Lumpy Skin Disease (LSD) is a viral disease predominantly affecting cattle and caused by a poxvirus belonging to the capripoxvirus genus. LSD is characterized by extensive cutaneous lesions, with severe consequent morbidity and sometimes mortality of the affected animal. Timely diagnosis and control of the spread of infections through measures including vaccination are therefore of great importance in preventing social and economic consequences of the disease. Genomic studies from outbreaks in the past have provided unique insights including the identification of recombinant variants in recent years. Genome sequencing and genomic surveillance of the disease therefore could provide useful insights into the evolution and epidemiology of the virus and could potentially also contribute to the development of diagnostic tools. Previous approaches for genome sequencing of the virus used a variety of approaches including amplicon-based sequencing as well as metagenomic approaches, which are tedious, time-consuming as well as costly. The wide availability of benchtop next-generation sequencing equipment and the application of sequencing-based approaches to enable genomic epidemiology of SARS-CoV-2 at scale, motivated us to create an amplicon-based approach based on the Illumina COVIDSeq assay1. for fast, scalable and cost-effective sequencing of the Lumpy Skin Disease Virus. This protocol is a modification of the previously published COVIDSeq assay 1 and can be adapted to any Illumina sequencing platform as an accelerated and scalable system for quick detection as well as genomic surveillance of LSD.
For complete details on the use and execution of this protocol, please refer to Bhatt et al. (2023).2