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
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
2011 Impact Factor: 5.402
2011 SCImago Journal Rankings: 0.745
DOIhttp://dx.doi.org/10.1128/JVI.02182-06
ISI Accession Number IDWOS:000244241400004
ReferencesReferences in Scopus
DC Field
Value
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
2011 Impact Factor: 5.402
2011 SCImago Journal Rankings: 0.745
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
Author Affiliations
  1. Guangdong Center for Disease Control and Prevention
  2. The University of Hong Kong
  3. Research Centre of Infection and Immunology