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BMC Res Notes. 2016 May 20;9(1):279. doi: 10.1186/s13104-016-2083-6.
The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure.
Vasin AV1,2, Petrova AV3,4, Egorov VV3, Plotnikova MA3, Klotchenko SA3, Karpenko MN4, Kiselev OI3.
Author information
Abstract
BACKGROUND:
Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures.
RESULTS:
We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages.
CONCLUSIONS:
These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle.
KEYWORDS:
Evolution; Influenza A virus; NS gene; Pathogenicity; RNA hairpin; RNA secondary structure
PMID: 27206548 [PubMed - in process] PMCID: PMC4875733 Free PMC Article
The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure.
Vasin AV1,2, Petrova AV3,4, Egorov VV3, Plotnikova MA3, Klotchenko SA3, Karpenko MN4, Kiselev OI3.
Author information
Abstract
BACKGROUND:
Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures.
RESULTS:
We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages.
CONCLUSIONS:
These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle.
KEYWORDS:
Evolution; Influenza A virus; NS gene; Pathogenicity; RNA hairpin; RNA secondary structure
PMID: 27206548 [PubMed - in process] PMCID: PMC4875733 Free PMC Article