Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece
Identifieur interne : 000E13 ( Pmc/Checkpoint ); précédent : 000E12; suivant : 000E14Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece
Auteurs : Athanasios Kossyvakis [Grèce] ; Ying Tao [États-Unis] ; Xiaoyan Lu [États-Unis] ; Vasiliki Pogka [Grèce] ; Sotirios Tsiodras [Grèce] ; Mary Emmanouil [Grèce] ; Andreas F. Mentis [Grèce] ; Suxiang Tong [États-Unis] ; Dean D. Erdman [États-Unis] ; Antonios Antoniadis [Grèce]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV) infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1st and 2nd day of patient hospitalization and tested using two real-time RT-PCR (rRT-PCR) assays targeting the UpE and Orf-1a regions of the MERS-CoV genome and RT-PCR and partial sequencing of RNA-dependent RNA polymerase and nucleocapsid genes. Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient’s history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.
Url:
DOI: 10.1371/journal.pone.0125809
PubMed: 25919137
PubMed Central: 4412533
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV) infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1<sup>st</sup>
and 2<sup>nd</sup>
day of patient hospitalization and tested using two real-time RT-PCR (rRT-PCR) assays targeting the UpE and Orf-1a regions of the MERS-CoV genome and RT-PCR and partial sequencing of RNA-dependent RNA polymerase and nucleocapsid genes. Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient’s history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.</p>
</div>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25919137</article-id>
<article-id pub-id-type="pmc">4412533</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0125809</article-id>
<article-id pub-id-type="publisher-id">PONE-D-14-51143</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Laboratory Investigation and Phylogenetic Analysis of an Imported Middle East Respiratory Syndrome Coronavirus Case in Greece</article-title>
<alt-title alt-title-type="running-head">Virological Analysis of a MERS-CoV Case</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kossyvakis</surname>
<given-names>Athanasios</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tao</surname>
<given-names>Ying</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lu</surname>
<given-names>Xiaoyan</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pogka</surname>
<given-names>Vasiliki</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tsiodras</surname>
<given-names>Sotirios</given-names>
</name>
<xref ref-type="aff" rid="aff003"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Emmanouil</surname>
<given-names>Mary</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mentis</surname>
<given-names>Andreas F.</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref rid="cor001" ref-type="corresp">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tong</surname>
<given-names>Suxiang</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Erdman</surname>
<given-names>Dean D.</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Antoniadis</surname>
<given-names>Antonios</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label>
<addr-line>National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, Athens, Greece</addr-line>
</aff>
<aff id="aff002"><label>2</label>
<addr-line>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America</addr-line>
</aff>
<aff id="aff003"><label>3</label>
<addr-line>Department of Epidemiological Surveillance and Intervention, Hellenic Centre for Disease Control and Prevention, Athens, Greece</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Vasilakis</surname>
<given-names>Nikos</given-names>
</name>
<role>Academic Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>University of Texas Medical Branch, UNITED STATES</addr-line>
</aff>
<author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: AK ME AM DE. Performed the experiments: AK YT XL VP ME. Analyzed the data: AK YT XL VP ST ME AM ST DE. Contributed reagents/materials/analysis tools: AA DE AM. Wrote the paper: AK YT XL VP ST ME AM ST DE AA. Decision to share specimens for testing: AM AA.</p>
</fn>
<corresp id="cor001">* E-mail: <email>mentis@pasteur.gr</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>28</day>
<month>4</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<volume>10</volume>
<issue>4</issue>
<elocation-id>e0125809</elocation-id>
<history><date date-type="received"><day>21</day>
<month>11</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>12</day>
<month>3</month>
<year>2015</year>
</date>
</history>
<permissions><license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0125809.pdf"></self-uri>
<abstract><p>Rapid and reliable laboratory diagnosis of persons suspected of Middle East respiratory syndrome coronavirus (MERS-CoV) infection is important for timely implementation of infection control practices and disease management. In addition, monitoring molecular changes in the virus can help elucidate chains of transmission and identify mutations that might influence virus transmission efficiency. This was illustrated by a recent laboratory investigation we conducted on an imported MERS-CoV case in Greece. Two oropharyngeal swab specimens were collected on the 1<sup>st</sup>
and 2<sup>nd</sup>
day of patient hospitalization and tested using two real-time RT-PCR (rRT-PCR) assays targeting the UpE and Orf-1a regions of the MERS-CoV genome and RT-PCR and partial sequencing of RNA-dependent RNA polymerase and nucleocapsid genes. Serum specimens were also collected and serological test were performed. Results from the first swab sample were inconclusive while the second swab was strongly positive for MERS-CoV RNA by rRT-PCR and confirmed positive by RT-PCR and partial gene sequencing. Positive serologic test results further confirmed MERS-CoV infection. Full-length nucleocapsid and spike gene coding sequences were later obtained from the positive swab sample. Phylogenetic analysis revealed that the virus was closely related to recent human-derived MERS-CoV strains obtained in Jeddah and Makkah, Saudi Arabia, in April 2014 and dromedary camels in Saudi Arabia and Qatar. These findings were consistent with the patient’s history. We also identified a unique amino acid substitution in the spike receptor binding domain that may have implications for receptor binding efficiency. Our initial inconclusive rRT-PCR results highlight the importance of collecting multiple specimens from suspect MERS-CoV cases and particularly specimens from the lower respiratory tract.</p>
</abstract>
<funding-group><funding-statement>These authors have no support or funding to report.</funding-statement>
</funding-group>
<counts><fig-count count="1"></fig-count>
<table-count count="0"></table-count>
<page-count count="6"></page-count>
</counts>
<custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name>
<meta-value>All relevant data are within the paper.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes><title>Data Availability</title>
<p>All relevant data are within the paper.</p>
</notes>
</front>
</pmc>
<affiliations><list><country><li>Grèce</li>
<li>États-Unis</li>
</country>
<region><li>Attique (région)</li>
<li>Géorgie (États-Unis)</li>
</region>
<settlement><li>Athènes</li>
</settlement>
</list>
<tree><country name="Grèce"><region name="Attique (région)"><name sortKey="Kossyvakis, Athanasios" sort="Kossyvakis, Athanasios" uniqKey="Kossyvakis A" first="Athanasios" last="Kossyvakis">Athanasios Kossyvakis</name>
</region>
<name sortKey="Antoniadis, Antonios" sort="Antoniadis, Antonios" uniqKey="Antoniadis A" first="Antonios" last="Antoniadis">Antonios Antoniadis</name>
<name sortKey="Emmanouil, Mary" sort="Emmanouil, Mary" uniqKey="Emmanouil M" first="Mary" last="Emmanouil">Mary Emmanouil</name>
<name sortKey="Mentis, Andreas F" sort="Mentis, Andreas F" uniqKey="Mentis A" first="Andreas F." last="Mentis">Andreas F. Mentis</name>
<name sortKey="Pogka, Vasiliki" sort="Pogka, Vasiliki" uniqKey="Pogka V" first="Vasiliki" last="Pogka">Vasiliki Pogka</name>
<name sortKey="Tsiodras, Sotirios" sort="Tsiodras, Sotirios" uniqKey="Tsiodras S" first="Sotirios" last="Tsiodras">Sotirios Tsiodras</name>
</country>
<country name="États-Unis"><region name="Géorgie (États-Unis)"><name sortKey="Tao, Ying" sort="Tao, Ying" uniqKey="Tao Y" first="Ying" last="Tao">Ying Tao</name>
</region>
<name sortKey="Erdman, Dean D" sort="Erdman, Dean D" uniqKey="Erdman D" first="Dean D." last="Erdman">Dean D. Erdman</name>
<name sortKey="Lu, Xiaoyan" sort="Lu, Xiaoyan" uniqKey="Lu X" first="Xiaoyan" last="Lu">Xiaoyan Lu</name>
<name sortKey="Tong, Suxiang" sort="Tong, Suxiang" uniqKey="Tong S" first="Suxiang" last="Tong">Suxiang Tong</name>
</country>
</tree>
</affiliations>
</record>
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