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Updated: Sep 19, 2025

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
Exploring the evolutionary journey of the lumpy skin disease virus through the phylogenetic and phylo-geo network
Manjunatha Reddy Gundallahalli Bayyappa1, Manoj Kumar Goud Pyatla2, Sai Mounica Pabbineedi1
1Capripoxvirus Lab, Veterinary Pathology, Indian Council of Agricultural Research (ICAR)-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru, Karnataka, India.
Introduction:
Lumpy Skin Disease Virus (LSDV), an emerging pathogen from the Capripoxvirus genus, continues to challenge global livestock health with its expanding host range and genetic adaptability.
Materials And Methods:
In this study, we report the first isolation and whole genome sequencing of LSDV from Bos frontalis, a semi-domesticated bovine species native to Northeast India, along with the assembly of an isolate from cattle.
Results:
Time to the Most Recent Common Ancestor (TMRCA) estimates support a relatively recent common origin for Indian strains, pointing to ongoing virus circulation and regional adaptation. The maximum likelihood phylogenetic tree of the whole genome and G protein-coupled chemokine receptor (GPCR) gene further demonstrated the clustering of global strains, emphasizing the virus's transboundary movement and genomic diversity. To strengthen phylogenetic inference, we identified shared SNPs, synonymous and non-synonymous mutations across the genome with a total of 2212 variants. Haplotype network and mutation pattern analyses across global genomes further highlighted the conservative evolution of Indian isolates within a distinct haplogroup.
Discussion:
Several mutation events between haplogroups highlight the virus's continuous genetic diversification, which correlates with known patterns of spread.
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