First complete genome characterization of swinepox virus directly from a clinical sample indicates divergence of a Eurasian-lineage virus

In this study, we report the complete genome sequence of swinepox virus from a clinical sample from a naturally occurring infection in India. The sequencing was done on a Nanopore MinION sequencer from Oxford Nanopore Technologies. Two new annotations were added to the genome. Three of the genes were found to have frameshifts, which might be of importance in relation to infection. When compared to the only other reported whole genome sequence of swinepox virus, which was obtained from an isolate from America in 1999, our sequence is only 98.19% identical at the nucleotide level. The average amino acid sequence identity of the viral proteins, based on the common 149 annotations, is also 98.19%, demonstrating that these viruses are distinctly divergent. Owing to the fact that swinepox virus infects only swine, it could not have entered America until the introduction of swine in the 16 th century from Europe. The swinepox viruses in both continents have continued to evolve independently. The sequence divergence identified here indicates a Eurasian-lineage virus that is geographically distinct from the American-lineage swinepox virus.