Yadav, P and Kumar, A and Nath, SS and Devasurmutt, Y and Shashidhar, G and Joshi, M and Puvar, A and Sharma, S and Raval, J and Pandit, R and Chavda, P and Nagaraj, S and Revanaiah, Y and Patil, D and Raval, SK and Raval, J and Kanani, A and Thakar, F and Kumar, N and Reddy, GBM and Joshi, C and Gulati, BR and Tatu, U (2024) Unravelling the genomic origins of lumpy skin disease virus in recent outbreaks. In: BMC Genomics, 25 (1).
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Abstract
Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in other countries. In this study, we used whole genome sequencing approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations compared to the Reference Neethling strain sequence and the previous field strains. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. Thirty-eight genes have more than 2 variations per gene, and these genes belong to viral-core proteins, viral binding proteins, replication, and RNA polymerase proteins. We highlight the importance of several SNPs in various genes, which may play an essential role in the pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues. © The Author(s) 2024.
| Item Type: | Journal Article |
|---|---|
| Publication: | BMC Genomics |
| Publisher: | BioMed Central Ltd |
| Additional Information: | The copyright for this article belongs to authors. |
| Keywords: | viral core protein, antigenicity; Article; Capripoxvirus; DNA extraction; fever; frameshift mutation; gene mutation; genetic variation; lumpy skin disease; Lumpy skin disease virus; multiplex polymerase chain reaction; nonhuman; phylogeny; Poxviridae; protein expression; sequencing by ligation; single nucleotide polymorphism; skin defect; skin nodule; Vero cell line; virus attachment; virus replication; whole genome sequencing; animal; bovine; epidemic; genetics; genomics; lumpy skin disease, Animals; Cattle; Disease Outbreaks; Genomics; Lumpy Skin Disease; Lumpy skin disease virus; Phylogeny |
| Department/Centre: | Division of Biological Sciences > Biochemistry |
| Date Deposited: | 05 Jul 2024 11:38 |
| Last Modified: | 05 Jul 2024 11:38 |
| URI: | http://eprints.iisc.ac.in/id/eprint/84601 |
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