A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study
Identifieur interne : 001402 ( Pmc/Checkpoint ); précédent : 001401; suivant : 001403A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study
Auteurs : Grace Ty Chung ; Rossa Wk Chiu ; Jo Lk Cheung ; Yongjie Jin ; Stephen Sc Chim ; Paul Ks Chan ; Ym Dennis LoSource :
- BMC Infectious Diseases [ 1471-2334 ] ; 2005.
Abstract
The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination.
Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing.
Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort.
We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.
The online version of this article (doi:10.1186/1471-2334-5-87) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2334-5-87
PubMed: 16229749
PubMed Central: 1276795
Affiliations:
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Jin</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Centre for Emerging Infectious Diseases,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Department of Chemical Pathology,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Chim, Stephen Sc" sort="Chim, Stephen Sc" uniqKey="Chim S" first="Stephen Sc" last="Chim">Stephen Sc Chim</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Centre for Emerging Infectious Diseases,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Department of Chemical Pathology,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Chan, Paul Ks" sort="Chan, Paul Ks" uniqKey="Chan P" first="Paul Ks" last="Chan">Paul Ks Chan</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id 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institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Centre for Emerging Infectious Diseases,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Department of Chemical Pathology,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</nlm:aff></affiliation></author></analytic><series><title level="j">BMC Infectious Diseases</title><idno type="eISSN">1471-2334</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination.</p></sec><sec><title>Methods</title><p>Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing.</p></sec><sec><title>Results</title><p>Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort.</p></sec><sec><title>Conclusion</title><p>We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2334-5-87) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author><author><name sortKey="Kuiken, T" uniqKey="Kuiken T">T Kuiken</name></author><author><name sortKey="Schutten, M" uniqKey="Schutten M">M Schutten</name></author><author><name sortKey="Van Amerongen, G" uniqKey="Van Amerongen G">G van Amerongen</name></author><author><name sortKey="Van Doornum, Gj" uniqKey="Van Doornum G">GJ van Doornum</name></author><author><name sortKey="Van Den Hoogen, Bg" uniqKey="Van Den Hoogen B">BG van den Hoogen</name></author><author><name sortKey="Peiris, M" uniqKey="Peiris M">M 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article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Infect Dis</journal-id><journal-id journal-id-type="iso-abbrev">BMC Infect. Dis</journal-id><journal-title-group><journal-title>BMC Infectious Diseases</journal-title></journal-title-group><issn pub-type="epub">1471-2334</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">16229749</article-id><article-id pub-id-type="pmc">1276795</article-id><article-id pub-id-type="publisher-id">235</article-id><article-id pub-id-type="doi">10.1186/1471-2334-5-87</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chung</surname><given-names>Grace TY</given-names></name><address><email>gracechung@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Chiu</surname><given-names>Rossa WK</given-names></name><address><email>rossachiu@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Cheung</surname><given-names>Jo LK</given-names></name><address><email>jo.lk.cheung@gmail.com</email></address><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Jin</surname><given-names>Yongjie</given-names></name><address><email>yoyo.jin@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Chim</surname><given-names>Stephen SC</given-names></name><address><email>sschim@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Chan</surname><given-names>Paul KS</given-names></name><address><email>paulkschan@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Lo</surname><given-names>YM Dennis</given-names></name><address><email>loym@cuhk.edu.hk</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Centre for Emerging Infectious Diseases,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Department of Chemical Pathology,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</aff><aff id="Aff3"><label>3</label><institution-wrap><institution-id institution-id-type="GRID">grid.415197.f</institution-id><institution-id institution-id-type="ISNI">0000000417647206</institution-id><institution>Department of Microbiology,</institution><institution>The Chinese University of Hong Kong, Prince of Wales Hospital,</institution></institution-wrap>Hong Kong</aff></contrib-group><pub-date pub-type="epub"><day>18</day><month>10</month><year>2005</year></pub-date><pub-date pub-type="pmc-release"><day>18</day><month>10</month><year>2005</year></pub-date><pub-date pub-type="collection"><year>2005</year></pub-date><volume>5</volume><elocation-id>87</elocation-id><history><date date-type="received"><day>08</day><month>6</month><year>2005</year></date><date date-type="accepted"><day>18</day><month>10</month><year>2005</year></date></history><permissions><copyright-statement>© Chung et al; licensee BioMed Central Ltd. 2005</copyright-statement><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination.</p></sec><sec><title>Methods</title><p>Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing.</p></sec><sec><title>Results</title><p>Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort.</p></sec><sec><title>Conclusion</title><p>We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2334-5-87) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Severe Acute Respiratory Syndrome</kwd><kwd>Single Nucleotide Variation</kwd><kwd>Severe Acute Respiratory Syndrome</kwd><kwd>Deletion Variant</kwd><kwd>Severe Acute Respiratory Syndrome Patient</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2005</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Chan, Paul Ks" sort="Chan, Paul Ks" uniqKey="Chan P" first="Paul Ks" last="Chan">Paul Ks Chan</name><name sortKey="Cheung, Jo Lk" sort="Cheung, Jo Lk" uniqKey="Cheung J" first="Jo Lk" last="Cheung">Jo Lk Cheung</name><name sortKey="Chim, Stephen Sc" sort="Chim, Stephen Sc" uniqKey="Chim S" first="Stephen Sc" last="Chim">Stephen Sc Chim</name><name sortKey="Chiu, Rossa Wk" sort="Chiu, Rossa Wk" uniqKey="Chiu R" first="Rossa Wk" last="Chiu">Rossa Wk Chiu</name><name sortKey="Chung, Grace Ty" sort="Chung, Grace Ty" uniqKey="Chung G" first="Grace Ty" last="Chung">Grace Ty Chung</name><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie Jin</name><name sortKey="Lo, Ym Dennis" sort="Lo, Ym Dennis" uniqKey="Lo Y" first="Ym Dennis" last="Lo">Ym Dennis Lo</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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