{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:10:37Z","timestamp":1790759437898,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pntd.0011141","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T00:00:00Z","timestamp":1680739200000}}],"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T00:00:00Z","timestamp":1679875200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"crossref","award":["21-74-20160"],"award-info":[{"award-number":["21-74-20160"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HSE University Basic Research Program"}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>Tick-borne encephalitis virus (TBEV) is a flavivirus which causes an acute or sometimes chronic infection that frequently has severe neurological consequences, and is a major public health threat in Eurasia. TBEV is genetically classified into three distinct subtypes; however, at least one group of isolates, the Baikal subtype, also referred to as \u201c886-84-like\u201d, challenges this classification. Baikal TBEV is a persistent group which has been repeatedly isolated from ticks and small mammals in the Buryat Republic, Irkutsk and Trans-Baikal regions of Russia for several decades. One case of meningoencephalitis with a lethal outcome caused by this subtype has been described in Mongolia in 2010. While recombination is frequent in <jats:italic>Flaviviridae<\/jats:italic>, its role in the evolution of TBEV has not been established. Here, we isolate and sequence four novel Baikal TBEV samples obtained in Eastern Siberia. Using a set of methods for inference of recombination events, including a newly developed phylogenetic method allowing for formal statistical testing for such events in the past, we find robust support for a difference in phylogenetic histories between genomic regions, indicating recombination at origin of the Baikal TBEV. This finding extends our understanding of the role of recombination in the evolution of this human pathogen.<\/jats:p>","DOI":"10.1371\/journal.pntd.0011141","type":"journal-article","created":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T17:31:58Z","timestamp":1679938318000},"page":"e0011141","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["The Baikal subtype of tick-borne encephalitis virus is evident of recombination between Siberian and Far-Eastern subtypes"],"prefix":"10.1371","volume":"17","author":[{"given":"Grigorii A.","family":"Sukhorukov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey I.","family":"Paramonov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oksana V.","family":"Lisak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irina V.","family":"Kozlova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2334-2751","authenticated-orcid":true,"given":"Georgii A.","family":"Bazykin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey D.","family":"Neverov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lyudmila S.","family":"Karan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,3,27]]},"reference":[{"key":"pntd.0011141.ref001","article-title":"Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022).","author":"PJ Walker","year":"2022","journal-title":"Arch Virol"},{"issue":"7","key":"pntd.0011141.ref002","doi-asserted-by":"crossref","first-page":"340","DOI":"10.3390\/v10070340","article-title":"Tick-Borne Flaviviruses and the Type I Interferon Response.","volume":"10","author":"R Lindqvist","year":"2018","journal-title":"Viruses"},{"key":"pntd.0011141.ref003","doi-asserted-by":"crossref","first-page":"298","DOI":"10.3389\/fcimb.2018.00298","article-title":"The Role of Mammalian Reservoir Hosts in Tick-Borne Flavivirus Biology.","volume":"8","author":"L Mlera","year":"2018","journal-title":"Front Cell Infect Microbiol"},{"issue":"2","key":"pntd.0011141.ref004","doi-asserted-by":"crossref","first-page":"453","DOI":"10.20506\/rst.34.2.2371","article-title":"Tick-borne encephalitis.","volume":"34","author":"J.F. Valarcher","year":"2015","journal-title":"Rev Sci Tech Int Off Epizoot"},{"issue":"1","key":"pntd.0011141.ref005","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1099\/0022-1317-80-1-179","article-title":"Sequence analysis and genetic classification of tick-borne encephalitis viruses from Europe and Asia","volume":"80","author":"M Ecker","year":"1999","journal-title":"J Gen Virol"},{"issue":"6","key":"pntd.0011141.ref006","first-page":"6","article-title":"Molecular epidemiology of tick-borne encephalitis","volume":"52","author":"VI Zlobin","year":"2007","journal-title":"Vopr Virusol"},{"key":"pntd.0011141.ref007","article-title":"Tick-borne encephalitis in Japan, Republic of Korea and China Tick-borne encephalitis in Japan, Republic of Korea and China.","volume":"1751","author":"K Yoshii","year":"2019","journal-title":"Nat Publ 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Adelshin","year":"2019","journal-title":"Ticks Tick-Borne Dis"},{"issue":"6","key":"pntd.0011141.ref042","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1002\/jmv.21765","article-title":"Genotyping and characterization of the geographical distribution of tick-borne encephalitis virus variants with a set of molecular probes","volume":"82","author":"TV Demina","year":"2010","journal-title":"J Med Virol"},{"issue":"11","key":"pntd.0011141.ref043","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.3390\/v12111240","article-title":"TBEV Subtyping in Terms of Genetic Distance.","volume":"12","author":"AA Deviatkin","year":"2020","journal-title":"Viruses"},{"issue":"9","key":"pntd.0011141.ref044","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0008133","article-title":"Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses","volume":"14","author":"JJ Clark","year":"2020","journal-title":"PLoS Negl Trop 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