Molecular characterization of a novel recombinant lumpy skin disease virus isolated during an outbreak in Tyumen, Russia, in 2019.

Lumpy skin disease virus causes a debilitating pox disease of domesticated cattle and water buffalos. In the last decade, LSDV has spread from Africa into the Middle East, Europe and most recently Asia. As of 2017, atypical outbreaks caused by novel LSDV strains were reported in Russia, followed by China and Vietnam between 2018 and 2020. In this work, we describe another unique recombinant LSDV strain recovered from Tyumen, Russia in 2019. Typing of the virus using currently available qPCR protocols produced inconclusive results and subsequently the complete genome of the isolate was determined. The consensus genome contained statistically significant signals of possible recombination events between parental strains KSGPO-240/Kenya/1958 and the live attenuated vaccine LW/1958. The novel strain carries 25 unique breakpoints different from the known recombinant strains. Additionally, the findings reiterate the importance of complete genome sequencing when analysing outbreak samples caused in particular by mosaic LSDV, in contrast to only performing specified qPCRs.