Foot-and-mouth Disease Virus RNA Research Articles

Detection of foot-and-mouth disease viruses from the A/AFRICA/G-I genotype in the Sultanate of Oman

Rapid identification and characterization of circulating foot-and-mouth disease virus (FMDV) strains is crucial for effective disease control. In Oman, a few serological and molecular studies have been conducted to identify the strains of FMDV responsible for the outbreaks that have been occurring within the country. In this study, 13 oral epithelial tissue samples from cattle were collected from suspected cases of FMD in Ash Sharqiyah North, Al Batinah North, Dhofar and Ad Dhakhyilia governorates of Oman between 2018 and 2021. FMDV RNA was detected in all samples by real-time RT-PCR and viruses were isolated after one- or two-blind passages in the porcine Instituto Biologico-Rim Suino-2 cell line. Antigen capture ELISA characterized all isolates as serotype A and VP1 phylogenetic analysis placed all sequences within a single clade of the G-I genotype within the A/AFRICA topotype. These sequences shared the closest nucleotide identities to viruses circulating in Bahrain in 2021 (93.5% to 99.5%) and Kenya in 2017 (93.4% to 99.1%). To the best of our knowledge, this is the first time that A/AFRICA/G-I viruses have been detected in Oman. Together with the closely related viruses detected recently in Bahrain, these findings reinforce the importance of deploying effective quarantine control measures to minimize the risks of transboundary transmission of FMD associated with the importation of cattle from East Africa.

Comparação de sete differentes RT-qPCR para detecção do virus da febre aftosa

Abstract The prompt and accurate diagnosis of foot-and-mouth disease outbreaks is crucial to curb the swift transmission of its causative agent, the foot-and-mouth disease virus (FMDV), which poses a substantial threat to the nation’s livestock. This study aimed to perform a comparative analysis of various RT-qPCR methods for the detection of FMDV. The methods evaluated for the 3D region demonstrated similar sensitivity and specificity. Nevertheless, noticeable distinctions emerged in samples with low RNA concentration. While these methods can be interchangeably utilized with consistent outcomes when handling a large number of samples sent to the laboratory to pinpoint an outbreak, minor variations may assume significance when working with a limited quantity of samples containing low FMDV RNA copies.

TaqMan probe-based one-step multiplex real-time RT-PCR assay for the diagnosis of foot-and-mouth disease

Effective control and monitoring the spread of foot-and-mouth disease (FMD) relies upon rapid and accurate laboratory detection of FMD virus (FMDV). Therefore, in this report, a multiplex TaqMan probe-based one-step RT-qPCR assay simultaneously targeting FMDV 5′UTR and 3Dpol regions, and 18S rRNA housekeeping gene (as an internal control) in a single reaction tube was developed and evaluated. The multiplex one-step RT-qPCR assay specifically detected viral genome in both FMDV-infected cell culture suspensions and clinical samples collected from known-FMD infected animals. The assay could detect FMDV RNA in the archived FMDV cell culture isolates (n = 120) collected during the last two decades in India. In addition, the new assay could also detect viral RNA in the FMD suspected clinical samples (n = 740) collected from various field outbreaks. At a cut-off Ct-value of <38, the assay could detect at least 20 and 10 copies of FMDV 3Dpol and 5′UTR genes, respectively. Further, the multiplex RT-qPCR assay proved to be robust, showing an inter-assay co-efficient of variations ranging from 1.3% to 3.03% for FMDV-3Dpol gene target, and from 1.44% to 4.69% for 5′UTR gene target. In addition, it was found that the new assay could be used to detect viral genome in a variety of samples (epithelium, saliva, OPF, milk and blood) without any significance difference in the detection limit of the assay. Hence, the multiplex one-step RT-qPCR assay could be considered a valuable tool for the detection of FMDV in India.

Patterns of foot-and-mouth disease virus detection in environmental samples in an endemic setting.

Foot-and-Mouth Disease virus (FMDV) is endemic in several regions and is a virus that can persist in the environment dependent on pH, relative humidity (RH), temperature, and matrix (i.e., soil, water, or air). Our previously published analysis of available viral persistence data showed that persistence is likely affected by interactions between RH, temperature, and matrix. Understanding these relationships will aid efforts to eliminate FMD, which has significant impacts on economies and food security. In Cameroon, West Africa, the livestock system consists of mobile (transhumant), transboundary trade and sedentary herds. Studying this system can provide information about the patterns of environmental detection of FMDV RNA that may influence approaches to virus elimination on premises during an outbreak. To improve our understanding of these patterns, we collected samples from individuals, vehicles, and along cattle pathways at three sedentary herds beginning on day one of owner-reported outbreaks, ending by day 30, and tested for the presence of FMD viral RNA using rRT-PCR. Our analysis suggests that detection decreases in soil surface samples with increased distance from herd and time from the first report of disease. Whereas time but not distance decreases detection in air samples. Interaction of RH and temperature suggests increased detection at high temperatures (>24°C) and RH (>75%), providing us with new information about the patterns of FMD viral RNA detection in and around cattle herds that could help to inform targeted virus elimination strategies, such as location and application of disinfectants.

The Host Protein CAD Regulates the Replication of FMDV through the Function of Pyrimidines' De Novo Synthesis.

Foot-and-mouth disease virus (FMDV) is a single-stranded picornavirus that causes economically devastating disease in even-hooved animals. There has been little research on the function of host cells during FMDV infection. We aimed to shed light on key host factors associated with FMDV replication during acute infection. We found that HDAC1 overexpression in host cells induced upregulation of FMDV RNA and protein levels. Activation of the AKT-mammalian target of rapamycin (mTOR) signaling pathway using bpV(HOpic) or SC79 also promoted FMDV replication. Furthermore, short hairpin RNA (shRNA)-induced suppression of carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), a transcription factor downstream of the AKT-mTOR signaling pathway, resulted in downregulation of FMDV RNA and protein levels. Coimmunoprecipitation assays showed that the ACTase domain of CAD could interact with the FMDV 2C protein, suggesting that the ACTase domain of CAD may be critical in FMDV replication. CAD proteins participate in de novo pyrimidine synthesis. Inhibition of FMDV replication by deletion of the ACTase domain of CAD in host cells could be reversed by supplementation with uracil. These results revealed that the contribution of the CAD ACTase domain to FMDV replication is dependent on de novo pyrimidine synthesis. Our research shows that HDAC1 promotes FMDV replication by regulating de novo pyrimidine synthesis from CAD via the AKT-mTOR signaling pathway. IMPORTANCE Foot-and-mouth disease virus is an animal virus of the Picornaviridae family that seriously harms the development of animal husbandry and foreign trade of related products, and there is still a lack of effective means to control its harm. Replication complexes would generate during FMDV replication to ensure efficient replication cycles. 2C is a common viral protein in the replication complex of Picornaviridae virus, which is thought to be an essential component of membrane rearrangement and viral replication complex formation. The host protein CAD is a key protein in the pyrimidines de novo synthesis. In our research, the interaction of CAD and FMDV 2C was demonstrated in FMDV-infected BHK-21 cells, and it colocalized with 2C in the replication complex. The inhibition of the expression of FMDV 3D protein through interference with CAD and supplementation with exogenous pyrimidines reversed this inhibition, suggesting that FMDV might recruit CAD through the 2C protein to ensure pyrimidine supply during replication. In addition, we also found that FMDV infection decreased the expression of the host protein HDAC1 and ultimately inhibited CAD activity through the AKT-mTOR signaling pathway. These results revealed a unique means of counteracting the virus in BHK-21 cells lacking the interferon (IFN) signaling pathway. In conclusion, our study provides some potential targets for the development of drugs against FMDV.

Molecular detection, genetic diversity, and phylogenetic analysis of foot-and-mouth disease virus (FMDV) type O in Iran during 2015-2016.

The major challenge of foot-and-mouth disease (FMD) control is attributed to the rapid mutations in the FMDV RNA genome, resulting in continuous antigenic changes of circulating strains. Despite widespread vaccination of livestock populations, the incidence of the FMDV serotype O outbreaks in Iran during 2015-2016 raised concerns about the emergence of new strains. The aim of this study is the genetic and antigenic evaluation of FMDV type O isolates from different outbreak areas including Alborz, Tehran, Isfahan, Markazi, Zahedan, and Qom provinces. For this purpose, 71 FMD-infected samples were collected from six provinces of Iran, of which 12 serotype O positive were selected for genetic analysis. All samples were in ME-SA topotypes/OPanAsia2 lineage, and the overall mean of genetic diversities at the 1D gene level was about 5% between the sequences. Blasting 1D gene sequences of isolated viruses showed more than 90% genetic identity with sequences registered from neighboring countries; therefore, it could be concluded that they had a common origin. Six isolates showed the highest genetic diversity (6% to 11%) with the OPanAsia2 vaccine strain (JN676146), which three of them (Qom, Alborz, and Zahedan isolates), had less than 30% antigenic homology with the OPanAsia2 virus (JN676146). Results of this study suggested OPanAsia2 vaccine had no enough coverage with some circulating strains in outbreak areas in Qom, Alborz, and Zahedan provinces, and the necessity of OPanAsia2 replacement with a new vaccine strain in Iran.

Heat Shock Protein 60 Is Involved in Viral Replication Complex Formation and Facilitates Foot and Mouth Virus Replication by Stabilizing Viral Nonstructural Proteins 3A and 2C.

ABSTRACTThe maintenance of viral protein homeostasis depends on the machinery of the infected host cells, giving us an insight into the interplay between host and virus. Accumulating evidence suggests that heat shock protein 60 (HSP60), as one molecular chaperone, is involved in regulating virus infection. However, the role of HSP60 during foot-and-mouth disease virus (FMDV) replication and its specific mechanisms have not been reported. We demonstrate that HSP60 modulates the FMDV life cycle. HSP60 plays a role at the postentry stage of the viral life cycle, including RNA replication and mRNA translation; however, HSP60 does not affect viral replication of Seneca Valley virus (SVA) or encephalomyocarditis virus (EMCV). We found that HSP60 is involved in FMDV replication complex (RC) formation. Furthermore, our results indicate that HSP60 interacts with FMDV nonstructural proteins 3A and 2C, key elements of the viral replication complex. We also show that HSP60 regulates the stability of 3A and 2C via caspase-dependent and autophagy-lysosome-dependent degradation, thereby promoting FMDV RNA synthesis and mRNA translation mediated by the RC. Additionally, we determined that the apical domain of HSP60 is responsible for interacting with 3A and 2C. The N terminus of 3A and ATPase domain of 2C are involved in binding to HSP60. Importantly, HSP60 depletion potently reduced FMDV pathogenicity in infected mice. Altogether, this study demonstrates a specific role of HSP60 in promoting FMDV replication. Furthermore, targeting host HSP60 will help us design the FMDV-specific antiviral drugs.

Full-Length Genomic RNA of Foot-and-Mouth Disease Virus Is Infectious for Cattle by Injection.

Safe sample transport is of great importance for infectious diseases diagnostics. Various treatments and buffers are used to inactivate pathogens in diagnostic samples. At the same time, adequate sample preservation, particularly of nucleic acids, is essential to allow an accurate laboratory diagnosis. For viruses with single-stranded RNA genomes of positive polarity, such as foot-and-mouth disease virus (FMDV), however, naked full-length viral RNA can itself be infectious. In order to assess the risk of infection from inactivated FMDV samples, two animal experiments were performed. In the first trial, six cattle were injected with FMDV RNA (isolate A22/IRQ/24/64) into the tongue epithelium. All animals developed clinical disease within two days and FMDV was reisolated from serum and saliva samples. In the second trial, another group of six cattle was exposed to FMDV RNA by instilling it on the tongue and spraying it into the nose. The animals were observed for 10 days after exposure. All animals remained clinically unremarkable and virus isolation as well as FMDV genome detection in serum and saliva were negative. No transfection reagent was used for any of the animal inoculations. In conclusion, cattle can be infected by injection with naked FMDV RNA, but not by non-invasive exposure to the RNA. Inactivated FMDV samples that contain full-length viral RNA carry only a negligible risk of infecting animals.

Effect of the Faradarmani Consciousness Field on immune response induced by an inactivated vaccine against Foot and Mouth disease virus (FMDV) in rats and replication of FMDV in vitro

Foot-and-mouth disease (FMD) is one of the highest risk factors affecting the animal industry throughout the world. Currently, available commercial FMD vaccines have numerous limitations, such as slow induction and short-term maintenance of antibody titers. Therefore, a novel approach is needed that can induce high neutralizing antibody titers to protect the host in the early stages of FMD virus (FMDV) infection and maintain high antibody titers for long periods after one vaccination dose. There are several T-Consciousness Fields (TCFs), introduced by Mohammad Ali Taheri. TCFs are not matter or energy, so they cannot be measured directly. However, we can evaluate their effects indirectly through several reproducible experiments in the laboratory. The present study aimed to evaluate the effect of Faradarmani CF as a type of the TCFs on FMDV replication, titer, and RNA copy number as well as the humoral immune response against two types of inactivated FMDV vaccines with different adjuvants in rats. Two types of FMD vaccines with different adjuvants (Freund and Alum) were prepared, and then 30 male Wistar rats were immunized with vaccines. Rats were divided into 6 groups (n=5 per group). Four groups of rats were studied using the different combinations of treatments and two groups served as positive and negative controls. Vaccination intervals were every 14 days three times. Serum neutralization test (SN) and Enzyme-linked immunosorbent assay (ELISA) were used to assess changes in antibody levels in the serum samples of rats after each immunization. The results showed that Faradarmani CF induced the replication of the virus in vitro. In addition, antibody levels in treated groups under both Freund adjuvant and Alum adjuvant vaccines increased significantly compared to groups without Faradarmani CF treatment. In conclusion, our data suggest that Faradarmani CF may provide an effective approach to increase the success of immunization and vaccination against FMDV serotype O. It is recommended that the effects of TCFs on different types of vaccines be investigated.

Molecular and Serological Epidemiology of Foot-and-Mouth Disease Virus in North Region of Cameroon

The serological prevalence of foot and mouth disease virus (FMDV) among the cattle population in the North region of Cameroon was determined using ELISA (Enzyme Linked Immunosorbent Assays) serological tests for structural as well as non-structural proteins. In these cattle, FMDV RNA was identified, amplified, sequenced and the sequences were used to construct a phylogenetic tree. A sedentary cattle population randomly selected from six veterinary centres in the North region was sampled twice, six months apart. High prevalence of FMDV antibody was recorded in the first (402/466 (85.84%)) and second (358/411 (86.90%)) sampling periods. There was no significant difference (P > 0.05) in prevalence of FMDV antibody between the two sampling periods. Goudali and Peulh breeds of cattle and animals of three to five years old were the most infected with FMDV and mostly in the months of May and August. A seroprevalence of 100% (n = 14) of FMDV against serotypes A and O was observed in sera from convalescent animals in the study area. FMDV antigen detection ELISA showed a prevalence of 18/37 (48.65%) for serotypes SAT1 (8.1%), SAT2 (35.1%), A (10.8%) and O (2.7%) among the clinically infected animals. There was no significant difference (P > 0.05) in prevalence of FMDV RNA between the sampling periods. A prevalence of FMDV RNA (17.5% (n = 120) and 16.7% (n = 240)) was observed among the sedentary animals that were sampled four to five months apart. FMDV RNA prevalence of 28/37 (75.6%) among clinically infected animals was also observed, thus confirming all the 12 outbreaks investigated. Sequence analysis of VP1 coding gene of the SAT2 serotype showed that it was homologous to the Libyan isolates (that caused epidemics in northern Africa in 2012) and also clustered with the serotypes isolated from both Nigeria and Sudan in 2007.

Fibroblast growth factor 11 inhibits foot-and-mouth disease virus gene expression and replication in vitro.

Foot-and-mouth disease virus (FMDV) causes highly contagious disease of cloven-hoofed animals such as cattle, swine, and sheep. Although FMD vaccine is the traditional way to protect against the disease, the use of FMD vaccines to protect early infection is limited. The alternative strategy of applying antiviral agents is required to control the spread of FMDV in outbreak situations. Fibroblast growth factor 11 (FGF11) is a member of the intracellular FGF. Here, we identified the inhibitory effect of FGF11 on FMDV gene expression through the transcriptional and translational regulation. For the quantitative analysis of FMDV transcription/translation level, we firstly constructed a plasmid reporter system (FMDV five prime untranslated region (5′ UTR) -luci) conjugating luciferase encoding gene with FMDV 5′ UTR region, which is a non-coding region to control FMDV transcription/translation and includes cis-acting replication element (CRE) and internal ribosome entry site (IRES). FGF11 decreased the gene expression of FMDV 5′ UTR-luci reporter in a dose-dependent manner. We further confirmed the inhibitory function of FGF11 on FMDV gene expression a replication in the FMDV-infected pig cells. FGF11 expression inhibited RNA production of FMDV RNA polymerase 3D gene in the FMDV-infected cells. In addition, while FMDV cell infection induced cytopathic effect (CPE) within 24 hr, FGF11 expression dramatically repressed CPE at the basal level. These results indicate that FGF11 inhibits FMDV gene expression and replication in vitro, implicating to provide intervention strategy for FMDV pathogenesis and transmission.

Environmental sampling for the detection of foot-and-mouth disease virus and peste des petits ruminants virus in a live goat market, Nepal.

Livestock markets are considered vital parts of the agricultural economy, particularly in developing countries where livestock keeping contributes to both food security and economic stability. Animals from diverse sources are moved to markets, they mix while they are there and are subsequently redistributed over wide geographic areas. Consequently, markets provide an opportunity for targeted surveillance for circulating pathogens. This study investigated the use of environmental sampling at a live goat market in Nepal for the detection of foot-and-mouth disease virus (FMDV) and peste des petits ruminants virus (PPRV), both of which are endemic. Five visits to the market were carried out between November 2016 and April 2018, with FMDV RNA detected on four visits and PPRV RNA detected on all five visits. Overall, 4.1% of samples (nine out of 217) were positive for FMDV RNA and 60.8% (132 out of 217) were positive for PPRV RNA, though the proportion of positive samples varied amongst visits. These results demonstrate that non-invasive, environmental sampling methods have the potential to be used to detect circulation of high priority livestock diseases at a live animal market and, hence, to contribute to their surveillance and control.

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

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

After nasopharyngeal infection, foot-and-mouth disease virus serotype A RNA is shed in bovine milk without associated mastitis.

Foot-and-mouth disease (FMD) is a highly contagious aphthoviral infection of cloven-hoofed animals, inducing vesiculopustular stomatitis, pododermatitis, and thelitis. Vesicular fluid represents a major pathway of virus excretion, but bovine milk is another important source of virus shedding. We describe here the time course of FMD virus (FMDV) excretion in the milk and characterize associated lesions in the mammary gland. Three dairy cows were infected by nasopharyngeal instillation of FMDV and monitored over 12 d. Autopsy was performed at the end of the study, and specimens were collected for histopathology, IHC, and RT-qPCR. All 3 cows developed fever, drooling, vesiculopustular stomatitis, interdigital dermatitis, and thelitis. FMDV RNA was detectable in whole milk until the end of the trial, but only transiently in saliva, nasal secretions, and blood serum. Although histology confirmed vesiculopustular lesions in the oral and epidermal specimens, the mammary glands did not have unequivocal evidence of FMDV-induced inflammation. FMDV antigen was detectable in skin and oral mucosa, but not in the mammary gland, and FMDV RNA was detectable in 9 of 29 samples of squamous epithelia but only in 1 of 12 samples of mammary gland.

Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing.

The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains. At present, sequencing of FMD virus (FMDV) relies upon the time-consuming transport of samples to well-resourced laboratories. The Oxford Nanopore Technologies' MinION portable sequencer has the potential to allow sequencing in remote, decentralised laboratories closer to the outbreak location. In this study, we investigated the utility of the MinION to generate sequence data of sufficient quantity and quality for the characterisation of FMDV serotypes O, A, Asia 1. Prior to sequencing, a universal two-step RT-PCR was used to amplify parts of the 5′UTR, as well as the leader, capsid and parts of the 2A encoding regions of FMDV RNA extracted from three sample matrices: cell culture supernatant, tongue epithelial suspension and oral swabs. The resulting consensus sequences were compared with reference sequences generated on the Illumina MiSeq platform. Consensus sequences with an accuracy of 100% were achieved within 10 and 30 min from the start of the sequencing run when using RNA extracted from cell culture supernatants and tongue epithelial suspensions, respectively. In contrast, sequencing from swabs required up to 2.5 h. Together these results demonstrated that the MinION sequencer can be used to accurately and rapidly characterise serotypes A, O, and Asia 1 of FMDV using amplicons amplified from a variety of different sample matrices.

Environmental and air sampling are efficient methods for the detection and quantification of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) can be found in all secretions and excretions and the breath of acutely infected animals. FMDV can survive in the environment, providing an opportunity for surveillance. The objective of this study was to assess the efficiency of sampling methods for the recovery and quantification of FMDV from a range of environmental surfaces and in aerosols. Selected surfaces, based on those likely to be found on farms, were spiked with a range of concentrations of FMDV, left to dry and then the surface was swabbed with an electrostatic dust cloth. For aerosol sampling, FMDV was nebulised at different concentrations and distances from the sampler. Recovery of viral RNA and infectious virus was measured by RT-qPCR and virus isolation respectively. FMDV RNA was detected from all surfaces at all concentrations except from glass. Infectious virus was recovered from all surfaces but only at higher concentrations. The higher the starting concentration of virus the more efficient the recovery was from surfaces and recovery was more consistent from non-porous surfaces than porous surfaces. FMDV was detected in aerosol samples and the amount of virus recovered decreased as the distance between the nebuliser and sampler increased. The higher the starting concentration of virus the more efficient the recovery was from sampled aerosols. The information provided in this study could be used to direct environmental and aerosol sampling approaches in the field and improve the detection efficiency of FMDV from an environment, thus extending the toolbox available for diagnosis and surveillance of this pathogen.

Foot-and-Mouth Disease Surveillance Using Pooled Milk on a Large-Scale Dairy Farm in an Endemic Setting.

Pooled milk is used for the surveillance of several diseases of livestock. Previous studies demonstrated the detection of foot-and-mouth disease virus (FMDV) in the milk of infected animals at high dilutions, and consequently, the collection of pooled milk samples could be used to enhance FMD surveillance. This study evaluated pooled milk for FMDV surveillance on a large-scale dairy farm that experienced two FMD outbreaks caused by the A/ASIA/G-VII and O/ME-SA/Ind-2001d lineages, despite regular vaccination and strict biosecurity practices. FMDV RNA was detected in 42 (5.7%) of the 732 pooled milk samples, and typing information was concordant with diagnostic reports of clinical disease. The FMDV positive milk samples were temporally clustered around reports of new clinical cases, but with a wider distribution. For further investigation, a model was established to predict real-time RT-PCR (rRT-PCR) CT values using individual cattle movement data, clinical disease records and virus excretion data from previous experimental studies. The model explained some of the instances where there were positive results by rRT-PCR, but no new clinical cases and suggested that subclinical infection occurred during the study period. Further studies are required to investigate the effect of vaccination on FMDV excretion in milk, and to evaluate more representative sampling methods. However, the results from this pilot study indicate that testing pooled milk by rRT-PCR may be valuable for FMD surveillance and has provided evidence of subclinical virus infection in vaccinated herds that could be important in the epidemiology of FMD in endemic countries where vaccination is used.

Foot and mouth disease virus undergoes non-progressive replication in mice peritoneal macrophages and induces M1 polarization

Despite the fact that macrophages link the innate and adaptive arms of immunity, it’s role in the early infection of foot and mouth disease virus (FMDV) is largely unknown. Recently, depletion of macrophages in vivo after vaccination has shown to drastically diminish the protection against FMDV challenge in mouse model. Even the ability of macrophages to reduce or resist FMDV infection is not known hitherto. Therefore, we examined the replication ability of FMDV in mice peritoneal macrophages and the responsiveness in terms of macrophage polarization and cytokine production. Negative strand specific RT-PCR indicated replication of FMDV RNA in macrophages. Absolute quantitation of FMDV transcripts, immunofluorescence studies and titre of the infectious progeny virus revealed that replication peaked at 12 hpi and significantly declined by 18 hpi indicating non-progressive replication in the infected macrophages. Further, significant up regulation of inducible nitric oxide synthase by 8 –12 hpi and increase of M1 specific CD11c + cells by 42.6 % after infection showed that FMDV induce M1 polarization. A significant up regulation of TNFα and IL12 transcripts at 8 hpi supported that M1 macrophages were functional. Further, we studied the expression of Type I to III interferons (IFN) and other antiviral molecules. The results indicate a marked up regulation of Type I IFNα and β by 9.2 and 11.2 fold, respectively at 8 hpi. Of the four IFN stimulated genes (ISG), viperin showed a significant up regulation by 286-fold at 12 hpi in the mice macrophages. In conclusion, the results suggest that replication of FMDV in mice peritoneal macrophages is non-progressive with up regulation of Type I IFN and ISGs. Further, FMDV induces M1 polarization in murine peritoneal macrophages.

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 αVβ6 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.

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.