Molecular and Epidemiological Analyses of Sheeppox Outbreaks in Russia from 2013 to 2021

Sheeppox (SPP) is a transboundary infectious disease that affects sheep and goats, leading to significant losses in countries with extensive small ruminant breeding programs. While sporadic SPP outbreaks have been observed in the Russian Northern Caucasus and the Far East, the number of SPP outbreaks in the Russian Central and Far East regions has increased recently. However, there is a lack of epidemiological data on SPP virus (SPPV) in the Northern latitudes. In this study, we conducted epidemiological and genetic analyses of SPP outbreaks in Russia from 2013 to 2021 using whole-genome sequences of five selected isolates. The epidemiological data revealed an elevated risk of SPP outbreaks during the summer months, although outbreaks were not limited to this period. A phylogenetic analysis of the whole-genome sequences of selected SPPVs obtained directly from clinical samples revealed a unique cluster of SPPV isolates circulating in Central Russia, which was related to previous isolates from the European part of Russia. In contrast, SPPVs obtained from the Russian Far East showed genetic similarity to isolates detected in Southeast Asia. The whole-genome sequences demonstrated that the reported outbreaks were not related to the NISKHI vaccine strain, which was used to combat lumpy skin disease and SPP in Russia. Based on the study findings and GenBank data, we propose a novel cluster designation system for SPPV genomic sequences.