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Article: Coronavirus genomics and bioinformatics analysis

TitleCoronavirus genomics and bioinformatics analysis
Authors
KeywordsBioinformatics
Coronavirus
Genome
Issue Date2010
PublisherMolecular Diversity Preservation International (MDPI) AG.. The Journal's web site is located at http://www.mdpi.com/journal/viruses
Citation
Viruses, 2010, v. 2 n. 8, p. 1805-1820 How to Cite?
AbstractThe drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4×10 -4 to 2×10 -2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses. © 2010 by the authors.
Persistent Identifierhttp://hdl.handle.net/10722/139521
ISSN
2015 Impact Factor: 3.042
2015 SCImago Journal Rankings: 1.873
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
Research Grants Council
University of Hong Kong
Consultancy Service for Enhancing Laboratory Surveillance of Emerging Infectious Disease for the HKSAR Department of Health
Funding Information:

This work was partly supported by a Research Grants Council Grant, The University of Hong Kong and Consultancy Service for Enhancing Laboratory Surveillance of Emerging Infectious Disease for the HKSAR Department of Health.

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorHuang, Yen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2011-09-23T05:51:03Z-
dc.date.available2011-09-23T05:51:03Z-
dc.date.issued2010en_HK
dc.identifier.citationViruses, 2010, v. 2 n. 8, p. 1805-1820en_HK
dc.identifier.issn1999-4915en_HK
dc.identifier.urihttp://hdl.handle.net/10722/139521-
dc.description.abstractThe drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4×10 -4 to 2×10 -2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses. © 2010 by the authors.en_HK
dc.languageengen_US
dc.publisherMolecular Diversity Preservation International (MDPI) AG.. The Journal's web site is located at http://www.mdpi.com/journal/virusesen_HK
dc.relation.ispartofVirusesen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectBioinformaticsen_HK
dc.subjectCoronavirusen_HK
dc.subjectGenomeen_HK
dc.titleCoronavirus genomics and bioinformatics analysisen_HK
dc.typeArticleen_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@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.authorityYuen, KY=rp00366en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.3390/v2081803en_HK
dc.identifier.pmid21994708-
dc.identifier.pmcidPMC3185738-
dc.identifier.scopuseid_2-s2.0-79952156407en_HK
dc.identifier.hkuros195245en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79952156407&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume2en_HK
dc.identifier.issue8en_HK
dc.identifier.spage1805en_HK
dc.identifier.epage1820en_HK
dc.identifier.isiWOS:000282477000020-
dc.publisher.placeSwitzerlanden_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.scopusauthoridHuang, Y=35597414700en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK

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