A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study
Identifieur interne : 001213 ( Ncbi/Merge ); précédent : 001212; suivant : 001214A 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.
Descripteurs français
- KwdFr :
- Allèles, Facteurs temps, Gènes viraux (génétique), Génotype, Humains, Phylogénie, Sondes oligonucléotidiques (analyse), Sondes oligonucléotidiques (génétique), Syndrome respiratoire aigu sévère (virologie), Syndrome respiratoire aigu sévère (épidémiologie), Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- analyse : Sondes oligonucléotidiques.
- génétique : Gènes viraux, Sondes oligonucléotidiques, Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- épidémiologie : Syndrome respiratoire aigu sévère.
- Allèles, Facteurs temps, Génotype, Humains, Phylogénie, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Oligonucleotide Probes.
- epidemiology : Severe Acute Respiratory Syndrome.
- genetics : Genes, Viral, Oligonucleotide Probes, SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Alleles, Evolution, Molecular, Genotype, Humans, Phylogeny, Time Factors.
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
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PMC:1276795Le document en format XML
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uniqKey="Chung G" first="Grace Ty" last="Chung">Grace Ty Chung</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="Chiu, Rossa Wk" sort="Chiu, Rossa Wk" uniqKey="Chiu R" first="Rossa Wk" last="Chiu">Rossa Wk 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id="Aff3"><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</nlm:aff></affiliation></author><author><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie 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 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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><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Evolution, Molecular</term><term>Genes, Viral (genetics)</term><term>Genotype</term><term>Humans</term><term>Oligonucleotide Probes (analysis)</term><term>Oligonucleotide Probes (genetics)</term><term>Phylogeny</term><term>SARS Virus (genetics)</term><term>Severe Acute Respiratory Syndrome (epidemiology)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Time Factors</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles</term><term>Facteurs temps</term><term>Gènes viraux (génétique)</term><term>Génotype</term><term>Humains</term><term>Phylogénie</term><term>Sondes oligonucléotidiques (analyse)</term><term>Sondes oligonucléotidiques (génétique)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Syndrome respiratoire aigu sévère (épidémiologie)</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Oligonucleotide Probes</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genes, Viral</term><term>Oligonucleotide Probes</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes viraux</term><term>Sondes oligonucléotidiques</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Evolution, Molecular</term><term>Genotype</term><term>Humans</term><term>Phylogeny</term><term>Time Factors</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Facteurs temps</term><term>Génotype</term><term>Humains</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords></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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pmid="16229749"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study</title><author><name sortKey="Chung, Grace Ty" sort="Chung, Grace Ty" uniqKey="Chung G" first="Grace Ty" last="Chung">Grace Ty Chung</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="Chiu, Rossa Wk" sort="Chiu, Rossa Wk" uniqKey="Chiu R" first="Rossa Wk" last="Chiu">Rossa Wk Chiu</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="Cheung, Jo Lk" sort="Cheung, Jo Lk" uniqKey="Cheung J" first="Jo Lk" last="Cheung">Jo Lk Cheung</name><affiliation><nlm:aff id="Aff3"><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</nlm:aff></affiliation></author><author><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie 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 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="Aff3"><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</nlm:aff></affiliation></author><author><name sortKey="Lo, Ym Dennis" sort="Lo, Ym Dennis" uniqKey="Lo Y" first="Ym Dennis" last="Lo">Ym Dennis Lo</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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">16229749</idno><idno type="pmc">1276795</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276795</idno><idno type="RBID">PMC:1276795</idno><idno type="doi">10.1186/1471-2334-5-87</idno><date when="2005">2005</date><idno type="wicri:Area/Pmc/Corpus">000290</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000290</idno><idno type="wicri:Area/Pmc/Curation">000290</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000290</idno><idno type="wicri:Area/Pmc/Checkpoint">001402</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001402</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study</title><author><name sortKey="Chung, Grace Ty" sort="Chung, Grace Ty" uniqKey="Chung G" first="Grace Ty" last="Chung">Grace Ty Chung</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="Chiu, Rossa Wk" sort="Chiu, Rossa Wk" uniqKey="Chiu R" first="Rossa Wk" last="Chiu">Rossa Wk Chiu</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="Cheung, Jo Lk" sort="Cheung, Jo Lk" uniqKey="Cheung J" first="Jo Lk" last="Cheung">Jo Lk Cheung</name><affiliation><nlm:aff id="Aff3"><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</nlm:aff></affiliation></author><author><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie 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 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="Aff3"><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</nlm:aff></affiliation></author><author><name sortKey="Lo, Ym Dennis" sort="Lo, Ym Dennis" uniqKey="Lo Y" first="Ym Dennis" last="Lo">Ym Dennis Lo</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></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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Lindh</name></author></analytic></biblStruct></listBibl></div1></back></TEI></pmc><pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study.</title><author><name sortKey="Chung, Grace T Y" sort="Chung, Grace T Y" uniqKey="Chung G" first="Grace T Y" last="Chung">Grace T Y. Chung</name><affiliation wicri:level="4"><nlm:affiliation>Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong. gracehung@cuhk.edu.hk</nlm:affiliation><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Chiu, Rossa W K" sort="Chiu, Rossa W K" uniqKey="Chiu R" first="Rossa W K" last="Chiu">Rossa W K. Chiu</name></author><author><name sortKey="Cheung, Jo L K" sort="Cheung, Jo L K" uniqKey="Cheung J" first="Jo L K" last="Cheung">Jo L K. Cheung</name></author><author><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie Jin</name></author><author><name sortKey="Chim, Stephen S C" sort="Chim, Stephen S C" uniqKey="Chim S" first="Stephen S C" last="Chim">Stephen S C. Chim</name></author><author><name sortKey="Chan, Paul K S" sort="Chan, Paul K S" uniqKey="Chan P" first="Paul K S" last="Chan">Paul K S. Chan</name></author><author><name sortKey="Lo, Y M Dennis" sort="Lo, Y M Dennis" uniqKey="Lo Y" first="Y M Dennis" last="Lo">Y M Dennis Lo</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16229749</idno><idno type="pmid">16229749</idno><idno type="doi">10.1186/1471-2334-5-87</idno><idno type="wicri:Area/PubMed/Corpus">002493</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002493</idno><idno type="wicri:Area/PubMed/Curation">002493</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002493</idno><idno type="wicri:Area/PubMed/Checkpoint">002852</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002852</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study.</title><author><name sortKey="Chung, Grace T Y" sort="Chung, Grace T Y" uniqKey="Chung G" first="Grace T Y" last="Chung">Grace T Y. Chung</name><affiliation wicri:level="4"><nlm:affiliation>Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong. gracehung@cuhk.edu.hk</nlm:affiliation><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Chiu, Rossa W K" sort="Chiu, Rossa W K" uniqKey="Chiu R" first="Rossa W K" last="Chiu">Rossa W K. Chiu</name></author><author><name sortKey="Cheung, Jo L K" sort="Cheung, Jo L K" uniqKey="Cheung J" first="Jo L K" last="Cheung">Jo L K. Cheung</name></author><author><name sortKey="Jin, Yongjie" sort="Jin, Yongjie" uniqKey="Jin Y" first="Yongjie" last="Jin">Yongjie Jin</name></author><author><name sortKey="Chim, Stephen S C" sort="Chim, Stephen S C" uniqKey="Chim S" first="Stephen S C" last="Chim">Stephen S C. Chim</name></author><author><name sortKey="Chan, Paul K S" sort="Chan, Paul K S" uniqKey="Chan P" first="Paul K S" last="Chan">Paul K S. Chan</name></author><author><name sortKey="Lo, Y M Dennis" sort="Lo, Y M Dennis" uniqKey="Lo Y" first="Y M Dennis" last="Lo">Y M Dennis Lo</name></author></analytic><series><title level="j">BMC infectious diseases</title><idno type="eISSN">1471-2334</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Evolution, Molecular</term><term>Genes, Viral (genetics)</term><term>Genotype</term><term>Humans</term><term>Oligonucleotide Probes (analysis)</term><term>Oligonucleotide Probes (genetics)</term><term>Phylogeny</term><term>SARS Virus (genetics)</term><term>Severe Acute Respiratory Syndrome (epidemiology)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Time Factors</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles</term><term>Facteurs temps</term><term>Gènes viraux (génétique)</term><term>Génotype</term><term>Humains</term><term>Phylogénie</term><term>Sondes oligonucléotidiques (analyse)</term><term>Sondes oligonucléotidiques (génétique)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Syndrome respiratoire aigu sévère (épidémiologie)</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Oligonucleotide Probes</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genes, Viral</term><term>Oligonucleotide Probes</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes viraux</term><term>Sondes oligonucléotidiques</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Evolution, Molecular</term><term>Genotype</term><term>Humans</term><term>Phylogeny</term><term>Time Factors</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Facteurs temps</term><term>Génotype</term><term>Humains</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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