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Microbiol."],"abstract":"<jats:p>The untranslated region (UTRs) of viral genome are important for viral replication and immune modulation. <jats:italic>Japanese encephalitis virus<\/jats:italic> (JEV) is the most significant cause of epidemic encephalitis worldwide. However, little is known regarding the characterization of the JEV UTRs. Here, systematic analyses of the UTRs of JEVs isolated from a variety of hosts worldwide spanning about 80 years were made. All the important <jats:italic>cis<\/jats:italic>-acting elements and structures were compared with other mosquito-borne <jats:italic>Flaviviruses<\/jats:italic> [<jats:italic>West Nile virus<\/jats:italic> (WNV), <jats:italic>Yellow fever virus<\/jats:italic> (YFV), <jats:italic>Zika virus<\/jats:italic> (ZIKV), <jats:italic>Dengue virus<\/jats:italic> (DENV)] and annotated in detail in the UTRs of different JEV genotypes. Our findings identified the JEV-specific structure and the sequence motif with unique JEV feature. (i) The 3\u2019 dbsHP was identified as a small hairpin located in the DB region in the 3\u2032 UTR of JEV, with the structure highly conserved among the JEV genotypes. (ii) The spacer sequence UARs of JEV consist of four discrete spacer sequences, whereas the UARs of other mosquito-borne <jats:italic>Flaviviruses<\/jats:italic> are continuous sequences. In addition, repetitive elements have been discovered in the UTRs of mosquito-borne <jats:italic>Flaviviruses<\/jats:italic>. The lengths, locations, and numbers of the repetitive elements of JEV also differed from other <jats:italic>Flaviviruses<\/jats:italic> (WNV, YFV, ZIKV, DENV). A 300 nt-length region located at the beginning of the 3\u2032 UTR exhibited significant genotypic specificity. This study lays the basis for future research on the relationships between the JEV specific structures and elements in the UTRs, and their important biological function.<\/jats:p>","DOI":"10.3389\/fmicb.2021.730045","type":"journal-article","created":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T08:59:35Z","timestamp":1635411575000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":14,"title":["The 5\u2032 and 3\u2032 Untranslated Regions of the Japanese Encephalitis Virus (JEV): Molecular Genetics and Higher Order Structures"],"prefix":"10.3389","volume":"12","author":[{"given":"Hong","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuzhen","family":"Niu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guodong","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,10,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"6631","DOI":"10.1128\/JVI.79.11.6631-6643.2005","article-title":"Long-range RNA-RNA interactions circularize the dengue virus genome.","volume":"79","author":"Alvarez","year":"2005","journal-title":"J. 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