Genetic and phylogenetic analysis of lumpy skin disease viruses (LSDV) isolated from the first and subsequent field outbreaks in India during 2019 reveals close proximity with unique signatures of historical Kenyan NI-2490/Kenya/KSGP-like field strains

Lumpy skin disease (LSD), an economically important viral disease of cattle caused by lumpy skin disease virus (LSDV) has recently spread into South and East Asia. LSD emerged in India in August 2019, first in Odisha State and spread to other areas, but there is scanty data on source and molecular epidemiology of LSDV involved in the initial outbreaks. Here we report genetic relationships and molecular features of LSDV, causing outbreaks in cattle spanning seven districts in Odisha and West Bengal States during August-December, 2019. Twelve LSDV isolates obtained using lamb testis cells were sequenced and analysed in four complete genes, GPCR, RPO30, P32 and EEV. The phylogenetic analysis revealed that all the Indian LSDV isolates from 2019 outbreaks are very closely related (99.7%-100%) to the historical Kenyan NI-2490/Kenya/KSGP-like field strains. Importantly, our results demonstrated that LSDV strains involved in 2019 outbreaks in India and Bangladesh are very similar in GPCR (99.7%), RPO30 (100%) and partial EEV (100%) sequences, indicating a common exotic source of LSDV introduction. Additionally, a 12-nucleotide insertion was found in GPCR gene of LSDV strains from 2019 outbreaks in India and Bangladesh. The findings of this study highlight the importance of continuous monitoring and molecular characterization of LSDV strains. These data should be useful while developing diagnostic and control strategies against LSD in India.