No abstract

Foot and mouth disease virus (FMDV) is an animal pathogen of global economic significance. Identifying the sources of outbreaks plays an important role in disease control; however, this can be confounded by the ease with which FMDV can spread via movement of infected livestock and animal products, aerosols or fomites, e.g. contaminated persons and objects. As sequencing technologies have advanced, this review highlights the uses of viral genomic data in helping to understand the global distribution and transboundary movements of FMDV, and the role that these approaches have played in control and surveillance programmes. The recent application of next-generation sequencing platforms to address important epidemiological and evolutionary challenges is discussed with particular reference to the advent of 'omics' technologies.

The recent emergence and spread of bluetongue virus (BTV) across the whole of Europe suggests that other orbiviruses could also emerge to threaten livestock species and wildlife populations in Europe and other parts of the world. The genus Orbivirus is the largest within the family Reoviridae, containing 22 virus species, as well as 14 unclassified orbiviruses. The orbiviruses are transmitted primarily by arthropod vectors (e.g. Culicoides, mosquitoes or ticks) and several are associated with severe and economically important diseases of livestock, including BTV in cattle and sheep, African horse sickness virus (AHSV), equine encephalosis virus (EEV) and Peruvian horse sickness virus (PHSV) in equids, as well as epizootic haemorrhagic disease virus (EHDV) in wild ungulates or cattle.Recent incursions of BTV in Europe, Southeastern USA, Australia and Asia, EHDV in North Africa, the Middle East and the Mediterranean region, AHSV in sub-Saharan Africa, and EEV in Israel and Gambia, indicate a need for the development of faster, more sensitive and more reliable diagnostic assays. These are required to detect and identify rapidly the viruses and virus types involved, monitor their incidence and movement, and identify infected animals. The Orbivirus genome is composed of 10 linear segments of double-stranded ribonucleic acid (dsRNA), each segment coding for at least one viral protein. The outer capsid proteins VP2 and VP5 are situated on or near the surface of the virus particle and are more variable than components of the virus core, or the non-structural proteins. VP2 (encoded by Seg-2) is the outermost of the BTV capsid proteins and represents the primary target antigen for neutralising antibodies, and hence Seg-2 is a target for the development of type-specific nucleicacid-based diagnostic assays. In contrast, the genome segments coding for protein components of the virus core and/or the nonstructural proteins can be used as targets for development of serogroup (virus-species) specific, reverse transcription -polymerase chain reaction (RT-PCR) based diagnostic assays.Virus species-specific and type-specific conventional (gel based) RT-PCR diagnostic assays, for the detection, identification and typing of some of these viruses (BTV, EHDV and AHSV), have been developed using the sequence data for segments 7 and 2, respectively. Initial evaluation studies indicate that these assays are reliable, specific, do not cross-react with related orbiviruses (group/species specific) or with related types (type specific). Although they are labour intensive, the results obtained can be confirmed by sequence analyses of the resulting complementary deoxyribonucleic acid complementary (c) DNA amplicons, and phylogenetic comparisons to determine the strain of virus involved. However, conventional RT-PCR assays are prone to cross-contamination, potentially leading to false positive results.The authors also describe group-specific real-time RT-PCR assays that use a 'closed-tube' format, which are therefore less susceptible to cross-co...