Molecular characterization of African swine fever virus from outbreaks in Namibia in 2018

Five samples were collected from four suspected outbreaks of African swine fever in Namibia in 2018. Sequencing of the C-terminus of the B646L gene (p72 protein), the central hypervariable region (CVR) of the B602L gene, the E183L gene (p54 protein) and the CD2v (used to determine the serogroup) was performed on DNA isolated from the samples. Phylogenetic analyses of the B646L (p72) revealed that one of the samples belonged to genotype I while the remaining samples could not be assigned to any currently known genotype. In contrast, by using the E183L gene three of the samples were shown to belong to genotype Id and only two were of unknown genotype. Based on the analysis of the partial CD2v amino acid sequences of four of the samples, one of the viruses clustered with serogroup 2 while the other three did not cluster within any of the eight known serogroups. Examination of the CVR identified three variants with 8, 18 and 24 tetrameric tandem repeat sequences. This study indicates that at least three different genetically distinct ASFV are currently present in Namibia.