The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure
Identifieur interne : 000C77 ( Ncbi/Merge ); précédent : 000C76; suivant : 000C78The 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
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<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>
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<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>
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</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Res Notes</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Res Notes</journal-id>
<journal-title-group><journal-title>BMC Research Notes</journal-title>
</journal-title-group>
<issn pub-type="epub">1756-0500</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27206548</article-id>
<article-id pub-id-type="pmc">4875733</article-id>
<article-id pub-id-type="publisher-id">2083</article-id>
<article-id pub-id-type="doi">10.1186/s13104-016-2083-6</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Short Report</subject>
</subj-group>
</article-categories>
<title-group><article-title>The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Vasin</surname>
<given-names>A. V.</given-names>
</name>
<address><phone>+78124991525</phone>
<email>vasin@influenza.spb.ru</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Petrova</surname>
<given-names>A. V.</given-names>
</name>
<address><email>alexandra.b_05@mail.ru</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Egorov</surname>
<given-names>V. V.</given-names>
</name>
<address><email>toizeg@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Plotnikova</surname>
<given-names>M. A.</given-names>
</name>
<address><email>biomalinka@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Klotchenko</surname>
<given-names>S. A.</given-names>
</name>
<address><email>klocha@list.ru</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Karpenko</surname>
<given-names>M. N.</given-names>
</name>
<address><email>mnkarpenko@mail.ru</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kiselev</surname>
<given-names>O. I.</given-names>
</name>
<address><email>office@influenza.spb.ru</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<aff id="Aff1"><label></label>
Research Institute of Influenza, 197376 St-Petersburg, Russia</aff>
<aff id="Aff2"><label></label>
Peter the Great St-Petersburg Polytechnic University, 195251 St-Petersburg, Russia</aff>
</contrib-group>
<pub-date pub-type="epub"><day>20</day>
<month>5</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>20</day>
<month>5</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><year>2016</year>
</pub-date>
<volume>9</volume>
<elocation-id>279</elocation-id>
<history><date date-type="received"><day>18</day>
<month>12</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>10</day>
<month>5</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s). 2016</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><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>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Influenza A virus</kwd>
<kwd>RNA secondary structure</kwd>
<kwd>RNA hairpin</kwd>
<kwd>Pathogenicity</kwd>
<kwd>NS gene</kwd>
<kwd>Evolution</kwd>
</kwd-group>
<funding-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100006769</institution-id>
<institution>Russian Science Foundation</institution>
</institution-wrap>
</funding-source>
<award-id>15-15-00170</award-id>
</award-group>
</funding-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2016</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<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. Vasin</name>
</country>
</tree>
</affiliations>
</record>
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