Application of the Nagoya Protocol to veterinary pathogens: concerns for the control of foot-and-mouth disease

The Nagoya Protocol is an international agreement adopted in 2010 (and entered into force in 2014) which governs access to genetic resources and the fair and equitable sharing of benefits from their utilisation. The agreement aims to prevent misappropriation of genetic resources and, through benefit sharing, create incentives for the conservation and sustainable use of biological diversity. While the equitable sharing of the benefits arising from the utilisation of genetic resources is a widely accepted concept, the way in which the provisions of the Nagoya Protocol are currently being implemented through national access and benefit-sharing legislation places significant logistical challenges on the control of transboundary livestock diseases such as foot-and-mouth disease (FMD). Delays to access FMD virus isolates from the field disrupt the production of new FMD vaccines and other tailored tools for research, surveillance and outbreak control. These concerns were raised within the FMD Reference Laboratory Network and were explored at a recent multistakeholder meeting hosted by the European Commission for the Control of FMD. The aim of this paper is to promote wider awareness of the Nagoya Protocol, and to highlight its impacts on the regular exchange and utilisation of biological materials collected from clinical cases which underpin FMD research activities, and work to develop new epidemiologically relevant vaccines and other diagnostic tools to control the disease.

Investigation into the protective ability of monovalent and bivalent A Malaysia 97 and A22 Iraq 64 vaccine strains against infection with an A/Asia/SEA-97 variant in pigs

Over the last 15 years, FMDV serotype A viruses in South-East Asia (A/ASIA/SEA-97 lineage) have diverged into several clusters. Variants from Thailand in 2011-2013 have caused vaccine failures and returned poor r₁-values (<0.30) to A₂₂ Iraq 64 (A22) and A Malaysia 97 (A May) vaccine strains. We investigated the protective ability of monovalent and bivalent A Malaysia 97 and A22 Iraq 64 vaccine strains against infection with an A/Asia/SEA-97 variant in pigs. Pigs were challenged with a variant of A/Asia/SEA-97 lineage either 21- or 7- days post-vaccination (V21 or V7) using the heal-bulb challenge. Only one in five pigs were protected in the V21 monovalent vaccine groups. Less severe clinical signs were observed in the A22 IRQ group compared to the A MAY 97 group. In the V21 combination group, 4 out of 5 pigs were protected and viraemia was significantly reduced compared to the monovalent V21 groups. V7 vaccine groups were not protected. The neutralising antibody response was below the detection limit in all groups on the challenge day, showing a poor correlation with protection. There was no evidence that the pigs protected from systemic disease had protective antibody responses sooner than other pigs in the study, implying other immune mechanisms might play a role in protecting these animals. FMDV was detected in the nasal and oral swab samples between 1 and 6 dpc. Viral loads were lower in the nasal swab samples from the V21 combination group than the other groups, but there was no difference in the oral swab samples. Since all unvaccinated controls were euthanised by 6-day post-challenge for ethical reasons, the ‘area under the curve (AUC)' method was used to compare the viraemia and virus excretion in different groups. We recommend that for the A/Asia/SEA97 variants, a combination vaccine with A Malaysia 97 and A22 Iraq 64 vaccine strains would be ideal compared to monovalent vaccines.

Chemical inactivation of foot-and-mouth disease virus in bovine tongue epithelium for safe transport and downstream processing

Epithelial tissue or vesicular fluid from an unruptured or recently ruptured vesicle is the sample of choice for confirmatory laboratory diagnosis of foot-and-mouth disease (FMD). However, in 'FMD-free' countries the transport and downstream processing of such samples from potentially infected animals present a biosafety risk, particularly during heightened surveillance, potentially involving decentralised testing in laboratories without adequate biocontainment facilities. In such circumstances, rapid inactivation of virus, if present, prior to transport becomes a necessity, while still maintaining the integrity of diagnostic analytes. Tongue epithelium collected from cattle infected with FMD virus (FMDV) of serotype O (O/ALG/3/2014 - Lineage O/ME-SA/Ind-2001d) or A (A/IRN/22/2015 - Lineage A/ASIA/G-VII) was incubated in the PAXGene Tissue System Fixative (pH 4) and Stabiliser (pH 6.5) components respectively, in McIlvaine's citrate-phosphate buffer (pH 2.6) or in phosphate-buffered saline (PBS, pH 7.4) at room temperature for 2, 6, 24 or 48h. Following incubation, tissues were homogenised and tested by virus isolation and titration using LFBK_αVβ6 cells. The integrity of FMD viral RNA was assessed by RT-qPCR (3D^pol coding region), Sanger sequencing of the VP1 region and transfection of LFBK_αVβ6 cells to recover infectious virus. Viable virus could be recovered from samples incubated in PBS for at least 48hours. The PAXgene Tissue System Stabiliser component yielded variable results dependent on virus serotype, requiring at least 6hours of incubation to inactivate A/IRN/22/2015 in most samples, whereas the Fixative component required up to 2hours in some samples. McIlvaine's citrate-phosphate buffer rapidly inactivated both viruses within 2hours of incubation. There was no demonstrable degradation of FMD viral RNA resulting from incubation in any of the buffers for up to 48hours, as assessed by RT-qPCR, and 24hours by sequencing and transfection to recover infectious virus. McIlvaine's citrate-phosphate buffer (pH 2.6) is easy to prepare, inexpensive and inactivates serotype A and O FMDV in epithelial tissue within 2hours, while maintaining RNA integrity for downstream diagnostic processes and virus characterisation.

A Vaccine Based on the A/ASIA/G-VII Lineage of Foot-and-Mouth Disease Virus Offers Low Levels of Protection against Circulating Viruses from the A/ASIA/Iran-05 lineage

The recent emergence and circulation of the A/ASIA/G-VII (A/G-VII) lineage of foot-and-mouth disease virus (FMDV) in the Middle East has resulted in the development of homologous vaccines to ensure susceptible animals are sufficiently protected against clinical disease. However, a second serotype A lineage called A/ASIA/Iran-05 (A/IRN/05) continues to circulate in the region and it is therefore imperative to ensure vaccine strains used will protect against both lineages. In addition, for FMDV vaccine banks that usually hold a limited number of strains, it is necessary to include strains with a broad antigenic coverage. To assess the cross protective ability of an A/G-VII emergency vaccine (formulated at 43 (95% CI 8-230) PD50/dose as determined during homologous challenge), we performed a heterologous potency test according to the European Pharmacopoeia design using a field isolate from the A/IRN/05 lineage as the challenge virus. The estimated heterologous potency in this study was 2.0 (95% CI 0.4-6.0) PD50/dose, which is below the minimum potency recommended by the World Organisation for Animal Health (OIE). Furthermore, the cross-reactive antibody titres against the heterologous challenge virus were poor (≤log10 0.9), even in those cattle that had received the full dose of vaccine. The geometric mean r1-value was 0.2 (95% CI 0.03-0.8), similar to the potency ratio of 0.04 (95% CI 0.004-0.3). Vaccination decreased viraemia and virus excretion compared to the unvaccinated controls. Our results indicate that this A/G-VII vaccine does not provide sufficient protection against viruses belonging to the A/IRN/05 lineage and therefore the A/G-VII vaccine strain cannot replace the A/IRN/05 vaccine strain but could be considered an additional strain for use in vaccines and antigen banks.

Comparing surveillance approaches to support regaining free status after a foot-and-mouth disease outbreak

Following an FMD eradication program, surveillance will be required to demonstrate that the program has been successful. The World Organization for Animal Health (OIE) provides guidelines including waiting periods and appropriate surveillance to support regaining FMD-free status. Serological surveillance is the recommended method for demonstrating freedom but is time consuming and expensive. New technologies such as real-time reverse transcription polymerase chain reaction (RT-qPCR) tests and sampling techniques such as bulk milk testing (BMT) of dairy cattle, oral swabs, and saliva collection with rope tethers in piggeries could enable surveillance to be done more efficiently. Epidemiological modelling was used to simulate FMD outbreaks, with and without emergency vaccination as part of the response, in Australia. Baseline post-outbreak surveillance approaches for unvaccinated and vaccinated animals based on the European FMD directive were compared with alternative approaches in which the sampling regime, sampling approaches and/or the diagnostic tests used were varied. The approaches were compared in terms of the resources required, time taken, cost, and effectiveness i.e., ability of the surveillance regime to correctly identify the infection status of herds. In the non-vaccination scenarios, the alternative approach took less time to complete and cost less, with the greatest benefits seen with larger outbreaks. In vaccinated populations, the alternative surveillance approaches significantly reduced the number of herds sampled, the total number of tests done and costs of the post-outbreak surveillance. There was no reduction in effectiveness using the alternative approaches, with one of the benefits being a reduction in the number of false positive herds. Alternative approaches to FMD surveillance based on non-invasive sampling methods and RT-qPCR tests have the potential to enable post outbreak surveillance substantiating FMD freedom to be done more quickly and less expensively than traditional approaches based on serological surveys.

Selection and use of reference panels: a case study highlighting current gaps in the materials available for foot and mouth disease

The World Organisation for Animal Health (OIE) Manual of Diagnostic Tests and Vaccines for Terrestrial Animals describes a diverse array of assays that can be used to detect, characterise and monitor the presence of infectious agents of farmed livestock. These methods have been developed in different laboratories, at different times, and often include tests or kits provided by the commercial sector. Reference panels are essential tools that can be used during assay development and in validation exercises to compare the performance of these varied (and sometimes competing) diagnostic technologies. World Organisation for Animal Health Reference Laboratories already provide approved international standard reagents to help calibrate diagnostic tests for a range of diseases, but there remain important gaps in their availability for comparative purposes and the calibration of test results across different laboratories. Using foot and mouth disease (FMD) as an example, this review highlights four specific areas where new reference reagents are required. These are to: reduce bias in estimates of the diagnostic sensitivity and inter-serotypic specificity of tests used to detect diverse strains of FMD virus (FMDV), provide bio-safe positive controls for new point-of-care test formats that can be deployed outside high containment, harmonise FMDV antigens for post-vaccination serology, and address inter-laboratory differences in serological assays used to measure virus-specific FMD antibody responses. Since there are often limited resources to prepare and distribute these materials, sustainable progress in this arena will only be achievable if there is consensus and coordination of these activities among OIE Reference Laboratories.

The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?

Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by an RNA virus subdivided into seven serotypes that are unevenly distributed in Asia, Africa, and South America. Despite the challenges of controlling FMD, since 1996 there have been only two outbreaks attributed to serotype C, in Brazil and in Kenya, in 2004. This article describes the historical distribution and origins of serotype C and its disappearance. The serotype was first described in Europe in the 1920s, where it mainly affected pigs and cattle but as a less common cause of outbreaks than serotypes O and A. No serotype C outbreaks have been reported in Europe since vaccination stopped in 1990. FMD virus is presumed to have been introduced into South America from Europe in the nineteenth century, although whether serotype C evolved there or in Europe is not known. As in Europe, this serotype was less widely distributed and caused fewer outbreaks than serotypes O and A. Since 1994, serotype C had not been reported from South America until four small outbreaks were detected in the Amazon region in 2004. Elsewhere, serotype C was introduced to Asia, in the 1950s to the 1970s, persisting and evolving for several decades in the Indian subcontinent and for eighteen years in the Philippines. Serotype C virus also circulated in East Africa between 1957 and 2004. Many serotype C viruses from European and Kenyan outbreaks were closely related to vaccine strains, including the most recently recovered Kenyan isolate from 2004. International surveillance has not confirmed any serotype C cases, worldwide, for over 15 years, despite more than 2,000 clinical submissions per year to reference laboratories. Serology provides limited evidence for absence of this serotype, as unequivocal interpretation is hampered by incomplete intra-serotype specificity of immunoassays and the continued use of this serotype in vaccines. It is recommended to continue strengthening surveillance in regions of FMD endemicity, to stop vaccination against serotype C and to reduce working with the virus in laboratories, since inadvertent escape of virus during such activities is now the biggest risk for its reappearance in the field.

Serological Evidence of Foot-and-Mouth Disease Infection in Goats in Lao PDR

Foot and Mouth Disease (FMD) causes significant economic loss in Lao PDR (Laos) and perpetuates the cycle of smallholder poverty mainly through large ruminant productivity losses, increased costs of production and potential limitations to market access for trade in livestock and their products. Goats are emerging as an important livestock species in Laos, and there is an increasing trend in the number of households with goats, often farmed alongside cattle and buffalo. Although an FMD susceptible species, very little is known about the role of goats in the epidemiology of the disease in Laos. A cross-sectional seroprevalence study was conducted by detecting antibodies to the non-structural proteins (NSP), an indication of a previous infection, and serotype-specific structural proteins (SP) that could be due to vaccination or infection. The study commenced in late 2017 and sera were collected from 591 goats in 26 villages of northern, central and southern Laos. For a subset of sera samples, paired oral swab samples were also collected by a simple random sampling method to detect the prevalence of FMD virus infection at the time of collection. The NSP seroprevalence in the provinces of Borkeo and Xayabouli in the north was 42 and 8%, respectively and in Khammoune in the center, it was 20%. In the other five provinces, Luang Namtha and Luang Prabang (northern Laos), Xieng Khouang and Savannaket (central Laos), and Champasak (southern Laos), the seroprevalence was close to zero. The multivariable analysis indicated that age (p < 0.001) was positively associated with animal-level seropositivity and males were less likely to be seropositive than females (OR: 0.29; 95%CI: 0.10–0.83; p = 0.017). Continued sero-surveillance for FMD in goats is recommended to improve our understanding of their role in the epidemiology of FMD in the region and to extend support to FMD control decisions, particularly regarding vaccination.

Virulence beneath the fleece; a tale of foot-and-mouth disease virus pathogenesis in sheep

Foot-and-mouth disease virus (FMDV) is capable of infecting all cloven-hoofed domestic livestock species, including cattle, pigs, goats, and sheep. However, in contrast to cattle and pigs, the pathogenesis of FMDV in small ruminants has been incompletely elucidated. The objective of the current investigation was to characterize tissue- and cellular tropism of early and late stages of FMDV infection in sheep following three different routes of simulated natural virus exposure. Extensive post-mortem harvest of tissue samples at pre-determined time points during early infection (24 and 48 hours post infection) demonstrated that tissues specifically susceptible to primary FMDV infection included the paraepiglottic- and palatine tonsils, as well as the nasopharyngeal mucosa. Additionally, experimental aerosol inoculation of sheep led to substantial virus replication in the lungs at 24-48 hours post-inoculation. During persistent infection (35 days post infection), the paraepiglottic- and palatine tonsils were the only tissues from which infectious FMDV was recovered. This is strikingly different from cattle, in which persistent FMDV infection has consistently been located to the nasopharyngeal mucosa. Analysis of tissue sections by immunomicroscopy revealed a strict epithelial tropism during both early and late phases of infection as FMDV was consistently localized to cytokeratin-expressing epithelial cells. This study expands upon previous knowledge of FMDV pathogenesis in sheep by providing detailed information on the temporo-anatomic distribution of FMDV in ovine tissues. Findings are discussed in relation to similar investigations previously performed in cattle and pigs, highlighting similarities and differences in FMDV pathogenesis across natural host species.

Inactivation of foot-and-mouth disease virus in epithelium samples for safe transport and processing in low-containment laboratories

During a foot-and-mouth disease (FMD) outbreak, transport and testing of potentially infectious samples, including epithelium from suspect lesions, presents a biosafety risk, particularly in FMD-free countries. Therefore, treatment to inactivate virus prior to transport is important. Tongue epithelium from cattle infected with FMD virus (FMDV) serotype O (O ALG/3/2014 - Lineage O/ME-SA/Ind-2001d) or A (A IRN/22/2015 - Lineage A/ASIA/G-VII) was incubated in RNAlater, RNA Shield or phosphate-buffered saline (pH 7.4) at room temperature for 2, 6, 24 or 48 h. After incubation, tissues were homogenised and tested by virus titration. Viral RNA in the homogenate was quantified by RT-qPCR, used for sequencing, and transfected into LFBK_αVβ6 cells to recover infectious virus. RNAlater reduced A IRN/22/2015 titres by 4 log₁₀ after 24 h, and completely after 48 h incubation. While O ALG/3/2014 was detected by VI after 2, 6 and 24 h, titration yielded no infectious virus, likely as a result of freeze-thawing. RNA Shield was cytotoxic at high concentrations but was effective at inactivating both strains after 24 h. Regardless of reagent or inactivation period, RT-qPCR, VP1 sequencing, and transfection of RNA to recover infectious virus were possible. RNA Shield appears a better choice for FMDV inactivation in tissues, however 24 h incubation is recommended.

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.

Assessment of a Rabies Virus Rapid Diagnostic Test for the Detection of Australian Bat Lyssavirus

Australian bat lyssavirus (ABLV) is closely related to the classical rabies virus and has been associated with three human fatalities and two equine fatalities in Australia. ABLV infection in humans causes encephalomyelitis, resulting in fatal disease, but has no effective therapy. The virus is maintained in enzootic circulation within fruit bats (Pteropid spp.) and at least one insectivorous bat variety (Saccolaimus flaviventris). Most frequently, laboratory testing is conducted on pteropodid bat brains, either following a potential human exposure through bites, scratches and other direct contacts with bats, or as opportunistic assessment of sick or dead bats. The level of medical intervention and post-exposure prophylaxis is largely determined on laboratory testing for antigen/virus as the demonstrable infection status of the in-contact bat. This study evaluates the comparative diagnostic performance of a lateral flow test, Anigen Rabies Ag detection rapid test (RDT), in pteropodid variant of ABLV-infected bat brain tissues. The RDT demonstrated 100% agreement with the reference standard fluorescent antibody test on 43 clinical samples suggesting a potential application in rapid diagnosis of pteropodid variant of ABLV infection. A weighted Kappa value of 0.95 confirmed a high level of agreement between both tests.

The protective capacity of high payload FMDV A22 IRQ vaccine in sheep against direct-contact challenge with a heterologous, contemporary FMDV A strain from South East Asia

Foot-and-mouth disease (FMD) is an acute, highly contagious viral disease of domestic and wild cloven-hoofed animals, caused by FMD virus (FMDV). An FMD outbreak can cause major production losses and have significant implications for trade. Vaccination can assist in controlling the disease, and emergency vaccination using high antigen payload vaccines (>6 PD₅₀/dose) is considered an important control approach in the event of an outbreak. In recent years there has been a divergence of serotype A viruses in South East Asia (SEA) into several distinct genetic and antigenic clusters. Numerous variants were found to poorly match serotype A vaccines commonly included in international antigen banks. This study examined the ability of single vaccination with high-potency monovalent A22 IRQ vaccine to protect sheep following challenge with the A/VIT/15/2012 strain, just four days following vaccination. The vaccine proved effective at limiting clinical disease but did not prevent infection.

Genetic characterization of African swine fever virus isolates from soft ticks at the wildlife/domestic interface in Mozambique and identification of a novel genotype

African swine fever virus (ASFV) is one of the most threatening infectious diseases of pigs. There are not sufficient data to indicate the importance of the sylvatic cycle in the spread and maintenance of the disease locally and potentially, globally. To assess the capacity to maintain ASF in the environment, we investigated the presence of soft tickreservoirs of ASFV in Gorongosa National Park (GNP) and its surrounding villages. A total of 1,658 soft ticks were recovered from warthog burrows and pig pens at the wildlife/livestock interface of the GNP and viral DNA was confirmed by nested PCR in 19% of Ornithodoros porcinus porcinus and 15% of O. p. domesticus. However, isolation of ASFV was only achieved in approximately 50% of the PCR-positive samples with nineteen haemadsorbing virus isolates recovered. These were genotyped using a combination of partial sequencing of the B646L gene (p72) and analysis of the central variable region (CVR) of the B602L gene. Eleven isolates were classified as belonging to genotype II and homologous to contemporary isolates from southern Africa, the Indian Ocean and eastern Europe. Three isolates grouped within genotype V and were similar to previous isolates from Mozambique and Malawi. The remaining five isolates constituted a new, previously unidentified genotype, designated genotype XXIV. This work confirms for the first time that the virus currently circulating in eastern Europe is likely to have a wildlife origin, and that the large diversity of ASFV maintained in wildlife areas can act as a permanent sources of different strains for the domestic pig value chain in Mozambique and beyond its boundaries. Their genetic similarity to ASFV strains currently spreading across Europe justifies the need to continue studying the sylvatic cycle in this African country and other parts of southern Africa in order to identify potential hot spots of ASF emergence and target surveillance and control efforts.

Efficacy of a high potency O1 Manisa monovalent vaccine against heterologous challenge with foot-and-mouth disease virus of O/SEA/Mya-98 lineage in sheep

Potency tests for commercial oil-adjuvanted foot-and-mouth disease (FMD) vaccines are usually carried out in cattle, using a full dose (2 ml) of vaccine and homologous virus challenge. However, in sheep the recommended vaccine dose is half of the cattle dose (1 ml) and most vaccines have not been potency tested for this species, especially with heterologous viruses. To determine the efficacy of a high potency (>6PD₅₀) FMD virus (FMDV) O1Manisa vaccine in sheep, we carried out a study using a heterologous FMDV (FMDV O/SKR/2010 - Mya-98 strain) challenge. Groups of seven animals each were vaccinated with 2×, 1×, 1/2× or 1/4× dose (2 ml, 1 ml, 0.5 ml or 0.25 ml respectively) and challenged at 7 days post vaccination (dpv). Only 3 of the 7 sheep in the group vaccinated with 2 ml were protected. With 2 additional groups, receiving double or single doses and challenged at 14 dpv, 4 of 7 sheep were protected in each group. None of the sheep had measurable neutralising antibodies against the vaccine or challenge virus at 7 dpv. However, all vaccinated animals challenged at 14 dpv had a homologous neutralising response against FMDV O1 Manisa on the day of challenge and all but one animal also had a heterologous response to FMDV O/SKR/2010. Infectious FMDV and viral RNA could be found in nasal swabs between 1 and 6 days post challenge (dpc) in most vaccinated sheep, but those vaccinated with higher doses or challenged at 14 dpv showed significant decreases in the level of FMDV detection. Intermittent virus shedding was noticed between 1 and 35 dpc in all vaccinated groups, but persistent infection could be demonstrated only in 4 sheep (20%). This study showed that at the recommended dose, a high potency (>6 PD₅₀) FMDV O1Manisa vaccine does not protect sheep against a heterologous challenge at 7 dpv. However, partial protection was observed when a double dose was used at 7 dpv or when double or single dose vaccinated sheep were challenged at 14 dpv.

Global Foot-and-Mouth Disease Research Update and Gap Analysis: 7 - Pathogenesis and Molecular Biology

We assessed research knowledge gaps in the fields of FMDV (foot-and-mouth disease virus) pathogenesis and molecular biology by performing a literature review (2011-15) and collecting research updates (2014) from 33 institutes from across the world. Findings were used to identify priority areas for future research. There have been important advances in FMDV pathogenesis; FMDV remains in lymph nodes of many recovered animals that otherwise do not appear persistently infected, even in species previously not associated with the carrier state. Whether virus retention helps maintain host immunity and/or virus survival is not known. Studies of FMDV pathogenesis in wildlife have provided insights into disease epidemiology, in endemic and epidemic settings. Many aspects of FMDV infection and virus entry remain unknown; however, at the cellular level, we know that expression level and availability of integrins (that permit viral entry), rate of clearance of infected cells and strength of anti-viral type I IFN (interferon) response are key determinants of tissue tropism. Extending findings to improved understanding of transmission requires a standardized approach and adoption of natural routes of infection during experimental study. There has been recognition of the importance of autophagosomes for FMDV entry into the cytoplasm following cell surface receptor binding, and that distinct internal cellular membranes are exploited for viral replication and immune evasion. New roles for viral proteins in blocking type I IFN production and downstream signalling have been identified facilitating research in anti-viral therapeutics. We know more about how infection affects cell protein expression, and research into molecular determinants of capsid stability has aided the development of stable vaccines. We have an expanding knowledge of viral and host molecular determinates of virulence and infectiousness, and of how phylogenetics may be used to estimate vaccine match and strain distribution. With ongoing advances, these areas could translate into significantly improved disease control.

Global Foot-and-Mouth Disease Research Update and Gap Analysis: 1 - Overview of Global Status and Research Needs

The Global Foot-and-mouth disease (FMD) Research Alliance periodically reviews the state of FMD research to assess progress and to identify new priorities. In this supplement we provide an update of global FMD research, comprising (i) this overview paper, which includes background information with key findings, and papers covering (ii) epidemiology, wildlife and economics, (iii) vaccines, (iv) diagnostics, (v) biotherapeutics and disinfectants, (vi) immunology and (vii) pathogenesis and molecular biology. FMD research publications were reviewed (2011-2015) and activity updates were obtained from 33 FMD research institutes from around the world. Although a continual threat, FMD has been effectively controlled in much of the world using existing tools. However, control remains a challenge in most developing countries, where little has been done to understand the ongoing burden of FMD. More research is needed to support control in endemically infected countries, particularly robust field studies. Traditional FMD vaccines have several limitations including short duration and spectrum of protection, cold chain requirements, and the costs and biosecurity risks associated with vaccine production. Significant progress has been made in the development of novel vaccine candidates, particularly in the use of recombinant vaccines and virus-like particles as an alternative to traditional inactivated whole virus vaccines. Continued investment is needed to turn these developments into improved vaccines produced at scale. Increased knowledge of cellular and mucosal immunity would benefit vaccine development, as would further advances in our ability to enhance vaccine capsid stability. Developments in molecular biology and phylogenetics underlie many of the recent advances in FMD research, including improved vaccines and diagnostics, and improved understanding of FMD epidemiology. Tools for genetic analyses continue to become both more powerful and more affordable enabling them to be used to address an ever-expanding range of questions. This rapidly advancing field potentiates many areas of FMD research and should be prioritized.

Global Foot-and-Mouth Disease Research Update and Gap Analysis: 3 - Vaccines

This study assessed research knowledge gaps in the field of FMDV (foot-and-mouth disease virus) vaccines. The study took the form of a literature review (2011-15) combined with research updates collected in 2014 from 33 institutes from across the world. Findings were used to identify priority areas for future FMD vaccine research. Vaccines play a vital role in FMD control, used both to limit the spread of the virus during epidemics in FMD-free countries and as the mainstay of disease management in endemic regions, particularly where sanitary controls are difficult to apply. Improvements in the performance or cost-effectiveness of FMD vaccines will allow more widespread and efficient disease control. FMD vaccines have changed little in recent decades, typically produced by inactivation of whole virus, the quantity and stability of the intact viral capsids in the final preparation being key for immunogenicity. However, these are exciting times and several promising novel FMD vaccine candidates have recently been developed. This includes the first FMD vaccine licensed for manufacture and use in the USA; this adenovirus-vectored FMD vaccine causes in vivo expression of viral capsids in vaccinated animals. Another promising vaccine candidate comprises stabilized empty FMDV capsids produced in vitro in a baculovirus expression system. Recombinant technologies are also being developed to improve otherwise conventionally produced inactivated vaccines, for example, by creating a chimeric vaccine virus to increase capsid stability and by inserting sequences into the vaccine virus for desired antigen expression. Other important areas of ongoing research include enhanced adjuvants, vaccine quality control procedures and predicting vaccine protection from immune correlates, thus reducing dependency on animal challenge studies. Globally, the degree of independent vaccine evaluation is highly variable, and this is essential for vaccine quality. Previously neglected, the importance of evaluating vaccination programme effectiveness and impact is increasingly being recognized.

Generation of mAbs to foot-and-mouth disease virus serotype A and application in a competitive ELISA for serodiagnosis

BACKGROUND

Foot-and-mouth disease (FMD) is an economically devastating disease that severely limits international trade of animals. Of the seven FMD virus (FMDV) serotypes, serotype A is one of the most widespread cross the world. Currently antibodies to FMDV are detected in animals using the virus neutralization test (VNT) and the enzyme-linked immunosorbent assay (ELISA). The VNT is laborious, time-consuming and reliant on live virus and cell cultures, while ELISA has the advantage of using inactivated antigens and often provides more reproducible results. The aim of this study was to develop a reliable and rapid competitive ELISA (cELISA) for the detection of antibodies to FMDV serotype A (FMDV/A).

RESULTS

A panel of FMDV/A specific monoclonal antibodies (mAbs) was generated and their ability to compete with a polyclonal serum from FMDV/A-infected cattle was examined. Two mAbs inhibited the binding of a polyclonal serum to FMDV/A viruses. The binding epitopes of each were determined as conformational and located on the VP2 viral capsid protein. The FMDV/A cELISA was developed using these two mAbs and FMDV/A inactivated virus as antigen. The diagnostic specificity and sensitivity were 99.7 and 99.3% (98.5-100%) respectively, based on a predetermined cut-off of 50% inhibition. When analysing sera from animals experimentally infected with FMDV/A, the cELISA detected antibodies from 5-days post infection (dpi) and remained positive for at least 21-28 days post infection. Comparison based on the Kappa coefficient showed strong agreement (90-94%) between cELISA and VNT.

CONCLUSION

The cELISA results are comparable to the VNT for antibody detection making it a simple and reliable test to detect antibodies against FMDV/A.

The B-cell response to foot-and-mouth-disease virus in cattle following vaccination and live-virus challenge

Antibodies play a pivotal role against viral infection, and maintenance of protection is dependent on plasma and memory B-cells. Understanding antigen-specific B-cell responses in cattle is essential to inform future vaccine design. We have previously defined T-cell-dependent and -independent B-cell responses in cattle, as a prelude to investigating foot-and-mouth-disease-virus (FMDV)-specific B-cell responses. In this study, we have used an FMDV O-serotype vaccination (O₁-Manisa or O SKR) and live-virus challenge (FMDV O SKR) to investigate the homologous and heterologous B-cell response in cattle following both vaccination and live-virus challenge. The FMDV O-serotype vaccines were able to induce a cross-reactive plasma-cell response, specific for both O₁-Manisa and O SKR, post-vaccination. Post-FMDV O SKR live-virus challenge, the heterologous O₁-Manisa vaccination provided cross-protection against O SKR challenge and cross-reactive O SKR-specific plasma cells were induced. However, vaccination and live-virus challenge were not able to induce a detectable FMDV O-serotype-specific memory B-cell response in any of the cattle. The aim of new FMDV vaccines should be to induce memory responses and increased duration of immunity in cattle.

The African swine fever control zone in South Africa and its current relevance

African swine fever (ASF) has been reported in South Africa since the early 20th century. The disease has been controlled and confined to northern South Africa over the past 80 years by means of a well-defined boundary line, with strict control measures and movement restrictions north of this line. In 2012, the first outbreak of ASF outside the ASF control zone since 1996 occurred. The objective of this study was to evaluate the current relevance of the ASF control line as a demarcation line between endemic ASF (north) areas and ASF-free (south) area and to determine whether there was a need to realign its trajectory, given the recent outbreaks of ASF, global climate changes and urban development since the line's inception. A study of ASF determinants was conducted in an area 20 km north and 20 km south of the ASF control line, in Limpopo, Mpumalanga, North West and Gauteng provinces between May 2008 and September 2012. The study confirmed that warthogs, warthog burrows and the soft tick reservoir, Ornithodoros moubata, are present south of the ASF control line, but no virus or viral DNA was detected in these ticks. There appears to be an increasing trend in the diurnal maximum temperature and a decrease in humidity along the line, but the impact of these changes is uncertain. No discernible changes in minimum temperatures and average rainfall along the disease control line were observed between 1992 and 2014. Even though the reservoirs were found south of the ASF boundary line, the study concluded that there was no need to realign the trajectory of the ASF disease control line, with the exception of Limpopo Province. However, the provincial surveillance programmes for the reservoir, vector and ASF virus south of this line needs to be maintained and intensified as changing farming practices may favour the spread of ASF virus beyond the control line.

Clinical and virological dynamics of a serotype O 2010 South East Asia lineage foot-and-mouth disease virus in sheep using natural and simulated natural inoculation and exposure systems

Within-host infection dynamics of a recent field isolate of foot-and-mouth disease virus (FMDV), serotype O, topotype South East Asia, lineage Myamar'98 were evaluated in sheep using four different systems for virus exposure. Two novel, simulated natural, inoculation systems consisting of intra-nasopharyngeal (INP) deposition and aerosol inoculation were evaluated in comparison with two conventional systems: coronary band inoculation and direct contact exposure. All four exposure systems were efficient in generating consistently severe, generalized FMD with synchronous clinical characteristics within exposure groups, indicating that this Myanmar98 strain is highly virulent in sheep. Clinical and virological dynamics were similarly rapid following INP- and coronary band inoculation, with both systems leading to significantly earlier detection of virus shedding when compared to aerosol inoculation and contact exposure. The data presented herein support application of the two optimized simulated natural inoculation systems as valid alternatives to conventionally used exposure systems for studies of FMDV pathogenesis and vaccinology in sheep. Furthermore, the data suggest that targeted exposure of the ovine pharynx is highly efficient for generating consistent FMDV infection, which supports critical involvement of this anatomic region as a site of primary virus replication in sheep.

Investigation into the Epidemiology of African Swine Fever Virus at the Wildlife - Domestic Interface of the Gorongosa National Park, Central Mozambique

An epidemiological study of African swine fever (ASF) was conducted between March 2006 and September 2007 in a rural area adjacent to the Gorongosa National park (GNP) located in the Central Mozambique. Domestic pigs and warthogs were sampled to determine the prevalence of antibodies against ASF virus and the salivary antigens of Ornithodoros spp. ticks, while ticks collected from pig pens were tested for the presence of ASFV. In addition, 310 framers were interviewed to gain a better understanding of the pig value chain and potential practices that could impact on the spread of the virus. The sero-prevalence to ASFV was 12.6% on farms and 9.1% in pigs, while it reached 75% in warthogs. Approximately 33% of pigs and 78% of warthogs showed antibodies against salivary antigens of ticks. The differences in sero-prevalence between farms close to the GNP, where there is greater chance for the sylvatic cycle to cause outbreaks, and farms located in the rest of the district, where pig to pig transmission is more likely to occur, were marginally significant. Ornithodoros spp. ticks were found in only 2 of 20 pig pens outside the GNP, and both pens had ticks testing positive for ASFV DNA. Interviews carried out among farmers indicated that biosecurity measures were mostly absent. Herd sizes were small with pigs kept in a free-ranging husbandry system (65%). Only 1.6% of farmers slaughtered on their premises, but 51% acknowledged allowing visitors into their farms to purchase pigs. ASF outbreaks seemed to have a severe economic impact with nearly 36% of farmers ceasing pig farming for at least 1 year after a suspected ASF outbreak. This study provides the first evidence of the existence of a sylvatic cycle in Mozambique and confirms the presence of a permanent source of virus for the domestic pig value chain.

Vaccine Potential of Two Previously Uncharacterized African Swine Fever Virus Isolates from Southern Africa and Heterologous Cross Protection of an Avirulent European Isolate

African swine fever (ASF) is a mostly fatal viral infection of domestic pigs for which there is no vaccine available. The disease is endemic to most of sub-Saharan Africa, causes severe losses and threatens food security in large parts of the continent. Naturally occurring attenuated ASF viruses have been tested as vaccine candidates, but protection was variable depending on the challenge virus. In this study, the virulence of two African isolates, one from a tick vector and the other from an indigenous pig, was determined in domestic pigs to identify a potential vaccine strain for southern Africa. Neither isolate was suitable as the tick isolate was moderately virulent and the indigenous pig virus was highly virulent. The latter was subsequently used as heterologous challenge in pigs first vaccinated with a naturally attenuated isolate previously isolated in Portugal. Although a statistically significant reduction in death rate and virus load was observed compared with unvaccinated pigs post-challenge, all pigs succumbed to infection and died.

Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa

Genetic information regarding the leader (L) and complete capsid-coding (P1) region of FMD serotype A and O viruses prevalent on the African continent is lacking. Here, we present the complete L-P1 sequences for eight serotype A and nine serotype O viruses recovered from FMDV outbreaks in East and West Africa over the last 33 years. Phylogenetic analysis of the P1 and capsid-coding regions revealed that the African isolates grouped according to serotype, and certain clusters were indicative of transboundary as well as intra-regional spread of the virus. However, similar analysis of the L region revealed random groupings of isolates from serotypes O and A. Comparisons between the phylogenetic trees derived from the structural coding regions and the L region pointed to a possibility of genetic recombination. The intertypic nucleotide and amino acid variation of all the isolates in this study supported results from previous studies where the externally located 1D was the most variable whilst the internally located 1A was the most conserved, which likely reflects the selective pressures on these proteins. Amino acids identified previously as important for FMDV structure and functioning were found to be highly conserved. The information gained from this study will contribute to the construction of structurally designed FMDV vaccines in Africa.

African swine fever virus eradication in Africa

African swine fever was reported in domestic pigs in 26 African countries during the period 2009-2011. The virus exists in an ancient sylvatic cycle between warthogs (Phacochoerus africanus) and argasid ticks of the Ornithodoros moubata complex in many of the countries reporting outbreaks and in two further countries in the region. Eradication of the virus from the countries in eastern and southern Africa where the classic sylvatic cycle occurs is clearly not an option. However, the virus has become endemic in domestic pigs in 20 countries and the great majority of outbreaks in recent decades, even in some countries where the sylvatic cycle occurs, have been associated with movement of infected pigs and pig meat. Pig production and marketing and ASF control in Africa have been examined in order to identify risk factors for the maintenance and spread of ASF. These include large pig populations, traditional free-range husbandry systems, lack of biosecurity in semi-intensive and intensive husbandry systems, lack of organisation in both pig production and pig marketing that results in lack of incentives for investment in pig farming, and ineffective management of ASF. Most of these factors are linked to poverty, yet pigs are recognised as a livestock species that can be used to improve livelihoods and contribute significantly to food security. The changes needed and how they might be implemented in order to reduce the risk of ASF to pig producers in Africa and to the rest of the world are explored.

Mapping of antigenic determinants on a SAT2 foot-and-mouth disease virus using chicken single-chain antibody fragments

Recombinant single-chain variable fragments (scFvs) of antibodies make it possible to localize antigenic and immunogenic determinants, identify protective epitopes and can be exploited for the design of improved diagnostic tests and vaccines. A neutralizing epitope, as well as other potential antigenic sites of a SAT2 foot-and-mouth disease virus (FMDV) were identified using phage-displayed scFvs. Three unique ZIM/7/83-specific scFvs, designated scFv1, scFv2 and scFv3, were isolated. Further characterization of these scFvs revealed that only scFv2 was capable of neutralizing the ZIM/7/83 virus and was used to generate neutralization-resistant virus variants. Sequence analysis of the P1 region of virus escaping neutralization revealed a residue change from His to Arg at position 159 of the VP1 protein. Residue 159 is not only surface exposed but is also located at the C-terminal base of the G-H loop, a known immunogenic region of FMDV. A synthetic peptide, of which the sequence corresponded to the predicted antigenic site of the VP1 G-H loop of ZIM/7/83, inhibited binding of scFv2 to ZIM/7/83 in a concentration-dependent manner. This region can therefore be considered in the design of SAT2 vaccine seed viruses for the regional control of FMD in Africa.

Classical swine fever (hog cholera): review of aspects relevant to control

Classical swine fever (CSF) has the ability to spread over large distances when human intervention such as illegal swill feeding facilitates its movement. This was apparent during 2005 when CSF appeared in South Africa (SA) after an absence of 87 years. In this review, various newly published developments in terms of the diagnosis of the disease and vaccination are described and applied to situations similar to SA. The role of wildlife such as feral pigs and European wild boar in the dissemination and maintenance of CSF virus are discussed, and the dearth of knowledge on the potential of other wild pig species prevalent on southern Africa noted. The modes of spread and control measures to prevent introduction as well as during outbreaks are discussed.

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics, but the prediction of viral cross-protection remains an important unsolved problem. For foot-and-mouth disease virus (FMDV) research in particular, improved methods for predicting this cross-protection are critical for predicting the severity of outbreaks within endemic settings where multiple serotypes and subtypes commonly co-circulate, as well as for deciding whether appropriate vaccine(s) exist and how much they could mitigate the effects of any outbreak. To identify antigenic relationships and their predictors, we used linear mixed effects models to account for variation in pairwise cross-neutralization titres using only viral sequences and structural data. We identified those substitutions in surface-exposed structural proteins that are correlates of loss of cross-reactivity. These allowed prediction of both the best vaccine match for any single virus and the breadth of coverage of new vaccine candidates from their capsid sequences as effectively as or better than serology. Sub-sequences chosen by the model-building process all contained sites that are known epitopes on other serotypes. Furthermore, for the SAT1 serotype, for which epitopes have never previously been identified, we provide strong evidence – by controlling for phylogenetic structure – for the presence of three epitopes across a panel of viruses and quantify the relative significance of some individual residues in determining cross-neutralization. Identifying and quantifying the importance of sites that predict viral strain cross-reactivity not just for single viruses but across entire serotypes can help in the design of vaccines with better targeting and broader coverage. These techniques can be generalized to any infectious agents where cross-reactivity assays have been carried out. As the parameterization uses pre-existing datasets, this approach quickly and cheaply increases both our understanding of antigenic relationships and our power to control disease.

New strains of viruses arise continually. Consequently, predicting when past exposure to closely related strains will protect against infection by novel strains is central to understanding the dynamics of a broad range of the world's most important infectious diseases. While previous research has developed valuable tools for describing the observed antigenic landscapes, our ability to predict cross-protection between different viral strains depends almost entirely on cumbersome and expensive live animal work, often restricted to model species rather than the natural host. The development of computer-based approaches to the estimation of cross-protection from viral sequence data would be hugely valuable, and our study represents a significant step towards this research goal.

A qualitative risk assessment of factors contributing to foot and mouth disease outbreaks in cattle along the western boundary of the Kruger National Park

Between November 2000 and the end of 2007, five outbreaks of foot and mouth disease (FMD) occurred in cattle in the area adjacentto the Kruger National Park (KNP) in the north-eastern corner of South Africa. To help understand the factors behind these outbreaks a qualitative risk assessment based on the World Organisation for Animal Health (OIE) assessment framework was adopted, using available data from published sources and various unpublished South African sources. Risk was assessed on the basis of the following factors: data on South African Territories (SAT) type infections of buffalo and impala in the KNP, permeability of the fence along the western boundary of the KNP, the potential for contact between livestock and wildlife susceptible to FMD in areas adjacent to the KNP, and the level of herd immunity in cattle generated by prophylactic vaccination. Scenario pathways for FMD occurrence outside the KNP are presented as a conceptual framework to qualitatively assess the risk of FMD outbreaks. Factors that are likely to have most influence on the risk were identified: fence permeability, vaccination coverage, or the efficiency of animal movement control measures. The method and results are provided as an approach that may be used as a basis to evaluate the risk of FMD outbreaks occurring in other wildlife/livestock interface areas of southern Africa.

Review of African swine fever: transmission, spread and control

African swine fever is one of the most important and serious diseases of domestic pigs. Its highly contagious nature and ability to spread over long distances make it one of the most feared diseases, since its devastating effects on pig production have been experienced not only in most of sub-Saharan Africa but also in western Europe, the Caribbean, Brazil and, most recently, the Caucasus. Unlike most diseases of livestock, there is no vaccine, and therefore prevention relies entirely upon preventing contact between the virus and the susceptible host. In order to do so it is necessary to understand the way in which the virus is transmitted and spreads. By implementing strict biosecurity measures that place barriers between the source of virus and the pigs it is possible to prevent infection. However, this has implications for free-ranging pig husbandry systems that are widespread in developing countries. Attempts to produce a vaccine are ongoing and new technology offers some hope for the future, but this will not remove the necessity for implementing adequate biosecurity on pig farms.

African swine fever: how can global spread be prevented?

African swine fever (ASF) is a devastating haemorrhagic fever of pigs with mortality rates approaching 100 per cent. It causes major economic losses, threatens food security and limits pig production in affected countries. ASF is caused by a large DNA virus, African swine fever virus (ASFV). There is no vaccine against ASFV and this limits the options for disease control. ASF has been confined mainly to sub-Saharan Africa, where it is maintained in a sylvatic cycle and/or among domestic pigs. Wildlife hosts include wild suids and arthropod vectors. The relatively small numbers of incursions to other continents have proven to be very difficult to eradicate. Thus, ASF remained endemic in the Iberian peninsula until the mid-1990s following its introductions in 1957 and 1960 and the disease has remained endemic in Sardinia since its introduction in 1982. ASF has continued to spread within Africa to previously uninfected countries, including recently the Indian Ocean islands of Madagascar and Mauritius. Given the continued occurrence of ASF in sub-Saharan Africa and increasing global movements of people and products, it is not surprising that further transcontinental transmission has occurred. The introduction of ASF to Georgia in the Caucasus in 2007 and dissemination to neighbouring countries emphasizes the global threat posed by ASF and further increases the risks to other countries. We review the mechanisms by which ASFV is maintained within wildlife and domestic pig populations and how it can be transmitted. We then consider the risks for global spread of ASFV and discuss possibilities of how disease can be prevented.

African swine fever virus isolate, Georgia, 2007

The virus isolate introduced to the Caucasus in 2007 is closely related to a group of viruses, genotype II, circulating in Mozambique, Madagascar, and Zambia.

African swine fever (ASF) is widespread in Africa but is rarely introduced to other continents. In June 2007, ASF was confirmed in the Caucasus region of Georgia, and it has since spread to neighboring countries. DNA fragments amplified from the genome of the isolates from domestic pigs in Georgia in 2007 were sequenced and compared with other ASF virus (ASFV) isolates to establish the genotype of the virus. Sequences were obtained from 4 genome regions, including part of the gene B646L that encodes the p72 capsid protein, the complete E183L and CP204L genes, which encode the p54 and p30 proteins and the variable region of the B602L gene. Analysis of these sequences indicated that the Georgia 2007 isolate is closely related to isolates belonging to genotype II, which is circulating in Mozambique, Madagascar, and Zambia. One possibility for the spread of disease to Georgia is that pigs were fed ASFV-contaminated pork brought in on ships and, subsequently, the disease was disseminated throughout the region.

Molecular characterization of SAT-2 foot-and-mouth disease virus isolates obtained from cattle during a four-month period in 2001 in Limpopo Province, South Africa

Foot-and-mouth disease (FMD) is an acute, highly contagious viral infection of domestic and wild cloven-hoofed animals. The virus is a single-stranded RNA virus that has a high rate of nucleotide mutation and amino acid substitution. In southern Africa the South African Territories (SAT) 1-3 serotypes of FMD virus are maintained by large numbers of African buffaloes (Syncerus caffer), which provide a potential source of infection for domestic livestock and wild animals. During February 2001, an outbreak of SAT-2 was recorded in cattle in the FMD control zone of South Africa, adjacent to the Kruger National Park (KNP). They had not been vaccinated against the disease since they form the buffer between the vaccination and free zones but in the face of the outbreak, they were vaccinated as part of the control measures to contain the disease. The virus was, however, isolated from some of them on several occasions up to May 2001. These isolates were characterized to determine the rate of genetic change in the main antigenic determinant, the 1D/2A gene. Nucleotide substitutions at 12 different sites were identified of which five led to amino acid changes. Three of these occurred in known antigenic sites, viz. the GH-loop and C-terminal part of the protein, and two of these have previously been shown to be subject to positive selection. Likelihood models indicated that the ratio of non-synonymous to synonymous changes among the outbreak sequences recovered from cattle was four times higher than among comparable sequences isolated from wildlife, suggesting that the virus may be under greater selective pressure during rapid transmission events.