Protocol for next-generation sequencing of the LSD virus genome using an amplicon-based approach

STAR Protoc. 2024 Sep 20;5(3):103020. doi: 10.1016/j.xpro.2024.103020. Epub 2024 Jul 30.

Abstract

Lumpy skin disease (LSD) is a viral disease predominantly affecting cattle caused by a poxvirus belonging to the capripoxvirus genus. Here, we present a protocol for next-generation sequencing of the LSD virus genome using an amplicon-based approach. We describe steps for DNA extraction, viral DNA enrichment, amplicon pooling and purification, and library preparation and pooling. We then detail procedures for sequencing and computational analysis. This protocol can be adapted to any Illumina sequencing platform as an accelerated and scalable system. For complete details on the use and execution of this protocol, please refer to Bhatt et al.1,2.

Keywords: Genomics; bioinformatics; high-throughput screening; sequence analysis; sequencing.

MeSH terms

  • Animals
  • Cattle
  • DNA, Viral / genetics
  • Genome, Viral* / genetics
  • High-Throughput Nucleotide Sequencing* / methods
  • Lumpy Skin Disease / genetics
  • Lumpy Skin Disease / virology
  • Lumpy skin disease virus / genetics
  • Lumpy skin disease virus / isolation & purification
  • Sequence Analysis, DNA / methods

Substances

  • DNA, Viral