{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T12:23:49Z","timestamp":1764937429183,"version":"3.41.2"},"reference-count":26,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,6,28]],"date-time":"2022-06-28T00:00:00Z","timestamp":1656374400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000277","name":"Department for Environment, Food and Rural Affairs, UK Government","doi-asserted-by":"publisher","award":["SE2210"],"award-info":[{"award-number":["SE2210"]}],"id":[{"id":"10.13039\/501100000277","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012095","name":"Scottish Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012095","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015846","name":"Llywodraeth Cymru","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015846","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak <jats:italic>via<\/jats:italic> full genome sequencing will be beneficial.<\/jats:p>","DOI":"10.3389\/fmicb.2022.909396","type":"journal-article","created":{"date-parts":[[2022,6,28]],"date-time":"2022-06-28T07:46:52Z","timestamp":1656402412000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK"],"prefix":"10.3389","volume":"13","author":[{"given":"Rebecca","family":"Strong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen","family":"McCleary","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvia","family":"Grierson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bhudipa","family":"Choudhury","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Falko","family":"Steinbach","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen R.","family":"Crooke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,6,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006885","article-title":"When are pathogen genome sequences informative of transmission events?","author":"Campbell","year":"2018","journal-title":"PLoS Pathog"},{"key":"B3","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1098\/rspb.2007.1442","article-title":"Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus","volume":"275","author":"Cottam","year":"","journal-title":"Proc Biol Sci"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000050","article-title":"Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007","author":"Cottam","year":"","journal-title":"PLoS Pathog"},{"key":"B5","doi-asserted-by":"publisher","first-page":"e99","DOI":"10.1016\/S2666-5247(20)30054-9","article-title":"An integrated national scale SARS-CoV-2 genomic surveillance network","volume":"1","year":"2020","journal-title":"Lancet Microbe"},{"key":"B6","doi-asserted-by":"publisher","first-page":"175","DOI":"10.20506\/rst.35.1.2426","article-title":"Genomics and outbreaks: foot and mouth disease","volume":"35","author":"Freimanis","year":"2016","journal-title":"Rev. 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