Genome Sequencing of Historical Encephalomyocarditis Viruses from South Africa Links the Historical 1993/4 Savanna Elephant () Outbreak to Cryptic Rodents.

From 1993 to 1994, 64 free-ranging elephants () succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. rodents were implicated as the reservoir host of the (EMCV) based on serology and RT-PCR. However, in the absence of sequence-confirmation of both the virus and the rodent host, definitive links between the elephant outbreak strains and rodent reservoir could not be established. In this study, we generate the first reference genome sequences for three historical EMCVs isolated from two rodents and one -associated mite, , in Gauteng Province, South Africa, in 1961. In addition, near-complete genome sequences were generated for two elephant outbreak virus strains, for which data were previously limited to the P1 and 3D genome regions. The consensus sequence of each virus was determined using a PCR-Sanger sequencing approach. Phylogenetic analysis confirmed the three near-identical (99.95-99.97%) -associated viruses to be sister to the two near-identical (99.85%) elephant outbreak strains, differing from each other at 6.4% of sites across the ~7400-nucleotide region characterised. This study demonstrates a link between -associated viruses and the historical elephant outbreak strains and implicates as reservoirs of EMCV in South Africa.