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. 2025 Jun 4:15:1575538.
doi: 10.3389/fcimb.2025.1575538. eCollection 2025.

Exploring the evolutionary journey of the lumpy skin disease virus through the phylogenetic and phylo-geo network analysis

Manjunatha Reddy Gundallahalli Bayyappa #  1 , Manoj Kumar Goud Pyatla #  2 , Sai Mounica Pabbineedi  1 , Narasimha Tanuj Gunturu  2 , Sai Manohar Peela  2 , Sudeep Nagaraj  1 , Sunil Tadakod  1 , Ravi Kumar Gandham  2 , Baldev Raj Gulati  1
Affiliations

Exploring the evolutionary journey of the lumpy skin disease virus through the phylogenetic and phylo-geo network analysis

Manjunatha Reddy Gundallahalli Bayyappa et al. Front Cell Infect Microbiol. .

Abstract

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.

Keywords: TMRCA; genetic diversity; haplotype network; lumpy skin disease virus; phylogenetic analysis; transboundary spread.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The handling editor RMA declared a shared parent affiliation with the author(s) MB, SPa, SN, ST, and BG at the time of review.

Figures

Figure 1
Figure 1
The map depicting the geographical distribution of the LSDV sequences retrieved from PubMed for the present study.
Figure 2
Figure 2
LSD virus isolation: The LSDV (5-Chitra isolate) infected MDBK cell line at 72hrs post-infection. The arrow indicates the clustering, rounding and characteristic foci formation of the MDBK cells infected by LSDV (B) compared to healthy cells (A).
Figure 3
Figure 3
Phylogenetic analysis of the full-length gene of GPCR of the LSDV isolates obtained in this study suing maximum-likelihood tree showing the LSDV isolates close relationship with GPV than SPV.
Figure 4
Figure 4
Phylogenetic analysis of the worldwide LSDV full genome sequences. The maximum likelihood tree was constructed using whole genome sequences. The LSD viruses from India (red color) are originated and evolutionarily more related to LSDV isolates from Kenya.
Figure 5
Figure 5
Analysis of phylogenomic geographic network of lumpy skin disease virus genomes 812 worldwide. Each of the circles represents either haplogroup or haplotype. The circle size states 813 the sequence load; the bigger the circle size represents the number of genome sequences there.
See this image and copyright information in PMC

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