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Article: Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features

TitleComparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features
Authors
Issue Date2007
PublisherAmerican Society for Microbiology. The Journal's web site is located at http://jvi.asm.org/
Citation
Journal Of Virology, 2007, v. 81 n. 4, p. 1574-1585 How to Cite?
Abstract
Twelve complete genomes of three novel coronaviruses - bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d) - were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories. Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Persistent Identifierhttp://hdl.handle.net/10722/78794
ISSN
2013 Impact Factor: 4.648
ISI Accession Number ID
References

 

Author Affiliations
  1. Guangdong Center for Disease Control and Prevention
  2. Research Centre of Infection and Immunology
  3. The University of Hong Kong
DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorWang, Men_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorXu, Hen_HK
dc.contributor.authorPoon, RWSen_HK
dc.contributor.authorGuo, Ren_HK
dc.contributor.authorWong, BHLen_HK
dc.contributor.authorGao, Ken_HK
dc.contributor.authorTsoi, HWen_HK
dc.contributor.authorHuang, Yen_HK
dc.contributor.authorLi, KSMen_HK
dc.contributor.authorLam, CSFen_HK
dc.contributor.authorChan, KHen_HK
dc.contributor.authorZheng, BJen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2010-09-06T07:46:52Z-
dc.date.available2010-09-06T07:46:52Z-
dc.date.issued2007en_HK
dc.identifier.citationJournal Of Virology, 2007, v. 81 n. 4, p. 1574-1585en_HK
dc.identifier.issn0022-538Xen_HK
dc.identifier.urihttp://hdl.handle.net/10722/78794-
dc.description.abstractTwelve complete genomes of three novel coronaviruses - bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d) - were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories. Copyright © 2007, 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.rightsJournal of Virology. Copyright © American Society for Microbiology.en_HK
dc.subject.meshAmino Acid Sequenceen_HK
dc.subject.meshAnimalsen_HK
dc.subject.meshChiroptera - virologyen_HK
dc.subject.meshCoronaviridae - classification - genetics - isolation & purificationen_HK
dc.subject.meshGenome, Viralen_HK
dc.subject.meshMolecular Sequence Dataen_HK
dc.subject.meshNucleic Acid Conformationen_HK
dc.subject.meshOpen Reading Frames - geneticsen_HK
dc.subject.meshPhylogenyen_HK
dc.subject.meshRNA, Viral - chemistryen_HK
dc.subject.meshSequence Alignmenten_HK
dc.subject.meshSpecies Specificityen_HK
dc.titleComparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup featuresen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0022-538X&volume=81&spage=1574&epage=1585&date=2007&atitle=Comparative+analysis+of+twelve+genomes+of+three+novel+group+2c+and+group+2d+coronaviruses+reveals+unique+group+and+subgroup+featuresen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailTsoi, HW:hwtsoi@hkucc.hku.hken_HK
dc.identifier.emailZheng, BJ:bzheng@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.authorityTsoi, HW=rp00439en_HK
dc.identifier.authorityZheng, BJ=rp00353en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1128/JVI.02182-06en_HK
dc.identifier.pmid17121802en_HK
dc.identifier.scopuseid_2-s2.0-33846799478en_HK
dc.identifier.hkuros127780en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33846799478&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume81en_HK
dc.identifier.issue4en_HK
dc.identifier.spage1574en_HK
dc.identifier.epage1585en_HK
dc.identifier.isiWOS:000244241400004-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridWang, M=7406685232en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridXu, H=7407448207en_HK
dc.identifier.scopusauthoridPoon, RWS=9334879200en_HK
dc.identifier.scopusauthoridGuo, R=15839273700en_HK
dc.identifier.scopusauthoridWong, BHL=7402023413en_HK
dc.identifier.scopusauthoridGao, K=36795368400en_HK
dc.identifier.scopusauthoridTsoi, HW=6603822102en_HK
dc.identifier.scopusauthoridHuang, Y=35597414700en_HK
dc.identifier.scopusauthoridLi, KSM=24759122500en_HK
dc.identifier.scopusauthoridLam, CSF=25950267400en_HK
dc.identifier.scopusauthoridChan, KH=7406034307en_HK
dc.identifier.scopusauthoridZheng, BJ=7201780588en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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