Phylogenomic Analysis of Lumpy Skin Disease Virus (LSDV) in South Asia

📌 Project Overview

This project investigates the evolutionary origins and genetic relationships of Lumpy Skin Disease Virus (LSDV) circulating in South Asia. Using whole-genome sequences from Bangladesh, India, Bhutan, and Pakistan combined with global reference genomes, the study reconstructs a maximum-likelihood phylogeny and computes genetic distances to determine:

1. How South Asian isolates cluster in the global LSDV phylogeny
2. Whether the regional outbreaks emerged from single or multiple introduction events
3. How divergent the lineages are within South Asia compared to global references

🧬 Data Sources

All whole-genome sequences and metadata were collected from:

NCBI Virus Database: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/

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🔧 Software & Tools Used

Command-line tools:

• seqkit v2.x — QC, filtering, header cleaning
• mafft v7.526 — Multiple sequence alignment
• trimal v1.5 — Automated trimming
• iqtree v2 — Model selection + ML tree
• curl + jq — Metadata automated download

R packages:

• ape — Distance matrix, alignment handling
• tidyverse — Data wrangling
• here — File path management

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📦 Reproducibility

All scripts used in analysis are included in the /Documentation and /scripts, directories, including:

• Full project documentation .qmd file
• download_refseqs_curl.sh
• R scripts for distance analysis and metadata management
• QC and alignment commands

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📚 Citation

If using this workflow, you may cite:

Basant Saud (2025). A Phylogenomic Analysis to Trace the Origin of Lumpy Skin Disease Virus (LSDV) in South Asia.

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📝 Contact

For questions or collaboration: Basant Saud Graduate Student, Veterinary Pathology Email: saudbasant.vet@gmail.com GitHub: https://github.com/saudbasant

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