Application of real-time RT-PCR assay for detection and typing of foot-and-mouth disease virus in Tanzania

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Sokoine University of Agriculture


Speed is paramount in the diagnosis of highly infectious Foot-and-mouth disease (FMD). Recent developments in molecular biology have enabled specific detection of FMD virus by real-time RT-qPCR and sequencing in endemic settings in Africa. In this study, a laboratory-based experimental design was used to standardize real-time RT-qPCR assay for detection and typing of FMDV in selected regions of Tanzania. The optimized conditions for both pan-serotypic and serotype-specific real-time RT-qPCR assays were: reverse transcription (at 60°C for 30minutes), denaturation of reverse transcriptase and activation of DNA polymerase (at 95°C for 10minutes followed by 95°C for 15 seconds), annealing and elongation temperature (at 60°C for 1 minute) for 52 cycles. FMD virus were detected in 100% (n = 14) archived samples that were collected between 2010 and 2013 from confirmed FMD-cases. The standardized real-time RT-qPCR assays revealed 100% sensitivity and 100% specificity for detection and typing of FMDV, respectively.The frequency of FMDV detection among FMD-suspected cases of cattle collected from 2008 to 2014 in selected regions of Tanzania was 92% (n = 23). Of the 23 positive samples, 56.5% (n = 13), 8.7% (n = 2), 21.7% (n = 5), and 8.7% (n = 2) were typed into serotypes O, A, SAT 1 and SAT 2 respectively. One sample (4.3%) was positive for both serotype A and SAT 1. These findings indicate that the standardized pan-serotypic and serotype-specific real-time RT-qPCR assays have a potential use in detection and typing of FMDV field strains in endemic settings of Tanzania and Africa at large. Application of standardized real-time RT-qPCR assays could hasten diagnosis of FMDV that guide selection of effective FMD-control measures in the region. In-depth studies, including sequencing of one sample that revealed positive for two serotypes, are required to elucidate the possibility of mixed infection among FMD cases.


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Real-time RT-PCR assay, Foot-and-mouth disease virus, Mouth disease, Tanzania