{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:54:50Z","timestamp":1791262490201,"version":"4.1.0"},"reference-count":66,"publisher":"Microbiology Society","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,1]]},"abstract":"<jats:p>Direct repeats (DRs) of 20\u201345\u2005nucleotide conserved sequences (CS) and repeated CS (RCS), separated by non-conserved sequences up to 100\u2005nucleotides long, were previously described in the 3\u2032 untranslated region (3\u2032UTR) of the three major mosquito-borne flavivirus (MBFV) subgroups, represented by <jats:italic>Japanese encephalitis virus<\/jats:italic>, <jats:italic>Yellow fever virus<\/jats:italic> and <jats:italic>Dengue virus<\/jats:italic>. Each subgroup exhibits a specific pattern of DRs, the biological significance of which has not yet been adequately addressed. The DRs were originally identified using conventional alignment programs based on the assumption that genetic variation is driven primarily by nucleotide substitutions. Since there are no recognized alignment programs that can adequately accommodate very divergent sequences, a method has been devised to construct and analyse a substantially improved 3\u2032UTR alignment between these highly divergent viruses, based on the concept that deletions and\/or insertions, in addition to substitutions, are important drivers of 3\u2032UTR evolution. This \u2018robust alignment\u2019 approach demonstrated more extensive homologies in the 3\u2032UTR than had been recognized previously and revealed the presence of similar DRs, either intact or as sequence \u2018remnants\u2019, in all the MBFV subgroups. The relevance of these observations is discussed in relation to (i) the function of DRs as elements of replication enhancement, (ii) the evolution of RNA secondary structures and (iii) the significance of DRs and secondary structures in MBFV transmissibility between vertebrate and invertebrate hosts.<\/jats:p>","DOI":"10.1099\/vir.0.82235-0","type":"journal-article","created":{"date-parts":[[2006,10,9]],"date-time":"2006-10-09T21:51:04Z","timestamp":1160430664000},"page":"3297-3305","source":"Crossref","is-referenced-by-count":55,"title":["Direct repeats in the 3\u2032 untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission"],"prefix":"10.1099","volume":"87","author":[{"given":"T. S.","family":"Gritsun","sequence":"first","affiliation":[{"name":"Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. 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