Evaluation of laboratory tests for SAT serotypes of foot-and-mouth disease virus with specimens collected from convalescent cattle in Zimbabwe.

During a field study in Zimbabwe, clinical specimens were collected from 403 cattle in six herds, in which the history of foot-and-mouth disease (FMD) vaccination and infection appeared to be known with some certainty. Five herds had reported outbreaks of disease one to five months previously but clinical FMD had not been observed in the sixth herd. A trivalent vaccine (South African Territories [SAT] types 1, 2 and 3) had been used in some of the herds at various times either before and/or after the recent outbreaks of FMD. The primary aim of this study was to evaluate the performance of serological tests for the detection of SAT-type FMD virus infection, particularly elisas for antibodies to non-structural proteins (NSPs) of FMD virus and solid phase competition ELISAS (SPCEs) for serotypes SAT1 and SAT2. Secondary aims were to examine NSP seroconversion rates in cattle that had been exposed to infection and to compare virus detection rates by virus isolation and real-time reverse transcriptase-PCR (rtRT-PCR) tests on both oesophagopharyngeal fluids and nasopharyngeal brush swabbings. In addition, the hooves of sampled animals were examined for growth arrest lines as clinical evidence of FMD convalescence. Laboratory tests provided evidence of FMD virus infection in all six herds; SAT2 viruses were isolated from oesophagopharyngeal fluids collected from two herds in northern Zimbabwe, and SAT1 viruses were isolated from three herds in southern Zimbabwe. Optimised rtRT-PCR was more sensitive than virus isolation at detecting FMD virus persistence and when the results of the two methods were combined for oesophagopharyngeal fluids, between 12 and 35 per cent of the cattle sampled in the convalescent herds were deemed to be carriers. In contrast, nasopharyngeal swabs yielded only two virus-positive specimens. The overall seroprevalence in the five affected herds varied with the different NSPS from 56 per cent to 75 per cent, compared with 81 per cent and 91 per cent by homologous SPCE and virus neutralisation tests respectively. However, if serological test results were considered only for the cattle in which persistent infection with FMD virus had been demonstrated, 70 to 90 per cent scored seropositive in the different NSPs.

Foot-and-mouth disease virus: a first inter-laboratory comparison trial to evaluate virus isolation and RT-PCR detection methods.

Five European reference laboratories participated in an exercise to evaluate the sensitivity and specificity of their routinely employed RT-PCR tests and cell cultures for the detection and isolation of foot-and-mouth disease (FMD) virus. Five identical sets of 20 coded samples were prepared from 10 vesicular epithelia, which were derived from submissions from suspect cases of FMD or swine vesicular disease (SVD). Sixteen samples were derived from six FMD virus positive epithelia representing four different serotypes (two each of types O and A and one each of types Asia 1 and SAT 2), two from samples which had been found to be negative by antigen ELISA and virus isolation (VI) in cell culture and two from SVD virus positive epithelia. Some of the FMD virus positive samples were prepared from 10-fold serial dilutions of three of the initial suspensions. Each laboratory tested the samples by one or more of its available RT-PCR procedures and inoculated cell cultures that it routinely uses for FMD diagnosis in attempts to isolate virus, the specificity of which was confirmed by antigen ELISA. The best of the RT-PCR assays used in each laboratory gave comparable results while the sensitivity of cell cultures was variable from high in one laboratory, moderate in two and low in two others. This prototype panel of samples would appear suitable for external quality assurance of these tests but would benefit from the inclusion of more negative samples and an extension in the serial dilution range of one or more of the FMD positive sample titration series.

Comparisons of original laboratory results and retrospective analysis by real-time reverse transcriptase-PCR of virological samples collected from confirmed cases of foot-and-mouth disease in the UK in 2001.

There were 2030 designated cases of foot-and-mouth disease (FMD) during the course of the epidemic in the UK in 2001 (including four from Northern Ireland). Samples from 1720 of the infected premises (IPs) were received in the laboratory and examined for either the presence of FMD virus (virological samples from 1421 IPs) or both FMD virus and antibody (virological and serological samples from 255 IPs) or antibody alone (from 44 IPs). The time taken to issue final diagnostic results ranged from a few hours in cases in which positive results were obtained by ELISA on epithelia containing sufficient virus to be detected, to several days for samples containing small amounts of virus requiring amplification through cell culture, negative samples or samples tested for antibody. Two subsets of samples were analysed retrospectively by real-time reverse transcriptase-PCR (RT-PCR); first, epithelia that were negative by both ELISA and virus isolation (VI) in cell culture, and secondly, samples that were negative by ELISA on epithelial suspension but positive by VI. There was broad agreement between the RT-PCR and VI/ELISA combined, except that the RT-PCR procedure did not detect a group of related virus isolates from Wales. These viruses had evidently evolved during the epidemic and had a nucleotide substitution in the RT-PCR probe site, which prevented them from being detected by the routine diagnostic probe. No evidence of FMD virus, antibody or nucleic acid was found in approximately 23 per cent (390 of 1730) of IPs from which samples were received, suggesting that the incidence of FMD during the outbreak may have been over-reported.

Diagnosis of foot-and-mouth disease by RT-PCR: evaluation of primers for serotypic characterisation of viral RNA in clinical samples.

Multiple primers designed from the 1D and 2AB regions of the foot-and-mouth disease (FMD) viral genome were evaluated extensively for the detection of all seven serotypes of the virus by reverse transcription polymerase chain reaction (RT-PCR) at the OIE/FAO World Reference Laboratory for FMD (WRL), Pirbright. The primers had been characterised previously elsewhere on a relatively small number of cell culture grown isolates and epithelial suspensions and had been shown to identify and differentiate all seven serotypes of FMD virus. The extended study evaluated several RT-PCR protocols on epithelial suspensions and supernatant fluids, resulting from their passage in cell culture, derived from clinical samples of diverse molecular characteristics. Each of the serotype-specific primers in selected RT-PCR protocols demonstrated suitable specificity and detected cell culture passaged isolates with some success but were not adequate for the serotyping of suspensions prepared from clinical samples of epithelium. The results showed that the primers can be used in RT-PCR procedures in conjunction with the routine detection methods of virus isolation and ELISA for the diagnosis and serotyping of FMD virus.

Development of a rapid chromatographic strip test for the pen-side detection of foot-and-mouth disease virus antigen.

Foot-and-mouth disease (FMD) is the most contagious animal virus disease of cloven-hoofed livestock and requires reliable and accurate diagnosis for the implementation of measures to control effectively its spread. Routine diagnosis of FMD is carried out at the OIE/FAO World Reference Laboratory for Foot-and-Mouth Disease (WRL for FMD), Pirbright by the combined use of ELISA and virus isolation in cell culture supplemented by reverse transcription polymerase chain reaction (RT-PCR) methods. These techniques require skilled personnel and dedicated laboratory facilities which are expensive. The development of a rapid and simple test for the detection of FMD virus antigen using Clearview chromatographic strip test technology for field application is described. This device detected FMD viral antigen in nasal swabs, epithelial suspensions and probangs from clinical samples submitted from the field, from animals infected experimentally and in supernatant fluids resulting from their passage in cell culture. The test system was more sensitive than ELISA for the diagnosis of all seven serotypes of FMD virus in the epithelial suspensions and nasal swabs and had equivalent sensitivity to the ELISA for the detection of contemporary virus strains in cell culture supernatant fluids. The study demonstrated the potential for this device to confirm a clinical diagnosis at the site of a suspected FMD outbreak, thereby offering the possibility of implementing control procedures more rapidly. Such pen-side diagnosis would have particular benefits in FMD emergencies, relevance to FMD control programmes which operate in endemic regions of the world such as South East Asia and for increasing disease awareness in other areas where efforts to control disease may be difficult. In each circumstance the availability of a pen-side device for diagnosis would reduce the necessity for sending routine diagnostic samples to an FMD laboratory and thereby reduce the delay in diagnosis, which can in some areas be considerable.

Primary diagnosis of foot-and-mouth disease by reverse transcription polymerase chain reaction.

Universal and serotype-specific primer sets were used in simple reverse transcription polymerase chain reaction (RT-PCR) assays on field samples of epithelium and vesicular fluid to determine their suitability for primary diagnosis of all seven serotypes of foot-and-mouth disease (FMD). The specificity of reactions was confirmed by using other vesicular disease viruses, namely: swine vesicular disease virus, vesicular stomatitis virus and three vesiviruses. This resulted in the identification of a universal O/A/C/Asia 1 primer set (1F/1R) located in the 5' untranslated region (UTR) of the FMD virus genome for the successful detection of virus of these serotypes in clinical samples although this primer set detected FMD virus of the SAT1/2/3 serotypes less efficiently. The 5' UTR universal primer set could be used for the primary diagnosis of FMD in conjunction with the routine diagnostic methods of virus isolation in cell culture and ELISA, although a more favourable reaction would be expected with FMD viruses of the O/A/C/Asia 1 group than with those of the SAT serotypes. The other examined universal and serotype-specific primer sets, located principally in the P1 capsid-coding region, were generally inferior to the 5' UTR universal primer set. It is envisaged that this evaluation of primers will lead to the development of alternative PCR strategies, for example nested PCR formats, with concomitant improvement in the speed of primary diagnosis of FMD which under present procedures can be lengthy.

Comparison of reverse transcription polymerase chain reaction, enzyme linked immunosorbent assay and virus isolation for the routine diagnosis of foot-and-mouth disease.

A reverse transcription polymerase chain reaction (RT-PCR) method was compared with virus isolation in cell culture and the antigen detection ELISA for the primary diagnosis of foot-and-mouth disease (FMD) on 166 clinical samples from the field. Eighty samples were positive by virus isolation/ELISA and 78 by RT-PCR. The RT-PCR detected FMD viral RNA in 11 of the 86 samples assessed as negative by virus isolation/ELISA but conversely failed to diagnose 13 samples identified as positive by the latter procedures. This RT-PCR is not serotype-specific so a cDNA product is indicative of the presence of FMD viral RNA only. Confirmation of the specificity of the cDNA product and the identification of the serotype requires nucleotide sequence analysis. The value of the RT-PCR is that it can rapidly facilitate the molecular analysis of field isolates and thus provide important epidemiological information regarding the source of outbreaks. However, it is a sophisticated technique requiring specialised equipment, expertise and refined reagents and has to be used in conjunction with current procedures for FMD diagnosis.

Development of a reverse transcription polymerase chain reaction procedure for the detection of marine caliciviruses with potential application for nucleotide sequencing.

A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detection of marine caliciviruses including vesicular exanthema of swine virus (VESV), San Miguel sea lion virus (SMSV), bovine Tillamook virus (BCV Bos-1) and caliciviruses (CV) isolated from dolphin (Cetacean CV), gorilla (Primate CV) and rattlesnake (Reptile CV) using primers (1F and 1R) designed from the capsid-coding region of the viral genome. These primers were compared with those described by Neill, J.D. and Seal, B.S., 1995: Development of PCR primers for specific amplification of two distinct regions of the genomes of San Miguel sea lion and vesicular exanthema of swine viruses, Mol. Cell. Probes 9, 33-38 (Hel1/Hel2), which had been designed from the 2C-like region of the calicivirus genome. Both sets proved to be extremely useful diagnostic tools for all of the known marine calicivirus serotypes with the exception of three: SMSV-8 and -12 and mink CV suggesting that these three caliciviruses may belong to a different group. Neither of the two primer sets reacted with strains of the vesicular disease viruses of foot-and-mouth disease (FMD), swine vesicular disease (SVD) or vesicular stomatitis (VS) nor with two feline caliciviruses (FCV). The 1F/1R primer set has the advantage over the Hel1/Hel2 set in that it generates a larger PCR product for nucleotide sequence investigations and so provides greater opportunity for identifying molecular differences between the viruses.

African swine fever virus infection of the bushpig (Potamochoerus porcus) and its significance in the epidemiology of the disease.

Warthog (Phacochoerus aethiopicus), giant forest hog (Hylochoerus meinertzhageni) and bushpig (Potamochoerus porcus) are known to be susceptible to infection with African swine fever (ASF) virus. Little however, is known about the ecology of the disease in the bushpig. This study has shown that the bushpig remains viraemic for between 35 and 91 days following infection during which time it is able to infect the tick vector O. moubata. These ticks were able to transmit the disease to pigs. The virus persists in the lymphatic tissues for less than 34 weeks. Bushpigs infected with LIL 20/l virus but not VIC T90/l virus transmitted infection to in-contact pigs. Infected domestic pigs did not transmit the infection to in-contact bushpigs. ASF virus was able to replicate in in vitro cultures of bushpig leucocytes and endothelial cells. Recovered bushpigs could be reinfected with some strains of virus but not others. While it has been demonstrated that bushpigs remain carriers of ASFV following infection a complete understanding of their significance in the epidemiology of the disease awaits further investigations of their association with O. moubata.

Use of automated real-time reverse transcription-polymerase chain reaction (RT-PCR) to monitor experimental swine vesicular disease virus infection in pigs.

Automated real-time RT-PCR was evaluated as a diagnostic tool for swine vesicular disease virus (SVDV) infection on a range of samples (vesicular epithelium, serum, nasal swabs, faeces) from four inoculated and three in-contact pigs over a period of 28 days. Traditional diagnostic procedures (virus isolation, and ELISAs for antigen and antibody) were used in parallel. Each inoculated pig developed a significant viraemia and clinical disease, and excreted virus, which was transmitted to the in-contact animals. The latter, however, developed only a short-lived, low-level viraemia and no clinical disease. The RT-PCR and virus isolation were generally comparable in detecting SVDV in the serum and nasal swabs from inoculated and in-contact pigs up to day 6 after infection; it was possible, however, to isolate virus for a longer period from the faeces of a few pigs. This suggested that further optimization of the template extraction method was required to counteract the effects of RT-PCR inhibitors in faeces. It was concluded that the automated real-time RT-PCR is a useful diagnostic method for SVD in clinically or subclinically affected pigs and contributed to the study of the pathogenesis of SVD in the pigs.

Enhanced laboratory diagnosis of foot and mouth disease by real-time polymerase chain reaction.

The performance of an automated real-time reverse transcription polymerase chain reaction (RT-PCR) was compared to virus isolation (VI) in cell culture and antigen detection enzyme-linked immunosorbent assay (ELISA) for the laboratory diagnosis of foot and mouth disease (FMD). The World Reference Laboratory for FMD in Woking, the United Kingdom, examined a collection of 334 epithelia received from eighteen countries between August 2002 and January 2004. The results showed that all VI positive (n = 195) and VI and ELISA positive samples combined (n = 204) were also positive by RT-PCR. Depending on the cut-off used, FMD virus genome was detected in a minimum of an additional 60 samples (18% of all samples tested). Furthermore, the RT-PCR generated results in less than one day from test commencement in contrast to up to 4 days to define some positive and all negative samples by VI. The study demonstrates that real-time RT-PCR provides an extremely sensitive and rapid procedure for improved laboratory diagnosis of FMD.

Serological study of pigs for antibody against African swine fever virus in two areas of southern Malawi.

A serological survey was conducted in July 1991 on domestic pigs in two areas of southern Malawi which were severely affected by the African swine fever (ASF) epizootic in 1989-1991. Sixty-six of the 216 owners questioned reported having witnessed ASF in their pigs. Forty-seven owners had pigs with antibodies against ASF virus, and the overall prevalence of pigs with anti-ASF virus antibodies was found to be 12.4%, in 445 pigs sampled in 35 villages. Spread of ASF was thought to occur principally through the slaughter and sale of infected animals, and due to the free-ranging of pigs. Permanent penning of pigs significantly reduced the attack rate (chi 2 = 7.59, P < 0.01, 1df) in pig pens in Thyolo, an area where permanent penning of pigs was widely practised. Feeding of kitchen scraps did not appear to have been an important means of virus spread. Ornithodoros ticks were found in only 1 of the 35 villages. Although virus was not isolated from 203 pooled sera from pigs in the Mulanje district or from collected ticks, the seroconversion of a small proportion of pigs born after the last reported date of ASF occurrence suggests that the virus had continued to circulate to a limited extent in this area.

Emergence of foot-and-mouth disease virus SAT 2 in Egypt during 2012.

The epidemiology of foot-and-mouth disease (FMD) in North Africa is complicated by the co-circulation of endemic FMD viruses (FMDV), as well as sporadic incursions of exotic viral strains from the Middle East and Sub-Saharan Africa. This report describes the molecular characterization of SAT 2 FMD viruses that have caused widespread field outbreaks of FMD in Egypt during February and March 2012. Phylogenetic analysis showed that viruses from these outbreaks fell into two distinct lineages within the SAT 2 topotype VII, which were distinct from a contemporary SAT 2 lineage of the same toptype from Libya. These were the first FMD outbreaks due to this serotype in Egypt since 1950 and required the development of a tailored real-time reverse-transcription PCR assay that can be used in the laboratory to distinguish FMD viruses of these lineages from other endemic FMD viruses that might be present in North Africa. These data highlight the ease by which FMDV can cross international boundaries and emphasize the importance of deploying systems to continuously monitor the global epidemiology of this disease.

Molecular characterisation of foot-and-mouth disease viruses from Pakistan, 2005-2008.

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

Molecular characterization of foot-and-mouth disease viruses collected from Sudan.

The aim of this study was to characterize foot-and-mouth disease (FMD) viruses collected between 2004 and 2008 from Sudan, a country where FMD is endemic. Using virus isolation and antigen ELISA, three FMD virus serotypes (O, A and SAT2) were detected in 24 samples that were submitted to the FAO World Reference Laboratory for FMD. Pan-serotypic real-time RT-PCR assays targeting the 5' untranslated region (5'UTR) and 3D genes of FMD virus were also used to contribute to the laboratory diagnosis of these cases. The lack of concordant results between the real-time RT-PCR assays for three serotype O viruses was attributed to four nucleotide mismatches in the 5'UTR PCR primer and probe sites (three substitutions for the sense-primer and one in the TaqMan(®) probe region). Taken together, the laboratory results showed that recent FMD outbreaks that occurred during 2008 in northern and central Sudan were caused by serotypes O and SAT2, while serotype A was last detected in 2006. Phylogenetic analyses of VP1 sequences from these viruses were used to determine the relationships with 23 older viruses from Sudan and other viruses from West and East Africa. For serotype O, closest genetic identities were between concurrent and historical Sudanese isolates, indicating that within-country circulation is an important mechanism by which FMD is maintained year-on-year in Sudan. A similar pattern was also evident for serotype A and SAT2 viruses; however, these lineages also contained recent representative FMD viral isolates from other countries in the region suggesting that long-distance animal movement can also contribute to FMD dispersal across sub-Saharan Africa. These findings provide the first molecular description of FMD viruses that are circulating in Sudan, and highlight that further sampling of representative viruses from the region is required before the complex epidemiology of FMD in sub-Saharan Africa can be fully understood.

Investigations into the cause of foot-and-mouth disease virus seropositive small ruminants in Cyprus during 2007.

In 2007, serological evidence for foot-and-mouth disease (FMD) infection was found as a result of differential diagnostic testing of Cypriot sheep suspected to be infected with bluetongue or contagious ecthyma. Seropositive sheep and goats were subsequently uncovered on ten geographically clustered flocks, while cattle and pigs in neighbouring herds were all seronegative. These antibodies were specific for serotype-O FMD virus, reacting with both structural and non-structural (NS) FMD viral proteins. However, no FMD virus could be recovered from the seropositive flocks. FMD had not been recorded in Cyprus since 1964 and there has been no vaccination programme since 1984. Since all the seropositive animals were at least 3 years old and home-bred, it was concluded that infection had occurred approximately 3 years previously had passed un-noticed and died out spontaneously. It therefore appears that antibodies to FMD virus NS proteins can still be detected around 3 years after infection of small ruminants, but that virus carriers cannot be detected at this time. This unusual situation of finding evidence of historical infection in a FMD-free country caused considerable disruption and alarm and posed questions about the definition of what constitutes a FMD outbreak.

Recent spread of a new strain (A-Iran-05) of foot-and-mouth disease virus type A in the Middle East.

This report describes the characterization of a new genotype of foot-and-mouth disease virus (FMDV) type A responsible for recent FMD outbreaks in the Middle East. Initially identified in samples collected in 2003 from Iran, during 2005 and 2006 this FMDV lineage (proposed to be named A-Iran-05) spread into Saudi Arabia and Jordan and then further west into Turkey reaching European Thrace in January 2007. Most recently A-Iran-05 has been found in Bahrain. To the east of Iran, it has been recognized in Afghanistan (2004-07) and Pakistan (2006-07). Throughout the region, this lineage is now the predominant genotype of FMDV serotype A sampled, and has appeared to have replaced the A-Iran-96 and A-Iran-99 strains which were previously encountered. In August 2007, a new A-Iran-05 sub-lineage (which we have called A-Iran-05(ARD-07)) was identified in Ardahan, Turkey, close to the border with Georgia. This new sub-lineage appeared to predominate in Turkey in 2008, but has, so far, not been identified in any other country. Vaccine matching tests revealed that the A-Iran-05 viruses are antigenically different to A-Iran-96 and more like A(22). These findings emphasize the importance of undertaking continued surveillance in the Middle East and Central Asia in order to detect and monitor the emergence and spread of new FMDV strains.

Swine vesicular disease: pathways of infection.

The pathways of infection in swine vesicular disease have been studied by (i) an estimation of the amounts of virus required to produce infection by different artificial inoculation procedures; (ii) the distribution and amounts of virus in various tissues of pigs killed at intervals after contact infection; (iii) an investigation of the susceptibility to virus infection of pig tissue explants. The results show that pigs can be infected by a number of pathways and that the skin, as the most susceptible tissue, is probably the most frequent route of infection.

Variable regions on the genome of Malawi isolates of African swine fever virus.

Restriction enzyme site mapping showed that most BamHI and all ClaI sites were conserved on the genomes of 17 African swine fever virus isolates from separate disease outbreaks that occurred between 1982 and 1989 in Malawi. However, frequent variation between virus genomes did occur due to addition or deletion of DNA sequences at various positions along the genome and 11 virus genotypes could thus be distinguished among the 17 isolates analysed. Length variations occurred at 10 different loci on the virus genome. These variable regions were located between the left DNA terminus and a position up to 48 kb from that terminus, in the centre of the genome 90 to 93 kb from the left DNA terminus and between the right DNA terminus and a position 22 kb from that terminus. Length variations in most of these regions were small (less than 1 kb) but variations of about 4 kb occurred in a region up to 20 kb from the left DNA terminus.