Using a new serotype-specific Polymerase Chain Reaction (PCR) and sequencing to differentiate between field and vaccine-derived African Horse Sickness viruses submitted in 2016/2017.

A new Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assay is described that can differentiate between the nine serotypes of African horse sickness virus (AHSV). A unique set of primers targeting regions in the corresponding genome segment-2 were designed for each serotype. Sequences of the individual amplicons have single nucleotide polymorphisms (SNPs) allowing discrimination between field samples and either reference strains or live attenuated viruses (ALVs). This assay was tested and used to determine the serotype prevalence of AHSV samples submitted during the 2016 / 2017 season as well as to determine the incidence of field samples derived from ALVs. The information was used to study the epidemiology of AHSV in Southern Africa.