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

Abstract

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.

Phylogenetic and sequence analysis of Lumpy skin disease virus circulating in some governorates of Egypt during 2019/2020.

“…The genome of LSDV is highly conserved and this explains the similarity between the genomic sequence of GPCR gene of the strains of this study and other strains of LSDV in agreement with Stram et al (2008) who demonstrate the inability to distinguish between the various LSDV, even though they were isolated from different locations at different times as LSDV has highly conserved nature. On comparing the three sequences of this study with the Indian strain (MW452639), which was nearly identical to the historical field strains (NI-2490/Kenya) and KSGP-like strains (KSGP O-240, Kenyavac, KS-1) from Kenya, we found 12 nucleotide deletions in the sequences of the study that can be explain as the strains of this study may be recombinant LSDV strains as described by Sudhakar et al (2022). Further multigenic sequencing was applied on one strain depending on three different genes (P32, ORF 95 and ORF 103) for adequate characterization of the field strain and comparing the ORF 103 sequence with that of a SPV field sample.…”

The changing epidemiology of lumpy skin disease in Russia since the first introduction from 2015 to 2020

“…To the best of our knowledge, KSGP has never been known to be present even on the regional scale in Eurasia. Interestingly, recent LSD cases in India, Bangladesh and Nepal are associated with KSGP‐related virus isolates (Sudhakar et al., 2021); however, no links apparently exist between these two clusters of epidemics. The massive spread of recombinant viruses along the border is concerning.…”

Experimentally controlled study indicates that the naturally occurring recombinant vaccine-like lumpy skin disease strain Udmurtiya/2019, detected during freezing winter in northern latitudes, is transmitted via indirect contact

“…The Russian Federation (RF) reported annual LSD outbreaks from 2015 to 2020, with a dramatic shift in the LSDV strains responsible for these outbreaks ( 5 ). Since 2019, China, India and other counties of South Asia have been affected by LSDV ( 6 , 7 ).…”