Genomic characterization of lumpy skin disease virus in southern China

Abstract

Lumpy skin disease virus (LSDV) is of high economic importance and has spread rapidly to many European and Asian countries in recent years. LSDV was introduced to China in 2019 and have caused severe outbreaks in several provinces. Here, we detected an LSDV strain (GD01/2020) from a cattle farm with typical LSD symptoms in Guangdong, southern China using a novel quantitative real‐time PCR assay targeting the viral GPCR gene. We obtained the whole genomic sequence of GD01/2020 through metagenomic analysis. The GD01/2020 was highly homologous to the LSDVs isolated in Xinjiang, China in 2019, and distinct from all the LSDVs identified in other countries, in their sequences of GPCR and RPO30 genes. The GD01/2020 was a vaccine‐recombinant strain, but distinct from two recombinant LSDVs identified in Russia. At least 25 putative recombination events between a vaccine strain and a field strain were identified in the genome of GD01/2020, which could affect the virulence and transmissibility of the virus. These results suggested that a virulent vaccine‐recombinant LSDV from an unknown origin was introduced into Xinjiang, China in 2019 and spread to Guangdong, China in 2020.

Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence?

“…Following the emergence of LSDV in Kazakhstan in 2016, the authorities launched a mass vaccination campaign with the Neethling-based Lumpivax vaccine (KEVEVAPI) [ 36 ]. As none of the other countries in the affected region used a homologous LSDV vaccine during the same period, it was suggested that the vaccine might have been responsible for the emergence of the recombinant strains [ 26 , 33 , 36 ]. In a previous study, Haegeman et al indeed obtained conflicting results when they analysed the Lumpivax vaccine with a series of PCR assays that allowed differentiation between infected and vaccinated animals (DIVA) [ 40 ].…”

“…Whole-genome sequencing (WGS) analyses have shown that the LSDV strains from the 2015–2016 epidemics in south-eastern Europe, Kazakhstan and Russia are most similar to a strain isolated in Israel in 2012 [ 28 , 29 , 30 , 31 ]. In contrast, most of the recent LSDV strains from Russia and Asia appear to be vaccine-like recombinant strains carrying genetic signatures from both Neethling- and KSGP-based LSDV vaccines [ 26 , 32 , 33 , 34 , 35 ]. It is noteworthy that while the use of homologous LSDV vaccines is not authorised in Russia, the Lumpivax vaccine (KEVEVAPI) was used in Kazakhstan shortly before the emergence of the vaccine-like strains [ 36 ].…”

Molecular detection and characterization of lumpy skin disease viruses from outbreaks in Thailand in 2021

“…In the present study, the phylogenetic analysis of GPCR, ANK and RPO30 gene sequences showed that all five LSDV isolates from Thailand were clustered separately from LSDV‐vaccine and LSDV‐field isolates and were closely correlated with LSDV strains from mainland China, Hong Kong territory and Vietnam. Generally, the phylogenies based on the GPCR and RPO30 genes are more widely used for the molecular evolution analysis of LSDV isolates (Azeem et al., 2021; Kumar et al., 2021; Ma et al., 2022; Ochwo et al., 2020). Additionally, either the p32 gene or the RPO30 gene is a well‐known candidate marker for differentiation between LSDV‐vaccine and LSDV‐field strains (Agianniotaki et al., 2017; Ma et al., 2022; Sameea Yousefi et al., 2018; Sudhakar et al., 2020).…”

“…Generally, the phylogenies based on the GPCR and RPO30 genes are more widely used for the molecular evolution analysis of LSDV isolates (Azeem et al., 2021; Kumar et al., 2021; Ma et al., 2022; Ochwo et al., 2020). Additionally, either the p32 gene or the RPO30 gene is a well‐known candidate marker for differentiation between LSDV‐vaccine and LSDV‐field strains (Agianniotaki et al., 2017; Ma et al., 2022; Sameea Yousefi et al., 2018; Sudhakar et al., 2020). Hence, this discrepancy in the phylogenetic classification of LSDV strains from Thailand may be due to the use of different gene regions.…”

“…Simultaneously, the Chinese LSDV strain (China/GD01/2020) isolated from cattle with typical LSD clinical signs in Guangdong, southern China, was highly homologous to the LSDVs isolated from Xinjiang, China, in 2019, and was distinct from all the LSDVs identified in other countries. The China/GD01/2020 strain was later confirmed as a virulent vaccine‐recombinant LSDV strain (Ma et al., 2022). In Thailand, the first LSD outbreak was occurred on March 29, 2021, at Roi‐Et province in the northeastern region.…”