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
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.