Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences
Identifieur interne : 000725 ( Pmc/Curation ); précédent : 000724; suivant : 000726Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences
Auteurs : Jin Il Kim ; Sehee Park ; Joon-Yong Bae ; Man-Seong ParkSource :
- Journal of Veterinary Science [ 1229-845X ] ; 2019.
Abstract
The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.
Url:
DOI: 10.4142/jvs.2019.20.e1
PubMed: 30944524
PubMed Central: 6441811
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences</title><author><name sortKey="Kim, Jin Il" sort="Kim, Jin Il" uniqKey="Kim J" first="Jin Il" last="Kim">Jin Il Kim</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Park, Sehee" sort="Park, Sehee" uniqKey="Park S" first="Sehee" last="Park">Sehee Park</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Bae, Joon Yong" sort="Bae, Joon Yong" uniqKey="Bae J" first="Joon-Yong" last="Bae">Joon-Yong Bae</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Park, Man Seong" sort="Park, Man Seong" uniqKey="Park M" first="Man-Seong" last="Park">Man-Seong Park</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30944524</idno><idno type="pmc">6441811</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441811</idno><idno type="RBID">PMC:6441811</idno><idno type="doi">10.4142/jvs.2019.20.e1</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000725</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000725</idno><idno type="wicri:Area/Pmc/Curation">000725</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000725</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences</title><author><name sortKey="Kim, Jin Il" sort="Kim, Jin Il" uniqKey="Kim J" first="Jin Il" last="Kim">Jin Il Kim</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Park, Sehee" sort="Park, Sehee" uniqKey="Park S" first="Sehee" last="Park">Sehee Park</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Bae, Joon Yong" sort="Bae, Joon Yong" uniqKey="Bae J" first="Joon-Yong" last="Bae">Joon-Yong Bae</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author><author><name sortKey="Park, Man Seong" sort="Park, Man Seong" uniqKey="Park M" first="Man-Seong" last="Park">Man-Seong Park</name><affiliation><nlm:aff id="A1"></nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Veterinary Science</title><idno type="ISSN">1229-845X</idno><idno type="eISSN">1976-555X</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Ji" uniqKey="Kim J">JI Kim</name></author><author><name sortKey="Kim, Yj" uniqKey="Kim Y">YJ Kim</name></author><author><name sortKey="Lemey, P" uniqKey="Lemey P">P Lemey</name></author><author><name sortKey="Lee, I" uniqKey="Lee I">I Lee</name></author><author><name sortKey="Park, S" uniqKey="Park S">S Park</name></author><author><name sortKey="Bae, Jy" uniqKey="Bae J">JY Bae</name></author><author><name sortKey="Kim, D" uniqKey="Kim D">D Kim</name></author><author><name sortKey="Kim, H" uniqKey="Kim H">H Kim</name></author><author><name sortKey="Jang, Si" uniqKey="Jang S">SI Jang</name></author><author><name sortKey="Yang, Js" uniqKey="Yang J">JS 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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Vet Sci</journal-id><journal-id journal-id-type="iso-abbrev">J. Vet. Sci</journal-id><journal-id journal-id-type="publisher-id">JVS</journal-id><journal-title-group><journal-title>Journal of Veterinary Science</journal-title></journal-title-group><issn pub-type="ppub">1229-845X</issn><issn pub-type="epub">1976-555X</issn><publisher><publisher-name>The Korean Society of Veterinary Science</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30944524</article-id><article-id pub-id-type="pmc">6441811</article-id><article-id pub-id-type="doi">10.4142/jvs.2019.20.e1</article-id><article-categories><subj-group subj-group-type="heading"><subject>Short Communication</subject></subj-group></article-categories><title-group><article-title>Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences</article-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0001-8833-2138</contrib-id><name><surname>Kim</surname><given-names>Jin Il</given-names></name><xref ref-type="aff" rid="A1"></xref><xref ref-type="author-notes" rid="FN1">†</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-4799-2241</contrib-id><name><surname>Park</surname><given-names>Sehee</given-names></name><xref ref-type="aff" rid="A1"></xref><xref ref-type="author-notes" rid="FN1">†</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-2483-4208</contrib-id><name><surname>Bae</surname><given-names>Joon-Yong</given-names></name><xref ref-type="aff" rid="A1"></xref></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-7427-486X</contrib-id><name><surname>Park</surname><given-names>Man-Seong</given-names></name><xref ref-type="aff" rid="A1"></xref></contrib></contrib-group><aff id="A1">Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841,<country>Korea</country>.</aff><author-notes><corresp>Corresponding author: Man-Seong Park. Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea. <email>manseong.park@gmail.com</email>; <email>ms0392@korea.ac.kr</email></corresp><fn id="FN1" fn-type="equal"><p><sup>†</sup>The first two authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><month>3</month><year>2019</year></pub-date><pub-date pub-type="epub"><day>19</day><month>2</month><year>2019</year></pub-date><volume>20</volume><issue>2</issue><elocation-id>e1</elocation-id><history><date date-type="received"><day>09</day><month>11</month><year>2018</year></date><date date-type="rev-recd"><day>26</day><month>11</month><year>2018</year></date><date date-type="accepted"><day>16</day><month>12</month><year>2018</year></date></history><permissions><copyright-statement>© 2019 The Korean Society of Veterinary Science</copyright-statement><copyright-year>2019</copyright-year><copyright-holder>The Korean Society of Veterinary Science</copyright-holder><license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by-nc/4.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by-nc/4.0">https://creativecommons.org/licenses/by-nc/4.0</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.</p></abstract><kwd-group kwd-group-type="author"><kwd>Middle East respiratory syndrome coronavirus</kwd><kwd>molecular evolution</kwd><kwd>phylogeny</kwd><kwd>zoonoses</kwd></kwd-group><funding-group><award-group><funding-source><institution-wrap><institution>National Research Foundation of Korea</institution><institution-id institution-id-type="CrossRef">https://doi.org/10.13039/501100003725</institution-id></institution-wrap></funding-source><award-id>NRF-2016M3A9B6916830</award-id></award-group><award-group><funding-source><institution-wrap><institution>Ministry of Health and Welfare</institution><institution-id institution-id-type="CrossRef">https://doi.org/10.13039/501100003625</institution-id></institution-wrap></funding-source><award-id>HI15C2870</award-id></award-group></funding-group></article-meta></front><floats-group><fig id="F1" fig-type="figure" orientation="portrait" position="float"><label>Fig. 1</label><caption><title>Phylogenetic relationship of the complete genes of human and camel MERS-CoV strains. The complete gene sequences of human and camel MERS-CoV strains were evaluated for their evolutionary relationships. Human strain sequences were colored black, whereas camel sequences were colored differently based on their individual distinct groups (camel G1, magenta; G2, sky blue; G3, purple; G4, light green; and G5, orange). The other camel strains not included in the camel G1–G5 groups were colored cantaloupe. The color of each node indicates its posterior probability score (0.0025–1).</title><p>MERS-CoV, Middle East respiratory syndrome coronavirus.</p></caption><graphic xlink:href="jvs-20-e1-g001"></graphic></fig><fig id="F2" fig-type="figure" orientation="portrait" position="float"><label>Fig. 2</label><caption><title>Phylogenetic relationship of the 4a and 4b coding regions of human and camel MERS-CoV strains. The 4a (A) and 4b (B) coding region sequences of human and camel MERS-CoV strains were evaluated for their evolutionary relationships. Human strain sequences were colored black, and camel sequences were colored differently based on their corresponding complete gene sequence group, as indicated and as in <xref ref-type="fig" rid="F1">Fig. 1</xref>. The color of each node indicates its posterior probability score (0.0013–1).</title><p>MERS-CoV, Middle East respiratory syndrome coronavirus.</p></caption><graphic xlink:href="jvs-20-e1-g002"></graphic></fig><table-wrap id="T1" orientation="portrait" position="float"><label>Table 1</label><caption><title>Estimated root years and evolutionary rates of the complete genes and the 4a and 4b coding regions of human and camel MERS-CoV strains</title></caption><alternatives><graphic xlink:href="jvs-20-e1-i001"></graphic><table frame="hsides" rules="rows"><col width="24.86%" span="1"></col><col width="18.78%" span="1"></col><col width="18.78%" span="1"></col><col width="18.78%" span="1"></col><col width="18.78%" span="1"></col><thead><tr><th valign="top" align="left" rowspan="2" colspan="1" style="background-color:rgb(238,248,254)">Gene (coding region)</th><th valign="top" align="center" rowspan="1" colspan="2" style="background-color:rgb(238,248,254)">tMRCA<sup>*</sup> (yr)</th><th valign="top" align="center" rowspan="1" colspan="2" style="background-color:rgb(238,248,254)">Evolutionary rate (10<sup>−3</sup> substitutions/site/yr)</th></tr><tr><th valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">Mean</th><th valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">95% HPD<sup>†</sup></th><th valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">Mean<sup>‡</sup></th><th valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">95% HPD</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">Complete gene</td><td valign="top" align="center" rowspan="1" colspan="1">2009.37</td><td valign="top" align="center" rowspan="1" colspan="1">2006.35–2011.46</td><td valign="top" align="center" rowspan="1" colspan="1">1.42 (0.74)</td><td valign="top" align="center" rowspan="1" colspan="1">1.19–1.72</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">4a</td><td valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">2009.84</td><td valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">2006.67–2011.65</td><td valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">1.89 (1.26)</td><td valign="top" align="center" rowspan="1" colspan="1" style="background-color:rgb(238,248,254)">0.98–3.02</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">4b</td><td valign="top" align="center" rowspan="1" colspan="1">2010.18</td><td valign="top" align="center" rowspan="1" colspan="1">2008.17–2011.83</td><td valign="top" align="center" rowspan="1" colspan="1">1.44 (1.27)</td><td valign="top" align="center" rowspan="1" colspan="1">0.94–2.01</td></tr></tbody></table></alternatives><table-wrap-foot><p>Values are presented as median (interquartile range) or number (%).</p><p>MERS-CoV, Middle East respiratory syndrome coronavirus; tMRCA, time to the most recent common ancestor; HPD, highest posterior density.</p><p><sup>*</sup>The time of most recent common ancestor; <sup>†</sup>Lower and upper limits of 95% highest probability density; <sup>‡</sup>Estimation results reported by Kim et al. [<xref rid="B3" ref-type="bibr">3</xref>] are indicated in parentheses.</p></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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