The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure
Identifieur interne : 000396 ( Main/Exploration ); précédent : 000395; suivant : 000397The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure
Auteurs : A. V. Vasin [Russie] ; A. V. Petrova [Russie] ; V. V. Egorov [Russie] ; M. A. Plotnikova [Russie] ; S. A. Klotchenko [Russie] ; M. N. Karpenko [Russie] ; O. I. Kiselev [Russie]Source :
- BMC Research Notes [ 1756-0500 ] ; 2016.
Abstract
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.
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.
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.
The online version of this article (doi:10.1186/s13104-016-2083-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13104-016-2083-6
PubMed: 27206548
PubMed Central: 4875733
Affiliations:
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Kiselev</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27206548</idno><idno type="pmc">4875733</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875733</idno><idno type="RBID">PMC:4875733</idno><idno type="doi">10.1186/s13104-016-2083-6</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000171</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000171</idno><idno type="wicri:Area/Pmc/Curation">000171</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000171</idno><idno type="wicri:Area/Pmc/Checkpoint">000279</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000279</idno><idno type="wicri:Area/Ncbi/Merge">000C77</idno><idno type="wicri:Area/Ncbi/Curation">000C77</idno><idno type="wicri:Area/Ncbi/Checkpoint">000C77</idno><idno type="wicri:Area/Main/Merge">000396</idno><idno type="wicri:Area/Main/Curation">000396</idno><idno type="wicri:Area/Main/Exploration">000396</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure</title><author><name sortKey="Vasin, A V" sort="Vasin, A V" uniqKey="Vasin A" first="A. V." last="Vasin">A. V. Vasin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg</wicri:regionArea><wicri:noRegion>195251 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Petrova, A V" sort="Petrova, A V" uniqKey="Petrova A" first="A. V." last="Petrova">A. V. Petrova</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg</wicri:regionArea><wicri:noRegion>195251 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Egorov, V V" sort="Egorov, V V" uniqKey="Egorov V" first="V. V." last="Egorov">V. V. Egorov</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Plotnikova, M A" sort="Plotnikova, M A" uniqKey="Plotnikova M" first="M. A." last="Plotnikova">M. A. Plotnikova</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Klotchenko, S A" sort="Klotchenko, S A" uniqKey="Klotchenko S" first="S. A." last="Klotchenko">S. A. Klotchenko</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Karpenko, M N" sort="Karpenko, M N" uniqKey="Karpenko M" first="M. N." last="Karpenko">M. N. Karpenko</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg</wicri:regionArea><wicri:noRegion>195251 St-Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Kiselev, O I" sort="Kiselev, O I" uniqKey="Kiselev O" first="O. I." last="Kiselev">O. I. Kiselev</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Research Institute of Influenza, 197376 St-Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Research Institute of Influenza, 197376 St-Petersburg</wicri:regionArea><wicri:noRegion>197376 St-Petersburg</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Research Notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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.</p></sec><sec><title>Results</title><p>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 H1N1<sub>pdm1918</sub> and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages.</p></sec><sec><title>Conclusions</title><p>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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13104-016-2083-6) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Vasin, Av" uniqKey="Vasin A">AV Vasin</name></author><author><name sortKey="Temkina, Oa" uniqKey="Temkina O">OA Temkina</name></author><author><name sortKey="Egorov, Vv" uniqKey="Egorov V">VV Egorov</name></author><author><name sortKey="Klotchenko, Sa" uniqKey="Klotchenko S">SA Klotchenko</name></author><author><name sortKey="Plotnikova, Ma" uniqKey="Plotnikova M">MA 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sortKey="Priore, Sf" uniqKey="Priore S">SF Priore</name></author><author><name sortKey="Moss, Wn" uniqKey="Moss W">WN Moss</name></author><author><name sortKey="Turner, Dh" uniqKey="Turner D">DH Turner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morens, Dm" uniqKey="Morens D">DM Morens</name></author><author><name sortKey="Taubenberger, Jk" uniqKey="Taubenberger J">JK Taubenberger</name></author><author><name sortKey="Harvey, Ha" uniqKey="Harvey H">HA Harvey</name></author><author><name sortKey="Memoli, Mj" uniqKey="Memoli M">MJ Memoli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tisoncik, Jr" uniqKey="Tisoncik J">JR Tisoncik</name></author><author><name sortKey="Korth, Mj" uniqKey="Korth M">MJ Korth</name></author><author><name sortKey="Simmons, Cp" uniqKey="Simmons C">CP Simmons</name></author><author><name sortKey="Farrar, J" uniqKey="Farrar J">J Farrar</name></author><author><name sortKey="Martin, Tr" uniqKey="Martin T">TR Martin</name></author><author><name sortKey="Katze, Mg" uniqKey="Katze M">MG Katze</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Russie</li></country></list><tree><country name="Russie"><noRegion><name sortKey="Vasin, A V" sort="Vasin, A V" uniqKey="Vasin A" first="A. V." last="Vasin">A. V. Vasin</name></noRegion><name sortKey="Egorov, V V" sort="Egorov, V V" uniqKey="Egorov V" first="V. V." last="Egorov">V. V. Egorov</name><name sortKey="Karpenko, M N" sort="Karpenko, M N" uniqKey="Karpenko M" first="M. N." last="Karpenko">M. N. Karpenko</name><name sortKey="Kiselev, O I" sort="Kiselev, O I" uniqKey="Kiselev O" first="O. I." last="Kiselev">O. I. Kiselev</name><name sortKey="Klotchenko, S A" sort="Klotchenko, S A" uniqKey="Klotchenko S" first="S. A." last="Klotchenko">S. A. Klotchenko</name><name sortKey="Petrova, A V" sort="Petrova, A V" uniqKey="Petrova A" first="A. V." last="Petrova">A. V. Petrova</name><name sortKey="Petrova, A V" sort="Petrova, A V" uniqKey="Petrova A" first="A. V." last="Petrova">A. V. Petrova</name><name sortKey="Plotnikova, M A" sort="Plotnikova, M A" uniqKey="Plotnikova M" first="M. A." last="Plotnikova">M. A. Plotnikova</name><name sortKey="Vasin, A V" sort="Vasin, A V" uniqKey="Vasin A" first="A. V." last="Vasin">A. V. 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