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Genomic characterization of Lumpy Skin Disease virus (LSDV) from 2019 outbreak in India reveals circulation of Kenyan-like LSDV strains with unique kelch-like proteins
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  • Amit Kumar,
  • Gnanavel Venkatesan,
  • Anand Kushwaha,
  • Poulinlu G,
  • Tapabrata Saha,
  • Ramakrisnan M A,
  • Pronab Dhar,
  • G. Sai Kumar,
  • Singh R K
Amit Kumar
Indian Veterinary Research Institute Mukteswar Campus

Corresponding Author:[email protected]

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Gnanavel Venkatesan
Indian Veterinary Research Institute Bengaluru Campus
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Anand Kushwaha
Indian Veterinary Research Institute Mukteswar Campus
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Poulinlu G
Indian Veterinary Research Institute Mukteswar Campus
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Tapabrata Saha
Government of West Bengal
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Ramakrisnan M A
Indian Veterinary Research Institute Bengaluru Campus
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Pronab Dhar
Indian Veterinary Research Institute
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G. Sai Kumar
Indian Veterinary Research Institute
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Singh R K
Indian Veterinary Research Institute
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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.