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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
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TitleComparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features
 
AuthorsWoo, PCY2 3
Wang, M1
Lau, SKP2 3
Xu, H1
Poon, RWS
Guo, R1
Wong, BHL
Gao, K1
Tsoi, HW
Huang, Y
Li, KSM
Lam, CSF
Chan, KH
Zheng, BJ2 3
Yuen, KY2 3 3
 
Issue Date2007
 
PublisherAmerican Society for Microbiology. The Journal's web site is located at http://jvi.asm.org/
 
CitationJournal Of Virology, 2007, v. 81 n. 4, p. 1574-1585 [How to Cite?]
DOI: http://dx.doi.org/10.1128/JVI.02182-06
 
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.
 
ISSN0022-538X
2012 Impact Factor: 5.076
2012 SCImago Journal Rankings: 2.559
 
DOIhttp://dx.doi.org/10.1128/JVI.02182-06
 
ISI Accession Number IDWOS:000244241400004
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWoo, PCY
 
dc.contributor.authorWang, M
 
dc.contributor.authorLau, SKP
 
dc.contributor.authorXu, H
 
dc.contributor.authorPoon, RWS
 
dc.contributor.authorGuo, R
 
dc.contributor.authorWong, BHL
 
dc.contributor.authorGao, K
 
dc.contributor.authorTsoi, HW
 
dc.contributor.authorHuang, Y
 
dc.contributor.authorLi, KSM
 
dc.contributor.authorLam, CSF
 
dc.contributor.authorChan, KH
 
dc.contributor.authorZheng, BJ
 
dc.contributor.authorYuen, KY
 
dc.date.accessioned2010-09-06T07:46:52Z
 
dc.date.available2010-09-06T07:46:52Z
 
dc.date.issued2007
 
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.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationJournal Of Virology, 2007, v. 81 n. 4, p. 1574-1585 [How to Cite?]
DOI: http://dx.doi.org/10.1128/JVI.02182-06
 
dc.identifier.doihttp://dx.doi.org/10.1128/JVI.02182-06
 
dc.identifier.epage1585
 
dc.identifier.hkuros127780
 
dc.identifier.isiWOS:000244241400004
 
dc.identifier.issn0022-538X
2012 Impact Factor: 5.076
2012 SCImago Journal Rankings: 2.559
 
dc.identifier.issue4
 
dc.identifier.openurl
 
dc.identifier.pmid17121802
 
dc.identifier.scopuseid_2-s2.0-33846799478
 
dc.identifier.spage1574
 
dc.identifier.urihttp://hdl.handle.net/10722/78794
 
dc.identifier.volume81
 
dc.languageeng
 
dc.publisherAmerican Society for Microbiology. The Journal's web site is located at http://jvi.asm.org/
 
dc.publisher.placeUnited States
 
dc.relation.ispartofJournal of Virology
 
dc.relation.referencesReferences in Scopus
 
dc.rightsJournal of Virology. Copyright © American Society for Microbiology.
 
dc.subject.meshAmino Acid Sequence
 
dc.subject.meshAnimals
 
dc.subject.meshChiroptera - virology
 
dc.subject.meshCoronaviridae - classification - genetics - isolation & purification
 
dc.subject.meshGenome, Viral
 
dc.subject.meshMolecular Sequence Data
 
dc.subject.meshNucleic Acid Conformation
 
dc.subject.meshOpen Reading Frames - genetics
 
dc.subject.meshPhylogeny
 
dc.subject.meshRNA, Viral - chemistry
 
dc.subject.meshSequence Alignment
 
dc.subject.meshSpecies Specificity
 
dc.titleComparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features
 
dc.typeArticle
 
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Author Affiliations
  1. Guangdong Center for Disease Control and Prevention
  2. Research Centre of Infection and Immunology
  3. The University of Hong Kong