Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.
Identifieur interne : 000609 ( PubMed/Corpus ); précédent : 000608; suivant : 000610Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.
Auteurs : Jing-Wen Ai ; Yi Zhang ; Hao-Cheng Zhang ; Teng Xu ; Wen-Hong ZhangSource :
- Emerging microbes & infections [ 2222-1751 ] ; 2020.
English descriptors
- KwdEn :
- Betacoronavirus (genetics), Betacoronavirus (isolation & purification), Clinical Laboratory Techniques, Coronavirus Infections (diagnosis), Coronavirus Infections (epidemiology), Coronavirus Infections (transmission), Humans, Molecular Diagnostic Techniques, Phylogeny, Pneumonia, Viral (diagnosis), Pneumonia, Viral (epidemiology), Pneumonia, Viral (transmission).
- MESH :
- diagnosis : Coronavirus Infections, Pneumonia, Viral.
- epidemiology : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- isolation & purification : Betacoronavirus.
- transmission : Coronavirus Infections, Pneumonia, Viral.
- Clinical Laboratory Techniques, Humans, Molecular Diagnostic Techniques, Phylogeny.
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.
DOI: 10.1080/22221751.2020.1738905
PubMed: 32174267
Links to Exploration step
pubmed:32174267Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.</title><author><name sortKey="Ai, Jing Wen" sort="Ai, Jing Wen" uniqKey="Ai J" first="Jing-Wen" last="Ai">Jing-Wen Ai</name><affiliation><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yi" sort="Zhang, Yi" uniqKey="Zhang Y" first="Yi" last="Zhang">Yi Zhang</name><affiliation><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></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><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Teng" sort="Xu, Teng" uniqKey="Xu T" first="Teng" last="Xu">Teng Xu</name><affiliation><nlm:affiliation>Vision Medicals Co., Ltd, Guangzhou, People's Republic of China.</nlm:affiliation></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><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32174267</idno><idno type="pmid">32174267</idno><idno type="doi">10.1080/22221751.2020.1738905</idno><idno type="wicri:Area/PubMed/Corpus">000609</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000609</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.</title><author><name sortKey="Ai, Jing Wen" sort="Ai, Jing Wen" uniqKey="Ai J" first="Jing-Wen" last="Ai">Jing-Wen Ai</name><affiliation><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yi" sort="Zhang, Yi" uniqKey="Zhang Y" first="Yi" last="Zhang">Yi Zhang</name><affiliation><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></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><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Teng" sort="Xu, Teng" uniqKey="Xu T" first="Teng" last="Xu">Teng Xu</name><affiliation><nlm:affiliation>Vision Medicals Co., Ltd, Guangzhou, People's Republic of China.</nlm:affiliation></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><nlm:affiliation>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, Shanghai, People's Republic of China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Emerging microbes & infections</title><idno type="eISSN">2222-1751</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Betacoronavirus (genetics)</term><term>Betacoronavirus (isolation & purification)</term><term>Clinical Laboratory Techniques</term><term>Coronavirus Infections (diagnosis)</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (transmission)</term><term>Humans</term><term>Molecular Diagnostic Techniques</term><term>Phylogeny</term><term>Pneumonia, Viral (diagnosis)</term><term>Pneumonia, Viral (epidemiology)</term><term>Pneumonia, Viral (transmission)</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Clinical Laboratory Techniques</term><term>Humans</term><term>Molecular Diagnostic Techniques</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32174267</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>17</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>17</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">2222-1751</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>1</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Emerging microbes & infections</Title><ISOAbbreviation>Emerg Microbes Infect</ISOAbbreviation></Journal><ArticleTitle>Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.</ArticleTitle><Pagination><MedlinePgn>597-600</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/22221751.2020.1738905</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ai</LastName><ForeName>Jing-Wen</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>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, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>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, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Hao-Cheng</ForeName><Initials>HC</Initials><AffiliationInfo><Affiliation>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, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Teng</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Vision Medicals Co., Ltd, Guangzhou, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Wen-Hong</ForeName><Initials>WH</Initials><AffiliationInfo><Affiliation>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, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016422">Letter</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Emerg Microbes Infect</MedlineTA><NlmUniqueID>101594885</NlmUniqueID><ISSNLinking>2222-1751</ISSNLinking></MedlineJournalInfo><SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName><SupplMeshName Type="Protocol" UI="C000657964">COVID-19 diagnostic testing</SupplMeshName><SupplMeshName Type="Organism" UI="C000656484">severe acute respiratory syndrome coronavirus 2</SupplMeshName></SupplMeshList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019411" MajorTopicYN="Y">Clinical Laboratory Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000635" MajorTopicYN="N">transmission</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D025202" MajorTopicYN="N">Molecular Diagnostic Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000635" MajorTopicYN="N">transmission</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">COVID-19</Keyword><Keyword MajorTopicYN="Y">SARS-CoV-2</Keyword><Keyword MajorTopicYN="Y">Unexplained pneumonia</Keyword><Keyword MajorTopicYN="Y">diagnosis</Keyword><Keyword MajorTopicYN="Y">molecular</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32174267</ArticleId><ArticleId IdType="doi">10.1080/22221751.2020.1738905</ArticleId><ArticleId IdType="pmc">PMC7144283</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>N Engl J Med. 2020 Feb 20;382(8):727-733</Citation><ArticleIdList><ArticleId IdType="pubmed">31978945</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>N Engl J Med. 2019 Jun 13;380(24):2327-2340</Citation><ArticleIdList><ArticleId IdType="pubmed">31189036</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2003 Jul 1;31(13):3497-500</Citation><ArticleIdList><ArticleId IdType="pubmed">12824352</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Emerg Microbes Infect. 2020 Dec;9(1):313-319</Citation><ArticleIdList><ArticleId IdType="pubmed">32020836</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>J Clin Microbiol. 2011 Dec;49(12):4083-8</Citation><ArticleIdList><ArticleId IdType="pubmed">21998418</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Lancet. 2020 Feb 15;395(10223):497-506</Citation><ArticleIdList><ArticleId IdType="pubmed">31986264</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>J Med Virol. 2020 Apr;92(4):408-417</Citation><ArticleIdList><ArticleId IdType="pubmed">31944312</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nature. 2020 Mar;579(7798):265-269</Citation><ArticleIdList><ArticleId IdType="pubmed">32015508</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Lancet. 2020 Feb 15;395(10223):514-523</Citation><ArticleIdList><ArticleId IdType="pubmed">31986261</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nature. 2020 Mar;579(7798):270-273</Citation><ArticleIdList><ArticleId IdType="pubmed">32015507</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Mol Biol Evol. 2018 Jun 1;35(6):1547-1549</Citation><ArticleIdList><ArticleId IdType="pubmed">29722887</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000609 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 000609 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= SrasV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:32174267
|texte= Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:32174267" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |