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

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

Rahul C Bhoyar  1 , Bani Jolly  2 , Harie Vignesh  1 , Lenin Bhatt  3 , Vigneshwar Senthivel  2 , Ravi Israni  3 , Vinod Scaria  4 , Sridhar Sivasubbu  5
Affiliations

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

Rahul C Bhoyar et al. STAR Protoc. .

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.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
The quality of the sequencing-ready libraries was confirmed by agarose gel electrophoresis (2%), and the expected band of ∼300 bp size was detected on the gel (L- 100 bp DNA ruler, S1-S8- sequencing-ready libraries)
See this image and copyright information in PMC

References

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    1. Bhatt L., Bhoyar R.C., Jolly B., Israni R., Vignesh H., Scaria V., Sivasubbu S. The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus. Arch. Virol. 2023;168:81. - PubMed
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