{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T06:15:53Z","timestamp":1771654553067,"version":"3.50.1"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,26]],"date-time":"2022-08-26T00:00:00Z","timestamp":1661472000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Tick-borne encephalitis virus (TBEV) is one of the most dangerous tick-borne viral pathogens for humans. It can cause severe tick-borne encephalitis (TBE), multiple neurological complications, and death. The European subtype (TBEV-Eu), Siberian subtype (TBEV-Sib), and Far-Eastern subtype (TBEV-FE) are three main TBEV subtypes, causing varying clinical manifestations. Though TBEV-FE is the most virulent TBEV subtype, the degree of variation in the amino acid sequence of TBEV polyprotein is not high, leaving an issue without proper explanation. We performed phylogenic analysis on 243 TBEV strains and then took Senzhang strain as a query strain and representative strains of three major TBEV subtypes as reference strains to perform the comparative genomic analysis, including synteny analysis, SNP analysis, InDel analysis, and multiple sequence alignment of their envelope (E) proteins. The results demonstrated that insertions or deletions of large fragments occurred at the 3\u2019 end but not at the 5\u2019 end or in the CDS region of TBEV Senzhang strain. In addition, SNP sites are mainly located in the CDS region, with few SNP sites in the non-coding region. Our data highlighted the insertions or deletions of large fragments at the 3\u2019 end and SNP sites in the CDS region as genomic properties of the TBEV Senzhang strain compared to representative strains with the main subtypes. These features are probably related to the virulence of the TBEV Senzhang strain and could be considered in future vaccine development and drug target screening for TBEV.<\/jats:p>","DOI":"10.1371\/journal.pone.0273565","type":"journal-article","created":{"date-parts":[[2022,8,26]],"date-time":"2022-08-26T17:49:40Z","timestamp":1661536180000},"page":"e0273565","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["The comparative genomic analysis provides insights into the phylogeny and virulence of tick-borne encephalitis virus vaccine strain Senzhang"],"prefix":"10.1371","volume":"17","author":[{"given":"Meng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingyong","family":"Tian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongying","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6303-8100","authenticated-orcid":true,"given":"Ming","family":"Cang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,8,26]]},"reference":[{"key":"pone.0273565.ref001","doi-asserted-by":"crossref","first-page":"430","DOI":"10.12998\/wjcc.v3.i5.430","article-title":"Tick-borne encephalitis: A review of epidemiology, clinical characteristics, and management","volume":"3","author":"P Bogovic","year":"2015","journal-title":"World J Clin Cases"},{"key":"pone.0273565.ref002","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1111\/ene.13356","article-title":"EAN consensus review on prevention, diagnosis and management of tick-borne encephalitis","volume":"24","author":"P Taba","year":"2017","journal-title":"Eur J Neurol"},{"key":"pone.0273565.ref003","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.meegid.2017.09.014","article-title":"Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history","volume":"55","author":"SY Kovalev","year":"2017","journal-title":"Infect Genet Evol"},{"key":"pone.0273565.ref004","first-page":"74","article-title":"A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau","volume":"7","author":"X Dai","year":"2018","journal-title":"China. 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