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Article: Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1

TitleComparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1
Authors
Issue Date2006
PublisherAmerican Society for Microbiology. The Journal's web site is located at http://jvi.asm.org/
Citation
Journal Of Virology, 2006, v. 80 n. 14, p. 7136-7145 How to Cite?
AbstractWe sequenced and compared the complete genomes of 22 strains of coronavirus HKU1 (CoV HKU1) obtained from nasopharyngeal aspirates of patients with respiratory tract infections over a 2-year period. Phylogenetic analysis of 24 putative proteins and polypeptides showed that the 22 CoV HKU1 strains fell into three clusters (genotype A, 13 strains; genotype B, 3 strains and genotype C, 6 strains). However, different phylogenetic relationships among the three clusters were observed in different regions of their genomes. From nsp4 to nsp6, the genotype A strains were clustered with the genotype B strains. For nsp7 and nsp8 and from nsp10 to nsp16, the genotype A strains were clustered with the genotype C strains. From hemagglutinin esterase (HE) to nucleocapsid (N), the genotype B strains were clustered closely with the genotype C strains. Bootscan analysis showed possible recombination between genotypes B and C from nucleotide positions 11500 to 13000, corresponding to the nsp6-nsp7 junction, giving rise to genotype A, and between genotypes A and B from nucleotide positions 21500 to 22500, corresponding to the nsp16-HE junction, giving rise to genotype C. Multiple alignments further narrowed the sites of crossover to a 143-bp region between nucleotide positions 11750 and 11892 and a 29-bp region between nucleotide positions 21502 and 21530. Genome analysis also revealed various numbers of tandem copies of a perfect 30-base acidic tandem repeat (ATR) which encodes NDDEDVVTGD and various numbers and sequences of imperfect repeats in the N terminus of nsp3 inside the acidic domain upstream of papain-like protease 1 among the 22 genomes. All 10 CoV HKU1 strains with incomplete imperfect repeats (1.4 and 4.4) belonged to genotype A. The present study represents the first evidence for natural recombination in coronavirus associated with human infection. Analysis of a single gene is not sufficient for the genotyping of CoV HKU1 strains but requires amplification and sequencing of at least two gene loci, one from nsp10 to nsp16 (e.g., pol or helicase) and another from HE to N (e.g., spike or N). Further studies will delineate whether the ATR is useful for the molecular typing of CoV HKU1. Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Persistent Identifierhttp://hdl.handle.net/10722/54323
ISSN
2015 Impact Factor: 4.606
2015 SCImago Journal Rankings: 3.347
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYip, CCYen_HK
dc.contributor.authorHuang, Yen_HK
dc.contributor.authorTsoi, HWen_HK
dc.contributor.authorChan, KHen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2009-04-03T07:43:17Z-
dc.date.available2009-04-03T07:43:17Z-
dc.date.issued2006en_HK
dc.identifier.citationJournal Of Virology, 2006, v. 80 n. 14, p. 7136-7145en_HK
dc.identifier.issn0022-538Xen_HK
dc.identifier.urihttp://hdl.handle.net/10722/54323-
dc.description.abstractWe sequenced and compared the complete genomes of 22 strains of coronavirus HKU1 (CoV HKU1) obtained from nasopharyngeal aspirates of patients with respiratory tract infections over a 2-year period. Phylogenetic analysis of 24 putative proteins and polypeptides showed that the 22 CoV HKU1 strains fell into three clusters (genotype A, 13 strains; genotype B, 3 strains and genotype C, 6 strains). However, different phylogenetic relationships among the three clusters were observed in different regions of their genomes. From nsp4 to nsp6, the genotype A strains were clustered with the genotype B strains. For nsp7 and nsp8 and from nsp10 to nsp16, the genotype A strains were clustered with the genotype C strains. From hemagglutinin esterase (HE) to nucleocapsid (N), the genotype B strains were clustered closely with the genotype C strains. Bootscan analysis showed possible recombination between genotypes B and C from nucleotide positions 11500 to 13000, corresponding to the nsp6-nsp7 junction, giving rise to genotype A, and between genotypes A and B from nucleotide positions 21500 to 22500, corresponding to the nsp16-HE junction, giving rise to genotype C. Multiple alignments further narrowed the sites of crossover to a 143-bp region between nucleotide positions 11750 and 11892 and a 29-bp region between nucleotide positions 21502 and 21530. Genome analysis also revealed various numbers of tandem copies of a perfect 30-base acidic tandem repeat (ATR) which encodes NDDEDVVTGD and various numbers and sequences of imperfect repeats in the N terminus of nsp3 inside the acidic domain upstream of papain-like protease 1 among the 22 genomes. All 10 CoV HKU1 strains with incomplete imperfect repeats (1.4 and 4.4) belonged to genotype A. The present study represents the first evidence for natural recombination in coronavirus associated with human infection. Analysis of a single gene is not sufficient for the genotyping of CoV HKU1 strains but requires amplification and sequencing of at least two gene loci, one from nsp10 to nsp16 (e.g., pol or helicase) and another from HE to N (e.g., spike or N). Further studies will delineate whether the ATR is useful for the molecular typing of CoV HKU1. Copyright © 2006, American Society for Microbiology. All Rights Reserved.en_HK
dc.languageengen_HK
dc.publisherAmerican Society for Microbiology. The Journal's web site is located at http://jvi.asm.org/en_HK
dc.relation.ispartofJournal of Virologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsJournal of virology. Copyright © American Society for Microbiology.en_HK
dc.rightsCopyright © American Society for Microbiology, Journal of virology, 2006, v. 80 n. 14, p. 7136-7145en_HK
dc.subject.meshCoronavirus - genetics - isolation & purificationen_HK
dc.subject.meshCoronavirus Infections - geneticsen_HK
dc.subject.meshCrossing Over, Geneticen_HK
dc.subject.meshGenes, Viral/ - geneticsen_HK
dc.subject.meshMultigene Family - geneticsen_HK
dc.titleComparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1en_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0022-538X&volume=80&issue=14&spage=7136&epage=7145&date=2006&atitle=Comparative+analysis+of+22+coronavirus+HKU1+genomes+reveals+a+novel+genotype+and+evidence+of+natural+recombination+in+coronavirus+HKU1en_HK
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hken_HK
dc.identifier.emailYip, CCY: yipcyril@hku.hken_HK
dc.identifier.emailTsoi, HW: hwtsoi@hkucc.hku.hken_HK
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYip, CCY=rp01721en_HK
dc.identifier.authorityTsoi, HW=rp00439en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturepostprinten_HK
dc.identifier.doi10.1128/JVI.00509-06en_HK
dc.identifier.pmid16809319-
dc.identifier.pmcidPMC1489027en_HK
dc.identifier.scopuseid_2-s2.0-33745782272en_HK
dc.identifier.hkuros120597-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33745782272&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume80en_HK
dc.identifier.issue14en_HK
dc.identifier.spage7136en_HK
dc.identifier.epage7145en_HK
dc.identifier.eissn1098-5514-
dc.identifier.isiWOS:000238770000042-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYip, CCY=14016999800en_HK
dc.identifier.scopusauthoridHuang, Y=35597414700en_HK
dc.identifier.scopusauthoridTsoi, HW=6603822102en_HK
dc.identifier.scopusauthoridChan, KH=7406034307en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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