Direct repeats in the 3' untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission

Gritsun, T. S.; Gould, E. A.. 2006 Direct repeats in the 3' untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission. Journal of General Virology, 87. 3297-3305.

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Direct repeats (DRs) of 20–45 nucleotide conserved sequences (CS) and repeated CS (RCS), separated by non-conserved sequences up to 100 nucleotides long, were previously described in the 3' untranslated region (3'UTR) of the three major mosquito-borne flavivirus (MBFV) subgroups, represented by Japanese encephalitis virus, Yellow fever virus and Dengue virus. 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'UTR alignment between these highly divergent viruses, based on the concept that deletions and/or insertions, in addition to substitutions, are important drivers of 3'UTR evolution. This ‘robust alignment’ approach demonstrated more extensive homologies in the 3'UTR than had been recognized previously and revealed the presence of similar DRs, either intact or as sequence ‘remnants’, 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.

Item Type: Publication - Article
Digital Object Identifier (DOI):
Programmes: CEH Programmes pre-2009 publications > Biodiversity
UKCEH and CEH Sections/Science Areas: _ Molecular Virology & Parasitology
ISSN: 0022-1317
NORA Subject Terms: Biology and Microbiology
Ecology and Environment
Date made live: 01 May 2008 08:15 +0 (UTC)

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