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Article: Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong

TitleCharacterizing 56 complete SARS-CoV S-gene sequences from Hong Kong
Authors
KeywordsMaximum-likelihood
Neighbour-joining
Phylogenetics
S-gene
SARS-CoV
Single nucleotide variation
Issue Date2007
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcv
Citation
Journal Of Clinical Virology, 2007, v. 38 n. 1, p. 19-26 How to Cite?
AbstractBackground: The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks. Objectives: To characterize complete SARS-CoV S-gene sequences from Hong Kong. Study design: Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March-May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank. Results: The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere. Conclusions: The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples. © 2006 Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/79274
ISSN
2015 Impact Factor: 2.647
2015 SCImago Journal Rankings: 1.503
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorTang, JWen_HK
dc.contributor.authorCheung, JLKen_HK
dc.contributor.authorChu, IMTen_HK
dc.contributor.authorIp, Men_HK
dc.contributor.authorHui, Men_HK
dc.contributor.authorPeiris, Men_HK
dc.contributor.authorChan, PKSen_HK
dc.date.accessioned2010-09-06T07:52:42Z-
dc.date.available2010-09-06T07:52:42Z-
dc.date.issued2007en_HK
dc.identifier.citationJournal Of Clinical Virology, 2007, v. 38 n. 1, p. 19-26en_HK
dc.identifier.issn1386-6532en_HK
dc.identifier.urihttp://hdl.handle.net/10722/79274-
dc.description.abstractBackground: The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks. Objectives: To characterize complete SARS-CoV S-gene sequences from Hong Kong. Study design: Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March-May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank. Results: The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere. Conclusions: The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples. © 2006 Elsevier B.V. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcven_HK
dc.relation.ispartofJournal of Clinical Virologyen_HK
dc.rightsJournal of Clinical Virology. Copyright © Elsevier BV.en_HK
dc.subjectMaximum-likelihooden_HK
dc.subjectNeighbour-joiningen_HK
dc.subjectPhylogeneticsen_HK
dc.subjectS-geneen_HK
dc.subjectSARS-CoVen_HK
dc.subjectSingle nucleotide variationen_HK
dc.titleCharacterizing 56 complete SARS-CoV S-gene sequences from Hong Kongen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1386-6532&volume=38&issue=1&spage=19&epage=26&date=2007&atitle=Characterizing+56+complete+SARS-CoV+S-gene+sequences+from+Hong+Kongen_HK
dc.identifier.emailPeiris, M: malik@hkucc.hku.hken_HK
dc.identifier.authorityPeiris, M=rp00410en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.jcv.2006.10.001en_HK
dc.identifier.pmid17112780-
dc.identifier.scopuseid_2-s2.0-33845346442en_HK
dc.identifier.hkuros134628en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33845346442&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume38en_HK
dc.identifier.issue1en_HK
dc.identifier.spage19en_HK
dc.identifier.epage26en_HK
dc.identifier.isiWOS:000243736900004-
dc.publisher.placeNetherlandsen_HK
dc.identifier.scopusauthoridTang, JW=10341387300en_HK
dc.identifier.scopusauthoridCheung, JLK=7202072287en_HK
dc.identifier.scopusauthoridChu, IMT=7103327448en_HK
dc.identifier.scopusauthoridIp, M=7102423261en_HK
dc.identifier.scopusauthoridHui, M=24075844900en_HK
dc.identifier.scopusauthoridPeiris, M=7005486823en_HK
dc.identifier.scopusauthoridChan, PKS=32067487100en_HK

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