FMDVs reported in this study all belonged to the earlier reported Group‐VII (Sindh‐08), which is currently a dominant strain in the West Eurasian region. Detection of two different serotypes of FMDV or/and two different strains of the same serotype in one animal/sample shows complexity in occurrence of FMD in the region.     

Model of persistent foot‐and‐mouth disease virus infection in multilayered cells derived from bovine dorsal soft palate

Foot‐and‐mouth disease virus (FMDV) causes a highly contagious vesicular disease in livestock, with serious consequences for international trade. The virus persists in the nasopharynx of cattle and this slows down the process to obtain an FMDV‐free status after an outbreak. To study biological mechanisms, or to identify molecules that can be targeted to diagnose or interfere with persistence, we developed a model of persistent FMDV infection in bovine dorsal soft palate (DSP). Primary DSP cells were isolated after commercial slaughter and were cultured in multilayers at the air‐liquid interface. After 5 weeks of culture without further passage, the cells were infected with FMDV strain O/FRA/1/2001. Approximately, 20% of cells still had a polygonal morphology and displayed tight junctions as in stratified squamous epithelia. Subsets of cells expressed cytokeratin and most or all cells expressed vimentin. In contrast to monolayers in medium, multilayers in air demonstrated only a limited cytopathic effect. Integrin α_Vβ₆ expression was observed in mono‐ but not in multilayers. FMDV antigen, FMDV RNA and live virus were detected from day 1 to 28, with peaks at day 1 and 2. The proportion of infected cells was highest at 24 hr (3% and 36% of cells at an MOI of 0.01 and 1, respectively). At day 28 after infection, at a time when animals that still harbour FMDV are considered carriers, FMDV antigen was detected in 0.2%–2.1% of cells, in all layers, and live virus was isolated from supernatants of 6/8 cultures. On the consensus level, the viral genome did not change within the first 24 hr after infection. Only a few minor single nucleotide variants were detected, giving no indication of the presence of a viral quasispecies. The air‐liquid interface model of DSP brings new possibilities to investigate FMDV persistence in a controlled manner.     

Opportunities for enhanced surveillance of foot‐and‐mouth disease in endemic settings using milk samples

Under‐reporting of foot‐and‐mouth disease (FMD) masks the true prevalence in parts of the world where the disease is endemic. Laboratory testing for the detection of FMD virus (FMDV) is usually reliant upon the collection of vesicular epithelium and fluid samples that can only be collected from acutely infected animals, and therefore animals with sub‐clinical infection may not be identified. Milk is a non‐invasive sample type routinely collected from dairy farms that has been utilized for surveillance of a number of other diseases. The aim of this study was to examine the application of milk as an alternative sample type for FMDV detection and typing, and to evaluate milk as a novel approach for targeted surveillance of FMD in East Africa. FMDV RNA was detected in 73/190 (38%) individual milk samples collected from naturally infected cattle in northern Tanzania. Furthermore, typing information by lineage‐specific rRT‐PCR assays was obtained for 58% of positive samples, and corresponded with the virus types identified during outbreak investigations in the study area. The VP1‐coding sequence data obtained from milk samples corresponded with the sequence data generated from paired epithelial samples collected from the same animal. This study demonstrates that milk represents a potentially valuable sample type for FMDV surveillance and might be used to overcome some of the existing biases of traditional surveillance methods. However, it is recommended that care is taken during sample collection and testing to minimize the likelihood of cross‐contamination. Such approaches could strengthen FMDV surveillance capabilities in East Africa, both at the individual animal and herd level.     

Characterization of SAT2 foot‐and‐mouth disease 2013/2014 outbreak viruses at the wildlife–livestock interface in South Africa

The Southern African Territories (SAT)‐type foot‐and‐mouth disease viruses (FMDV) are endemic to the greater Kruger National Park (KNP) area in South Africa, where they are maintained through persistent infections in African buffalo. The occurrence of FMDV within the Greater KNP area constitutes a continual threat to the livestock industry. To expand on knowledge of FMDV diversity, the genetic and antigenic relatedness of SAT2‐type viruses isolated from cattle during a FMD outbreak in Mpumalanga Province in 2013 and 2014 were investigated. Cattle from twelve diptanks tested positive on polymerase chain reaction (PCR), and molecular epidemiological relationships of the viruses were determined by VP1 sequencing. Phylogenetic analysis of the SAT2 viruses from the FMD outbreak in Mpumalanga in 2013/2014 revealed their genetic relatedness to other SAT2 isolates from topotype I (South Africa, Zimbabwe and Mozambique), albeit genetically distinct from previous South African outbreak viruses (2011 and 2012) from the same topotype. The fifteen SAT2 field isolates clustered into a novel genotype with ≥98.7% nucleotide identity. High neutralization antibody titres were observed for four 2013/2014 outbreak viruses tested against the SAT2 reference antisera representative of viruses isolated from cattle and buffalo from South Africa (topotype I) and Zimbabwe (topotype II). Comparison of the antigenic relationship (r₁ values) of the outbreak viruses with reference antisera indicated a good vaccine match with 90% of r₁ values > 0.3. The r₁ values for the 2013/2014 outbreak viruses were 0.4 and above for the three South African vaccine/reference strains. These results confirm the presence of genetic and antigenic variability in SAT2 viruses and suggest the emergence of new variants at the wildlife–livestock interface in South Africa. Continuous characterization of field viruses should be performed to identify new virus strains as epidemiological surveillance to improve vaccination efforts.     

Utilizing milk from pooling facilities as a novel approach for foot‐and‐mouth disease surveillance

This study investigated the potential of pooled milk as an alternative sample type for foot‐and‐mouth disease (FMD) surveillance. Real‐time RT‐PCR (rRT‐PCR) results of pooled milk samples collected weekly from five pooling facilities in Nakuru County, Kenya, were compared with half‐month reports of household‐level incidence of FMD. These periodic cross‐sectional surveys of smallholder farmers were powered to detect a threshold household‐level FMD incidence of 2.5% and collected information on trends in milk production and sales. FMD virus (FMDV) RNA was detected in 9/219 milk samples, and using a type‐specific rRT‐PCR, serotype SAT 1 was identified in 3/9 of these positive samples, concurrent with confirmed outbreaks in the study area. Four milk samples were FMDV RNA‐positive during the half‐months when at least one farmer reported FMD; that is, the household‐level clinical incidence was above a threshold of 2.5%. Additionally, some milk samples were FMDV RNA‐positive when there were no reports of FMD by farmers. These results indicate that the pooled milk surveillance system can detect FMD household‐level incidence at a 2.5% threshold when up to 26% of farmers contributed milk to pooling facilities, but perhaps even at lower levels of infection (i.e., below 2.5%), or when conventional disease reporting systems fail. Further studies are required to establish a more precise correlation with estimates of household‐level clinical incidence, to fully evaluate the reliability of this approach. However, this pilot study highlights the potential use of this non‐invasive, routinely collected, cost‐effective surveillance tool, to address some of the existing limitations of traditional surveillance methods.     

Managing complexity: Simplifying assumptions of foot‐and‐mouth disease models for swine

Compartmental models have often been used to test the effectiveness and efficiency of alternative control strategies to mitigate the spread of infectious animal diseases. A fundamental principle of epidemiological modelling is that models should start as simple as possible and become as complex as needed. The simplest version of a compartmental model assumes that the population is closed, void of births and deaths and that this closed population mixes homogeneously, meaning that each infected individual has an equal probability of coming into contact with each susceptible individual in the population. However, this assumption may oversimplify field conditions, leading to conclusions about disease mitigation strategies that are suboptimal. Here, we assessed the impact of the homogeneous mixing/closed population assumption, which is commonly assumed for within‐farm models of highly contagious diseases of swine, such as foot‐and‐mouth disease (FMD ), on predictions about disease spread. Incorporation of farm structure (different barns or rooms for breeding and gestation, farrowing, nursery and finishing) and demography (piglet births and deaths, and animal movement within and off of the farm) resulted in transmission dynamics that differed in the latter portion of an outbreak. Specifically, farm structure and demography, which were included in the farrow to finish and farrow to wean farms, resulted in FMD virus persistence within the population under certain conditions. Results here demonstrate the impact of incorporating farm structure and demography into models of FMD spread in swine populations and will ultimately contribute to the design and evaluation of effective disease control strategies to mitigate the impact of potential incursions.     

Safety profile of a replication‐deficient human adenovirus‐vectored foot‐and‐mouth disease virus serotype A24 subunit vaccine in cattle

The safety of a replication‐deficient, human adenovirus‐vectored foot‐and‐mouth disease virus (FMDV ) serotype A24 Cruzeiro capsid‐based subunit vaccine (AdtA24) was evaluated in five independent safety studies. The target animal safety studies were designed in compliance with United States (U.S.) regulatory requirements (Title 9, U.S. Code of Federal Regulation [9CFR ]) and international standard guidelines (VICH Topic GL ‐44) for veterinary live vaccines. The first three studies were conducted in a total of 22 vaccinees and demonstrated that the AdtA24 master seed virus (MSV ) was safe, did not revert to virulence and was not shed or spread from vaccinees to susceptible cattle or pigs. The fourth safety study conducted in 10 lactating cows using an AdtA24 vaccine serial showed that the vaccine was completely absent from milk. The fifth safety study was conducted under typical U.S. production field conditions in 500 healthy beef and dairy cattle using two AdtA24 vaccine serials. These results demonstrated that the vaccine was safe when used per the product label recommendations. Additional data collected during these five studies confirmed that AdtA24 vaccinees developed FMDV A24 and the HA d5 vaccine vector serum neutralization antibodies that test negative in a FMDV non‐structural protein antibody test, confirming AdtA24 vaccine's capability to differentiate infected from vaccinated animals (DIVA ). In conclusion, results from this comprehensive set of cattle studies demonstrated the safety of the replication‐deficient AdtA24 vaccine and fulfilled safety‐related requirements for U.S. regulatory requirements.     

Quantitative characteristics of the foot‐and‐mouth disease carrier state under natural conditions in India

The goal of this study was to characterize the properties and duration of the foot‐and‐mouth disease (FMD ) carrier state and associated serological responses subsequent to vaccination and naturally occurring infection at two farms in northern India. Despite previous vaccination of cattle in these herds, clinical signs of FMD occurred in October 2013 within a subset of animals at the farms containing juvenile‐yearling heifers and steers (Farm A) and adult dairy cattle (Farm B). Subsequent to the outbreak, FMD virus (FMDV ) asymptomatic carriers were identified in both herds by seroreactivity to FMDV non‐structural proteins and detection of FMDV genomic RNA in oropharyngeal fluid. Carriers’ seroreactivity and FMDV genome detection status were subsequently monitored monthly for 23 months. The mean extinction time of the carrier state was 13.1 ± 0.2 months, with extinction having occurred significantly faster amongst adult dairy cattle at Farm B compared to younger animals at Farm A. The rate of decrease in the proportion of carrier animals was calculated to be 0.07 per month. Seroprevalence against FMDV non‐structural proteins decreased over the course of the study period, but was found to increase transiently following repeated vaccinations. These data provide novel insights into viral and host factors associated with the FMDV carrier state under natural conditions. The findings reported herein may be relevant to field veterinarians and governmental regulatory entities engaged in FMD response and control measures.     

The impact of changing farm structure on foot‐and‐mouth disease spread and control: A simulation study

Foot‐and‐mouth disease (FMD) is a highly contagious viral disease that affects ruminants and pigs. Countries with large exports of livestock products are highly vulnerable to economic damage following an FMD incursion. The faster disease spread is controlled, the lower the economic damage. During the past decades, the structure of livestock production has dramatically changed. To maintain the relevance of contingency plans, it is important to understand the effects of changes in herd structure on the spread and control of infectious diseases. In this study, we compare the spread and control of FMD based on 2006/2007 and 2018 livestock data. Spread of FMD in Denmark was simulated using the DTU‐DADS model, applying different control measures. The number of cattle, swine and sheep/goat herds reduced from about 50,000 in total in 2006/2007 to about 33,000 in 2018. During this period, the average number of outgoing animal movements and the exports of swine and swine products increased by about 35% and 22%, respectively. This coincided with an overall increase in herd size of 14%. Using the EU and national control measures (Basic: 3 days standstill, depopulation of detected herds followed by cleaning and disinfection and establishment of control zones, where tracing, surveillance and contact restrictions are implemented), we found that the simulated epidemics in 2018 would be about 50% shorter in duration, affect about 50% fewer herds but cause more economic damage, compared to epidemics using 2006/2007 data. When 2006/2007 data were used, Basic + pre‐emptive depopulation (Depop) overall was the optimal control strategy. When 2018 data were used, this was the case only when epidemics were initiated in cattle herds, whereas when epidemics were initiated in sow or sheep/goats herds, basic performed as well as Depop. The results demonstrate that regular assessment of measures to control the spread of infectious diseases is necessary for contingency planning.     

Foot‐and‐mouth disease virus transmission dynamics and persistence in a herd of vaccinated dairy cattle in India

Foot‐and‐mouth disease (FMD ) is an important transboundary disease with substantial economic impacts. Although between‐herd transmission of the disease has been well studied, studies focusing on within‐herd transmission using farm‐level outbreak data are rare. The aim of this study was to estimate parameters associated with within‐herd transmission, host physiological factors and FMD virus (FMDV ) persistence using data collected from an outbreak that occurred at a large, organized dairy farm in India. Of 1,836 regularly vaccinated, adult dairy cattle, 222 had clinical signs of FMD over a 39‐day period. Assuming homogenous mixing, a frequency‐dependent compartmental model of disease transmission was built. The transmission coefficient and basic reproductive number were estimated to be between 16.2–18.4 and 67–88, respectively. Non‐pregnant animals were more likely to manifest clinical signs of FMD as compared to pregnant cattle. Based on oropharyngeal fluid (probang) sampling and FMDV ‐specific RT ‐PCR , four of 36 longitudinally sampled animals (14%) were persistently infected carriers 10.5 months post‐outbreak. There was no statistical difference between subclinical and clinically infected animals in the duration of the carrier state. However, prevalence of NSP ‐ELISA antibodies differed significantly between subclinical and clinically infected animals 12 months after the outbreak with 83% seroprevalence amongst clinically infected cattle compared to 69% of subclinical animals. This study further elucidates within‐herd FMD transmission dynamics during the acute‐phase and characterizes duration of FMDV persistence and seroprevalence of FMD under natural conditions in an endemic setting.     

Investigating the temporal and spatial distribution of foot‐and‐mouth disease virus serotype C in the Region of South America, 1968‐2016.

This study investigates the historical temporal trend and geographical distribution of the foot‐and‐mouth disease virus (FMDv) serotype C in South America; discussing the findings within the context of the actions and strategies carried out for the elimination of foot‐and‐mouth disease (FMD). This is the first time that such a comprehensive historical compilation has been carried out in the Region; hence, the study is intended as a reference and source of evidence about the presence/absence of FMDv serotype C in South America. Data on the occurrence of FMD were sourced from the Weekly Epidemiological Reports submitted by the countries to Pan American Foot‐and‐Mouth Disease Center (PANAFTOSA‐PAHO/WHO) since 1972, and complemented with other sources of information from the 1968–1971 period. The temporal distribution was examined with local weighted regression (LOESS) to identify two temporal trends, that is, “smoothed” and “over‐adjusted”, utilising the time‐series with the total number of cases per year, at Regional level. Thereafter the outbreaks were aggregated by decades and mapped by the first subnational administrative level. As a result, two major peaks of occurrence were identified, one in the 70s, with up to 1,193 outbreaks, and another in the 80s, with 380. Overall, the investigations show a clear regressive trend in the occurrence of serotype C, with a reduction in the number of outbreaks over‐time, and with the subsequent reduction of affected locations. This study illustrates the contrast between the very limited presence over the last 20 years – with only one event in 2004 – and the epidemic situation in the 1970s and 1980s, and suggests that serotype C of FMDv is no longer present in the Region.     

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

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