An amplicon-based approach for fast and scalable genome sequencing of lumpy skin disease virus on benchtop next-generation sequencers

An amplicon-based approach for fast and scalable genome sequencing of lumpy skin disease virus on benchtop next-generation sequencers | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article An amplicon-based approach for fast and scalable genome sequencing of lumpy skin disease virus on benchtop next-generation sequencers Rahul C. Bhoyar, Bani Jolly, Harie Vignesh, Lenin Bhatt, Vigneshwar Senthivel, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-2987962/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract 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 assay 1 . 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 Animal Science Veterinary Epidemiology Bioinformatics Lumpy Skin Disease Lumpy Skin Disease Virus (LSDV) Whole-genome sequencing Illumina Sequencing platform Full Text Supplementary Files Table1LSDVMultiplexPrimers.xlsx LSDV Multiplex Primers Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-2987962","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":204356419,"identity":"deca498d-4d03-48c8-a3c2-c224bcc0c8bf","order_by":0,"name":"Rahul C. 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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. 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