Genetic characterization of lumpy skin disease virus (LSDV) from 2022 to 2023 outbreaks in yaks (Bos grunniens) and cattle in the Himalayan state of Sikkim, India, reveals dominant circulation of the LSDV 1.2.1 variant strain.

Abstract

Lumpy skin disease (LSD) is a major threat to global cattle production with an expanding host range. In India, although LSDV-associated mortality in yaks (Bos grunniens) is a major concern, LSD epidemiology in yaks is poorly understood and genetic profile of LSDV from the Northeast is scarce. This study aimed to molecularly detect and genetically characterize the LSDV strains from the 2022-2023 LSD outbreaks in yaks and cattle in the Himalayan state of Sikkim. Infected yaks exhibited clinical signs akin to cattle and necropsy revealed lesions on vital organs. Testing of 23 yak samples and 123 cattle samples by LSDV real-time PCR and antibody ELISA demonstrated LSDV infection. Sequencing and phylogenetic analysis of four selected marker genes (GPCR, RPO30, EEV, and B22R) revealed that LSDV sequences from yaks and cattle belonged to the 1.2.1 sub-cluster, closely related to the circulating 1.2.1 variants from India and Tibet. However, they were distinct from the dominant LSDV strains circulating in India (1.2.2) and China (2.5 recombinant). Detection of identical LSDV sequences and close proximity between yaks and local cattle implied a spillover from cattle. Additionally, our findings showed that concatenated sequence-based analysis could function as a proxy to whole-genome sequence analysis, and the C-terminal 717 bp of the B22R gene may represent a potential single-gene sequencing target for classifying LSDV into well-supported clusters. These findings improved our understanding of LSDV molecular epidemiology and host range and highlight the necessity of LSD control in yaks, and monitoring of cross-border transmission.