ABSTRACT
Lumpy skin disease (LSD) is an economically important poxviral disease endemic to Asia, Europe, and Africa. Recently, LSD has spread to naïve countries, including India, China, Bangladesh, Pakistan, Myanmar, Vietnam, and Thailand. Here, we describe the complete genomic characterization of LSDV from India, LSDV-WB/IND/19 isolated from a calf in Vero cells determined by Illumina next-generation sequencing (NGS). The LSDV-WB/IND/19 has a genome size of 150969 bp encoding 156 putative ORFs. Phylogenetic analysis based on complete genome sequence suggested that LSDV-WB/IND/19 is closely related to Kenyan LSDV strains with 10-12 variants with non-synonymous changes confined to LSD_019, LSD_049, LSD_089, LSD_094, LSD_096, LSD_140, and LSD_144 genes. In contrast, to complete kelch-like proteins in Kenyan LSDV strains, LSDV-WB/IND/19 LSD_019 and LSD_144 genes were found to encode truncated versions (019a, 019b, and 144a, 144b). LSD_019a and LSD_019b proteins of LSDV-WB/IND/19 resemble that of wild-type LSDV strains based on SNPs and the C-terminal part of LSD_019b except for deletion at K229, whereas the LSD_144a and LSD_144b proteins resemble that of Kenyan LSDV strains based on SNPs, however, C-terminal part of LSD_144a resembles that of vaccine-associated LSDV strains due to premature truncation. The NGS findings were confirmed by Sanger sequencing of these genes in Vero cell isolate as well as in the original skin scab along with similar findings in another Indian LSDV from scab specimens. LSD_019 and LSD_144 genes are thought to modulate virulence and host range in capripoxviruses. This study demonstrates the circulation of unique LSDV strains in India and highlights the importance of constant monitoring of the molecular evolution of LSDV and associated factors in the region in light of the emergence of recombinant LSDV strains.
Keywords: Lumpy skin disease virus, kelch-like proteins, Phylogenetic analysis, whole genome
Introduction
Lumpy skin disease is a contagious viral disease caused by lumpy skin disease virus (LSDV) belonging to the Capripoxvirus genus of thePoxviridae family and affects cattle and domestic water buffaloes. It incurs huge economic losses to the livestock industry due to a decrease in milk production, infertility, abortions, hide damage as well as trade restrictions (Tuppurainen et al., 2017). The disease was originally described in Zambia in 1929, later spreading to South Africa and Kenya. Initially, the disease was contained to Africa and the Middle East (Davies, 1982), later spreading to Europe followed by outbreaks in several Asian countries including India (Sudhakar et al., 2019), Nepal (Acharya and Subedi, 2020), Bangladesh (Hasib et al., 2021), Vietnam (Tran et al., 2021), Thailand (Arjkumpa et al., 2021), Myanmar (Maw et al., 2022), China (Lu et al., 2021), and Hongkong (Flannery et al., 2021) has raised serious concerns. The clinical manifestations of lumpy skin disease include pyrexia, characteristic nodules on different body parts, lymphadenopathy, drop in milk production, weight loss, infertility, abortion, and sometimes death (Tuppurainen et al., 2017). The morbidity rate can be as high as 100% whereas the mortality rate is usually less than 10%. LSDV is mainly transmitted by arthropod vectors. LSDV has a genome size of ~151 kbp encoding putative 156 proteins (Tulman et al., 2001; Biswas et al., 2020). LSDV is antigenically related to other members of Genus Capripoxvirus , sheeppox virus (SPPV), and goatpox virus (GTPV). Full genome sequences of LSDV strains circulating across the world are available (Table 1). The information on the genomic sequence of LSDV strains circulating in India has not been widely available yet, although previous sequence analyses were based on partial gene sequence data (Kumar et al., 2021; Sudhakar et al., 2021, Sethi et al., 2022). In this study, we have therefore determined the complete genome sequence of LSDV from cattle in India to offer additional insights into molecular epidemiology and the factors affecting the evolution of capripoxviruses.