Genomic analysis and spatiotemporal distribution of newly emerging lumpy skin disease virus in malaysia identify recombinant strain from transboundary spread

Abstract

Lumpy skin disease is a transboundary viral disease affecting bovine species. This disease had never been recorded in Malaysia prior to May of 2021, and had spread to 65 of 92 districts in Peninsular Malaysia by December of the same year. In this study, we conducted a whole-genome sequencing, phylogenetic analysis and geographical mapping of the outbreak from lumpy skin disease virus isolated from the first wave of outbreaks to better understand the origin, transmission, and genetic diversity of the virus. The whole genome sequences of these isolates were deposited in GenBank with accession number PP145891 and PP145892. Malaysia LSDV isolates were found clustered with recombinant strains in clade 2.5, particularly subclade 2.5.1, which included strains from China, Vietnam, Thailand, and Indonesia. The spread of the disease in Malaysia was closely linked to cross-border cattle movements from Thailand, as evidenced by the spatiotemporal distribution of the outbreaks. This study emphasizes the need for ongoing genomic surveillance to detect emerging variants and inform targeted control strategies, including vaccination and cross-border cooperation to curb future outbreaks.

Keywords: Lumpy skin disease virus; PP145891; PP145892; Poxvirus; Spatio-temporal analysis; Whole genome sequence.