Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned
Identifieur interne : 000262 ( Pmc/Checkpoint ); précédent : 000261; suivant : 000263Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned
Auteurs : Jing-Wen Ai [République populaire de Chine] ; Yi Zhang [République populaire de Chine] ; Hao-Cheng Zhang [République populaire de Chine] ; Teng Xu [République populaire de Chine] ; Wen-Hong Zhang [République populaire de Chine]Source :
- Emerging Microbes & Infections [ 2222-1751 ] ; 2020.
Abstract
Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT–PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.
Url:
DOI: 10.1080/22221751.2020.1738905
PubMed: 32174267
PubMed Central: 7144283
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Zhang</name><affiliation wicri:level="1"><nlm:aff id="AF1"><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hao Cheng" sort="Zhang, Hao Cheng" uniqKey="Zhang H" first="Hao-Cheng" last="Zhang">Hao-Cheng Zhang</name><affiliation wicri:level="1"><nlm:aff id="AF1"><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key 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Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32174267</idno><idno type="pmc">7144283</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144283</idno><idno type="RBID">PMC:7144283</idno><idno type="doi">10.1080/22221751.2020.1738905</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000A84</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A84</idno><idno 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Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Yi" sort="Zhang, Yi" uniqKey="Zhang Y" first="Yi" last="Zhang">Yi Zhang</name><affiliation wicri:level="1"><nlm:aff id="AF1"><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hao Cheng" sort="Zhang, Hao Cheng" uniqKey="Zhang H" first="Hao-Cheng" last="Zhang">Hao-Cheng Zhang</name><affiliation wicri:level="1"><nlm:aff id="AF1"><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Xu, Teng" sort="Xu, Teng" uniqKey="Xu T" first="Teng" last="Xu">Teng Xu</name><affiliation wicri:level="1"><nlm:aff id="AF2"><institution>Vision Medicals Co., Ltd</institution>, Guangzhou,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Wen Hong" sort="Zhang, Wen Hong" uniqKey="Zhang W" first="Wen-Hong" last="Zhang">Wen-Hong Zhang</name><affiliation wicri:level="1"><nlm:aff id="AF1"><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Emerging Microbes & Infections</title><idno type="eISSN">2222-1751</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT–PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhu, N" uniqKey="Zhu N">N Zhu</name></author><author><name sortKey="Zhang, D" uniqKey="Zhang D">D Zhang</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Juan, D" uniqKey="Juan D">D. Juan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Huang, C" uniqKey="Huang C">C Huang</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chenna, R" uniqKey="Chenna R">R Chenna</name></author><author><name sortKey="Sugawara, H" uniqKey="Sugawara H">H Sugawara</name></author><author><name sortKey="Koike, T" uniqKey="Koike T">T Koike</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</name></author><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, N" uniqKey="Zhang N">N Zhang</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, Jf W" uniqKey="Chan J">JF-W Chan</name></author><author><name sortKey="Yuan, S" uniqKey="Yuan S">S Yuan</name></author><author><name sortKey="Kok, K H" uniqKey="Kok K">K-H Kok</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P Zhou</name></author><author><name sortKey="Yang, Xl" uniqKey="Yang X">XL Yang</name></author><author><name sortKey="Wang, Xg" uniqKey="Wang X">XG Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, F" uniqKey="Wu F">F Wu</name></author><author><name sortKey="Zhao, S" uniqKey="Zhao S">S Zhao</name></author><author><name sortKey="Yu, B" uniqKey="Yu B">B Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, L" uniqKey="Chen L">L Chen</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilson, Mr" uniqKey="Wilson M">MR Wilson</name></author><author><name sortKey="Sample, Ha" uniqKey="Sample H">HA Sample</name></author><author><name sortKey="Zorn, Kc" uniqKey="Zorn K">KC Zorn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loeffelholz, Mj" uniqKey="Loeffelholz M">MJ Loeffelholz</name></author><author><name sortKey="Pong, Dl" uniqKey="Pong D">DL Pong</name></author><author><name sortKey="Pyles, Rb" uniqKey="Pyles R">RB Pyles</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="letter"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Emerg Microbes Infect</journal-id><journal-id journal-id-type="iso-abbrev">Emerg Microbes Infect</journal-id><journal-id journal-id-type="publisher-id">TEMI</journal-id><journal-id journal-id-type="publisher-id">temi20</journal-id><journal-title-group><journal-title>Emerging Microbes & Infections</journal-title></journal-title-group><issn pub-type="epub">2222-1751</issn><publisher><publisher-name>Taylor & Francis</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32174267</article-id><article-id pub-id-type="pmc">7144283</article-id><article-id pub-id-type="publisher-id">1738905</article-id><article-id pub-id-type="doi">10.1080/22221751.2020.1738905</article-id><article-categories><subj-group subj-group-type="heading"><subject>Letter</subject></subj-group></article-categories><title-group><article-title>Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned</article-title><alt-title alt-title-type="running-title">Emerging Microbes & Infections</alt-title><alt-title alt-title-type="running-authors">J.-W. Ai et al.</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ai</surname><given-names>Jing-Wen</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yi</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Hao-Cheng</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="author-notes" rid="an1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Teng</given-names></name><xref ref-type="aff" rid="AF2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Wen-Hong</given-names></name><xref ref-type="aff" rid="AF1"><sup>a</sup></xref><xref ref-type="corresp" rid="cor1"><sup>CONTACT</sup></xref></contrib><aff id="AF1"><label>a</label><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai,<country>People’s Republic of China</country></aff><aff id="AF2"><label>b</label><institution>Vision Medicals Co., Ltd</institution>, Guangzhou,<country>People’s Republic of China</country></aff></contrib-group><author-notes><corresp id="cor1"><label>CONTACT</label> Wen-Hong Zhang <email xlink:href="wenhongzhang_hs@126.com">wenhongzhang_hs@126.com</email><institution>Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University</institution>, Shanghai 200040, <country>People’s Republic of China</country></corresp><fn id="an1"><label>*</label><p>These authors contributed equally to this manuscript.</p></fn></author-notes><pub-date pub-type="collection"><year>2020</year></pub-date><pub-date pub-type="epub"><day>16</day><month>3</month><year>2020</year></pub-date><volume>9</volume><issue>1</issue><fpage seq="66">597</fpage><lpage>600</lpage><history><date date-type="received"><day>11</day><month>2</month><year>2020</year></date><date date-type="rev-recd"><day>22</day><month>2</month><year>2020</year></date><date date-type="accepted"><day>24</day><month>2</month><year>2020</year></date></history><permissions><copyright-statement>© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>The Author(s)</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution 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 the original work is properly cited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="TEMI_9_1738905.pdf"></self-uri><abstract><title>ABSTRACT</title><p>Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT–PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.</p></abstract><kwd-group kwd-group-type="author"><title>KEYWORDS</title><kwd>Unexplained pneumonia</kwd><kwd>diagnosis</kwd><kwd>SARS-CoV-2</kwd><kwd>COVID-19</kwd><kwd>molecular</kwd></kwd-group><funding-group><award-group><funding-source><named-content content-type="funder-name">Key Technologies Research and Development Program</named-content><named-content content-type="funder-identifier">10.13039/501100012165</named-content></funding-source><award-id>2018ZX10305-409-001-003</award-id></award-group><funding-statement>This study was supported by Key Technologies Research and Development Program for Infectious Diseases of China under [grant number 2018ZX10305-409-001-003].</funding-statement></funding-group><counts><fig-count count="1"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="13"></ref-count><page-count count="4"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ai, Jing Wen" sort="Ai, Jing Wen" uniqKey="Ai J" first="Jing-Wen" last="Ai">Jing-Wen Ai</name></noRegion><name sortKey="Xu, Teng" sort="Xu, Teng" uniqKey="Xu T" first="Teng" last="Xu">Teng Xu</name><name sortKey="Zhang, Hao Cheng" sort="Zhang, Hao Cheng" uniqKey="Zhang H" first="Hao-Cheng" last="Zhang">Hao-Cheng Zhang</name><name sortKey="Zhang, Wen Hong" sort="Zhang, Wen Hong" uniqKey="Zhang W" first="Wen-Hong" last="Zhang">Wen-Hong Zhang</name><name sortKey="Zhang, Yi" sort="Zhang, Yi" uniqKey="Zhang Y" first="Yi" last="Zhang">Yi Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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