Coronavirus Genomics and Bioinformatics Analysis
Identifieur interne : 002561 ( Main/Exploration ); précédent : 002560; suivant : 002562Coronavirus Genomics and Bioinformatics Analysis
Auteurs : Patrick C. Y. Woo ; Yi Huang ; Susanna K. P. Lau ; Kwok-Yung YuenSource :
- Viruses [ 1999-4915 ] ; 2010.
Abstract
The 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,
Url:
DOI: 10.3390/v2081803
PubMed: 21994708
PubMed Central: 3185738
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Coronavirus Genomics and Bioinformatics Analysis</title><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21994708</idno><idno type="pmc">3185738</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185738</idno><idno type="RBID">PMC:3185738</idno><idno type="doi">10.3390/v2081803</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">001935</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001935</idno><idno type="wicri:Area/Pmc/Curation">001935</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001935</idno><idno type="wicri:Area/Pmc/Checkpoint">000C42</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000C42</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:21994708</idno><idno type="wicri:Area/PubMed/Corpus">001656</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001656</idno><idno type="wicri:Area/PubMed/Curation">001656</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001656</idno><idno type="wicri:Area/PubMed/Checkpoint">001696</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001696</idno><idno type="wicri:Area/Ncbi/Merge">002398</idno><idno type="wicri:Area/Ncbi/Curation">002398</idno><idno type="wicri:Area/Ncbi/Checkpoint">002398</idno><idno type="wicri:Area/Main/Merge">002599</idno><idno type="wicri:Area/Main/Curation">002561</idno><idno type="wicri:Area/Main/Exploration">002561</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Coronavirus Genomics and Bioinformatics Analysis</title><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="af1-viruses-02-01804"> State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; China; E-Mail:<email>kyyuen@hkucc.hku.hk</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-02-01804"> Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af3-viruses-02-01804"> Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong; China</nlm:aff><wicri:noCountry code="subfield">Hong Kong; China</wicri:noCountry></affiliation><affiliation><nlm:aff id="af4-viruses-02-01804"> Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong; China; E-Mail:<email>huangyil@hkucc.hku.hk</email></nlm:aff></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The 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, <italic>Alphacoronavirus</italic>, <italic>Betacoronavirus</italic> and <italic>Gammacoronavirus</italic>, with <italic>Betacoronavirus</italic> consisting of subgroups A, B, C and D, exist. A fourth genus, <italic>Deltacoronavirus</italic>, 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<sup>−4</sup> to 2×10<sup>−2</sup> 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Snijder, Ej" uniqKey="Snijder E">EJ Snijder</name></author><author><name sortKey="Bredenbeek, Pj" uniqKey="Bredenbeek P">PJ Bredenbeek</name></author><author><name sortKey="Dobbe, Jc" uniqKey="Dobbe J">JC Dobbe</name></author><author><name sortKey="Thiel, V" uniqKey="Thiel V">V Thiel</name></author><author><name sortKey="Ziebuhr, J" uniqKey="Ziebuhr J">J Ziebuhr</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y Guan</name></author><author><name sortKey="Rozanov, M" uniqKey="Rozanov M">M Rozanov</name></author><author><name sortKey="Spaan, Wj" 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Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="Woo, Pc" uniqKey="Woo P">PC Woo</name></author><author><name sortKey="Yuen, Ky" uniqKey="Yuen K">KY Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, Pc" uniqKey="Woo P">PC Woo</name></author><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Yuen, Ky" uniqKey="Yuen K">KY Yuen</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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