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

Area of Science:

• Veterinary Virology
• Genomics
• Molecular Biology

Background:

• Lumpy Skin Disease (LSD) is a significant viral disease impacting cattle populations globally.
• The causative agent is a poxvirus within the capripoxvirus genus.
• Accurate and efficient viral genome sequencing is crucial for disease surveillance and control.

Purpose of the Study:

• To present a detailed protocol for next-generation sequencing (NGS) of the Lumpy Skin Disease virus (LSDV) genome.
• To establish an amplicon-based approach for accelerated and scalable viral genome analysis.
• To provide a comprehensive guide for researchers working with LSDV and related capripoxviruses.

Main Methods:

• DNA extraction from infected samples.
• Viral DNA enrichment and amplification using an amplicon-based strategy.
• Next-generation sequencing library preparation, pooling, and sequencing.
• Bioinformatic analysis of generated sequence data.

Main Results:

• A robust and reproducible protocol for LSDV genome sequencing was developed.
• The amplicon-based approach facilitates efficient and scalable genomic analysis.
• The protocol is adaptable to various Illumina sequencing platforms.

Conclusions:

• The presented protocol enables rapid and efficient sequencing of the LSDV genome.
• This method supports enhanced surveillance and research into Lumpy Skin Disease.
• The protocol serves as a valuable tool for the molecular characterization of capripoxviruses.