{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T05:37:45Z","timestamp":1775453865602,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000},"content-version":"vor","delay-in-days":323,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The spread of a severe and often fatal form of lumpy skin disease (LSD) in cattle and water buffaloes has caused widespread mortality and morbidity of these animals in India. To track and understand the genetic changes occurring in the virus and to enable routine surveillance of the virus, multiplexed polymerase chain reaction (PCR) and sequencing methods were developed and validated in this study. Multiplexed nested PCR for LSD virus (LSDV) detection was optimized using skin lesion swabs and nasal samples collected from symptomatic and asymptomatic animals. For genotyping, overlapping PCRs to amplify the entire LSDV genome were developed and tested on field samples collected from the Maharashtra and Odisha states of India. Analysis of LSDV genomes from 41 field samples collected in 2022 and 2023 revealed the presence of highly conserved novel mutations. Phylogenetic analysis shows that a distinct genotype of LSDV has spread across India, which warrants genomic surveillance of the virus in the coming years to track the evolution and transmission of the virus. The non-invasive sample collection, detection, and genotyping methods described in this study can facilitate large-scale surveillance of LSDV in dairy animals.<\/jats:p>","DOI":"10.1093\/ve\/veaf090","type":"journal-article","created":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:56:12Z","timestamp":1763470572000},"source":"Crossref","is-referenced-by-count":3,"title":["Detection and variant characterization of lumpy skin disease virus from dairy cattle in India"],"prefix":"10.1093","volume":"11","author":[{"given":"Manali","family":"Bajpai","sequence":"first","affiliation":[{"name":"Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road , Pune, Maharashtra 411008 ,","place":["India"]},{"name":"Academy of Scientific and Innovative Research (AcSIR) , Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ajinkya","family":"Khilari","sequence":"additional","affiliation":[{"name":"Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road , Pune, Maharashtra 411008 ,","place":["India"]},{"name":"Academy of Scientific and Innovative Research (AcSIR) , Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bhagyashree","family":"Likhitkar","sequence":"additional","affiliation":[{"name":"Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road , Pune, Maharashtra 411008 ,","place":["India"]},{"name":"Academy of Scientific and Innovative Research (AcSIR) , Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pankaj","family":"Musale","sequence":"additional","affiliation":[{"name":"Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road , Pune, Maharashtra 411008 ,","place":["India"]},{"name":"Academy of Scientific and Innovative Research (AcSIR) , Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002 ,","place":["India"]},{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santoshkumar","family":"Jadhav","sequence":"additional","affiliation":[{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Velu","family":"Dhanikachalam","sequence":"additional","affiliation":[{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Payal","family":"Kakramkar","sequence":"additional","affiliation":[{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaustubh","family":"Bhave","sequence":"additional","affiliation":[{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marimuthu","family":"Swaminathan","sequence":"additional","affiliation":[{"name":"Freelance Consultant, Central Research Station, BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune - 412202,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sachin","family":"Joshi","sequence":"additional","affiliation":[{"name":"BAIF Development Research Foundation , BAIF Road, Uruli Kanchan, Pune, Maharashtra 412202 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3341-4846","authenticated-orcid":false,"given":"Dhanasekaran","family":"Shanmugam","sequence":"additional","affiliation":[{"name":"Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road , Pune, Maharashtra 411008 ,","place":["India"]},{"name":"Academy of Scientific and Innovative Research (AcSIR) , Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,11,20]]},"reference":[{"key":"2025120500171005700_ref1","first-page":"6","article-title":"Lumpy skin disease: review of literature","volume":"3","author":"Al-Salihi","year":"2014","journal-title":"Mirror Res Vet Sci Anim"},{"key":"2025120500171005700_ref2","volume-title":"*RAMPART*, Version 1.0.0","author":"Artic Network","year":"2020"},{"key":"2025120500171005700_ref3","doi-asserted-by":"publisher","first-page":"1567","DOI":"10.1038\/s41598-017-01703-6","article-title":"BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing","volume":"7","author":"Au","year":"2017","journal-title":"Sci Rep"},{"key":"2025120500171005700_ref4","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1007\/s00705-023-05705-w","article-title":"The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus","volume":"168","author":"Bhatt","year":"2023","journal-title":"Arch Virol"},{"key":"2025120500171005700_ref5","doi-asserted-by":"publisher","DOI":"10.3390\/v15071471","article-title":"Lumpy skin disease virus genome sequence analysis: putative Spatio-temporal epidemiology, single gene versus whole genome phylogeny and genomic evolution","volume":"15","author":"Breman","year":"2023","journal-title":"Viruses."},{"key":"2025120500171005700_ref6","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics."},{"key":"2025120500171005700_ref7","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2025120500171005700_ref8","doi-asserted-by":"publisher","first-page":"4660","DOI":"10.1038\/s41467-019-12493-y","article-title":"Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing","volume":"10","author":"Edge","year":"2019","journal-title":"Nat Commun"},{"key":"2025120500171005700_ref9","doi-asserted-by":"publisher","first-page":"451","DOI":"10.5455\/OVJ.2022.v12.i4.6","article-title":"Molecular diagnosis of three outbreaks during three successive years (2018, 2019, and 2020) of Lumpy skin disease virus in cattle in Sharkia Governorate","volume":"12","author":"Fawzi","year":"2022","journal-title":"Egypt Open Vet J"},{"key":"2025120500171005700_ref10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae038","article-title":"BCFtools\/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies","volume":"40","author":"Genovese","year":"2024","journal-title":"Bioinformatics"},{"key":"2025120500171005700_ref11","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/s11259-020-09780-1","article-title":"A review: lumpy skin disease and its emergence in India","volume":"44","author":"Gupta","year":"2020","journal-title":"Vet Res Commun"},{"key":"2025120500171005700_ref12","doi-asserted-by":"publisher","first-page":"064","DOI":"10.17352\/ijvsr.000115","article-title":"Epidemiology and diagnostic methods of lumpy skin disease: a short review","volume":"8","author":"Guyassa","year":"2022","journal-title":"Int J Vet Sci Res"},{"key":"2025120500171005700_ref13","doi-asserted-by":"publisher","first-page":"1616","DOI":"10.1002\/vms3.524","article-title":"Lumpy skin disease outbreak in cattle population of Chattogram","volume":"7","author":"Hasib","year":"2021","journal-title":"Bangladesh Vet Med Sci"},{"key":"2025120500171005700_ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.15761\/MCA.1000161","article-title":"Comparative studies on lumpy skin disease virus in human","volume":"3","author":"Kamal","year":"2019","journal-title":"Med Clin Arch"},{"key":"2025120500171005700_ref15","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025120500171005700_ref16","doi-asserted-by":"publisher","first-page":"e0241022","DOI":"10.1371\/journal.pone.0241022","article-title":"Isolation and characterization of lumpy skin disease virus from cattle in India","volume":"16","author":"Kumar","year":"2021","journal-title":"PLoS One"},{"key":"2025120500171005700_ref17","doi-asserted-by":"publisher","first-page":"2190647","DOI":"10.1080\/21505594.2023.2190647","article-title":"Evaluation of the safety, immunogenicity and efficacy of a new live-attenuated lumpy skin disease vaccine in India","volume":"14","author":"Kumar","year":"2023","journal-title":"Virulence"},{"key":"2025120500171005700_ref18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2021\/8862180","article-title":"Molecular characterization of lumpy skin disease virus isolates from outbreak cases in cattle from Sawena District of Bale Zone, Oromia","volume":"2021","author":"Leliso","year":"2021","journal-title":"Ethiopia Vet Med Int"},{"key":"2025120500171005700_ref19","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025120500171005700_ref20","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics."},{"key":"2025120500171005700_ref21","doi-asserted-by":"publisher","first-page":"114464","DOI":"10.1016\/j.jviromet.2022.114464","article-title":"A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses","volume":"301","author":"Mathijs","year":"2022","journal-title":"J Virol Methods"},{"key":"2025120500171005700_ref22","doi-asserted-by":"publisher","DOI":"10.31646\/gbio.187","article-title":"Outbreak of Lumpy skin disease in India 2022-an emerging threat to livestock & livelihoods","volume":"5","author":"Mathivanan","year":"2023","journal-title":"Global Biosecur"},{"key":"2025120500171005700_ref23","doi-asserted-by":"publisher","first-page":"1266759","DOI":"10.3389\/fmicb.2023.1266759","article-title":"Lumpy skin disease: history, current understanding and research gaps in the context of recent geographic expansion","volume":"14","author":"Mazloum","year":"2023","journal-title":"Front Microbiol"},{"key":"2025120500171005700_ref24","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2025120500171005700_ref25","doi-asserted-by":"publisher","first-page":"106485","DOI":"10.1016\/j.micpath.2023.106485","article-title":"Lumpy skin disease: insights into current status and geographical expansion of a transboundary viral disease","volume":"186","author":"Moudgil","year":"2024","journal-title":"Microb Pathog"},{"key":"2025120500171005700_ref26","doi-asserted-by":"crossref","first-page":"535","DOI":"10.4172\/2157-7579.1000535","article-title":"Review: Lumpy skin disease","volume":"9","author":"Mulatu","year":"2018","journal-title":"J Vet Sci Technol"},{"key":"2025120500171005700_ref27","volume-title":"*Guppy Basecaller*, Version 6.1.5","author":"Oxford Nanopore Technologies","year":"2024"},{"key":"2025120500171005700_ref28","volume-title":"*Medaka*, Version 1.8.0","author":"Oxford Nanopore Technologies","year":"2024"},{"key":"2025120500171005700_ref29","doi-asserted-by":"publisher","first-page":"13","DOI":"10.12691\/ajidm-11-1-3","article-title":"Can lumpy skin disease be considered a zoonosis?","volume":"11","author":"Pal","year":"2023","journal-title":"Am J Infect Dis Microbiol"},{"key":"2025120500171005700_ref30","doi-asserted-by":"publisher","first-page":"e0037522","DOI":"10.1128\/mra.00375-22","article-title":"Coding-complete genome sequence of a Lumpy Skin Disease virus isolated during the 2021 Thailand outbreak","volume":"11","author":"Paungpin","year":"2022","journal-title":"Microbiol Resour Announc"},{"key":"2025120500171005700_ref31","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1007\/s11262-023-01967-3","article-title":"First complete genome sequence of lumpy skin disease virus directly from a clinical sample in South India","volume":"59","author":"Putty","year":"2023","journal-title":"Virus Genes"},{"key":"2025120500171005700_ref32","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"Quick","year":"2017","journal-title":"Nat Protoc"},{"key":"2025120500171005700_ref33","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025120500171005700_ref34","doi-asserted-by":"publisher","first-page":"277","DOI":"10.5958\/0973-970X.2023.00051.2","article-title":"Epidemiology of Lumpy skin disease in India-Mini review","volume":"47","author":"Reddy","year":"2023","journal-title":"Indian J Vet Pathol"},{"key":"2025120500171005700_ref35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2016\/6257984","article-title":"Serum biochemistry of lumpy skin disease virus-infected cattle","volume":"2016","author":"\u015eevik","year":"2016","journal-title":"Biomed Res Int"},{"key":"2025120500171005700_ref36","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1111\/tbed.13579","article-title":"Lumpy skin disease (LSD) outbreaks in cattle in Odisha state, India in august 2019: epidemiological features and molecular studies","volume":"67","author":"Sudhakar","year":"2020","journal-title":"Transbound Emerg Dis"},{"key":"2025120500171005700_ref37","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.3201\/eid2907.230043","article-title":"Lumpy skin disease virus infection in free-ranging Indian gazelles (Gazella bennettii), Rajasthan","volume":"29","author":"Sudhakar","year":"2023","journal-title":"India Emerg Infect Dis"},{"key":"2025120500171005700_ref38","doi-asserted-by":"publisher","DOI":"10.1007\/s00705-025-06252-2","article-title":"Genetic characterization of lumpy skin disease virus (LSDV) isolates from an outbreak on Great Nicobar Island, India, in 2022 reveals the involvement of a cluster 2.5 recombinant LSDV strain (East\/Southeast Asian lineage)","volume":"170","author":"Sudhakar","year":"2025","journal-title":"Arch Virol"},{"key":"2025120500171005700_ref39","first-page":"1154","article-title":"A short review on transmission of lumpy skin disease","volume":"12","author":"Thota","year":"2023","journal-title":"Pharm Innov J"},{"key":"2025120500171005700_ref40","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.3390\/vaccines9101136","article-title":"Review: vaccines and vaccination against lumpy skin disease","volume":"9","author":"Tuppurainen","year":"2021","journal-title":"Vaccines (Basel)"},{"key":"2025120500171005700_ref41","article-title":"Book Chapter 28: Capripox (Lumpy skin disease, sheep pox, and goat pox)","author":"","journal-title":"Veterinary Vaccines: Principles and Applications"},{"key":"2025120500171005700_ref42","doi-asserted-by":"publisher","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2014new capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025120500171005700_ref43","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1186\/s12864-024-10061-3","article-title":"Unravelling the genomic origins of lumpy skin disease virus in recent outbreaks","volume":"25","author":"Yadav","year":"2024","journal-title":"BMC Genomics"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaf090\/65408091\/veaf090.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf090\/65408091\/veaf090.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf090\/65408091\/veaf090.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T05:17:21Z","timestamp":1764911841000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaf090\/8329248"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,9]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaf090","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"veaf090"}}