Mosaic Structure of Human Coronavirus NL63, One Thousand Years of Evolution
Identifieur interne : 001742 ( Ncbi/Merge ); précédent : 001741; suivant : 001743Mosaic Structure of Human Coronavirus NL63, One Thousand Years of Evolution
Auteurs : Krzysztof Pyrc [Pays-Bas] ; Ronald Dijkman [Pays-Bas] ; Lea Deng [Nouvelle-Zélande] ; Maarten F. Jebbink [Pays-Bas] ; Howard A. Ross [Nouvelle-Zélande] ; Ben Berkhout [Pays-Bas] ; Lia Van Der Hoek [Pays-Bas]Source :
- Journal of Molecular Biology [ 0022-2836 ] ; 2006.
Descripteurs français
- KwdFr :
- Algorithmes, Coronavirus (), Coronavirus (génétique), Données de séquences moléculaires, Facteurs temps, Génome viral, Humains, Infections à coronavirus (virologie), Laryngite diphtérique, Phylogénie, RT-PCR, Similitude de séquences d'acides nucléiques, Spécificité d'espèce, Séquence nucléotidique, Évolution biologique.
- MESH :
- génétique : Coronavirus.
- virologie : Infections à coronavirus.
- Algorithmes, Coronavirus, Données de séquences moléculaires, Facteurs temps, Génome viral, Humains, Laryngite diphtérique, Phylogénie, RT-PCR, Similitude de séquences d'acides nucléiques, Spécificité d'espèce, Séquence nucléotidique, Évolution biologique.
English descriptors
- KwdEn :
- Algorithms, Base Sequence, Biological Evolution, Coronavirus (classification), Coronavirus (genetics), Coronavirus Infections (virology), Croup, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Nucleic Acid, Species Specificity, Time Factors.
- MESH :
- classification : Coronavirus.
- genetics : Coronavirus.
- virology : Coronavirus Infections.
- Algorithms, Base Sequence, Biological Evolution, Croup, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Nucleic Acid, Species Specificity, Time Factors.
Abstract
Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be ∼ 3 × 10− 4 substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.
Url:
DOI: 10.1016/j.jmb.2006.09.074
PubMed: 17054987
PubMed Central: 7094706
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<front><div type="abstract" xml:lang="en"><p>Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be ∼ 3 × 10<sup>− 4</sup>
substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.</p>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Mosaic Structure of Human Coronavirus NL63, One Thousand Years of Evolution</title>
<author><name sortKey="Pyrc, Krzysztof" sort="Pyrc, Krzysztof" uniqKey="Pyrc K" first="Krzysztof" last="Pyrc">Krzysztof Pyrc</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
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<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
</affiliation>
</author>
<author><name sortKey="Dijkman, Ronald" sort="Dijkman, Ronald" uniqKey="Dijkman R" first="Ronald" last="Dijkman">Ronald Dijkman</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands</nlm:aff>
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<placeName><settlement type="city">Amsterdam</settlement>
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</author>
<author><name sortKey="Deng, Lea" sort="Deng, Lea" uniqKey="Deng L" first="Lea" last="Deng">Lea Deng</name>
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<wicri:noRegion>Auckland</wicri:noRegion>
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</author>
<author><name sortKey="Jebbink, Maarten F" sort="Jebbink, Maarten F" uniqKey="Jebbink M" first="Maarten F." last="Jebbink">Maarten F. Jebbink</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
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<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
</affiliation>
</author>
<author><name sortKey="Ross, Howard A" sort="Ross, Howard A" uniqKey="Ross H" first="Howard A." last="Ross">Howard A. Ross</name>
<affiliation wicri:level="1"><nlm:aff id="aff2">School of Biological Sciences and Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland, New Zealand</nlm:aff>
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<wicri:regionArea>School of Biological Sciences and Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland</wicri:regionArea>
<wicri:noRegion>Auckland</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name>
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<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam</wicri:regionArea>
<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
</affiliation>
</author>
<author><name sortKey="Van Der Hoek, Lia" sort="Van Der Hoek, Lia" uniqKey="Van Der Hoek L" first="Lia" last="Van Der Hoek">Lia Van Der Hoek</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam</wicri:regionArea>
<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
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</analytic>
<series><title level="j">Journal of Molecular Biology</title>
<idno type="ISSN">0022-2836</idno>
<idno type="eISSN">1089-8638</idno>
<imprint><date when="2006">2006</date>
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<front><div type="abstract" xml:lang="en"><p>Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be ∼ 3 × 10<sup>− 4</sup>
substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.</p>
</div>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Mosaic structure of human coronavirus NL63, one thousand years of evolution.</title>
<author><name sortKey="Pyrc, Krzysztof" sort="Pyrc, Krzysztof" uniqKey="Pyrc K" first="Krzysztof" last="Pyrc">Krzysztof Pyrc</name>
<affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands. k.a.pyrc@amc.uva.nl</nlm:affiliation>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam</wicri:regionArea>
<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
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<author><name sortKey="Dijkman, Ronald" sort="Dijkman, Ronald" uniqKey="Dijkman R" first="Ronald" last="Dijkman">Ronald Dijkman</name>
</author>
<author><name sortKey="Deng, Lea" sort="Deng, Lea" uniqKey="Deng L" first="Lea" last="Deng">Lea Deng</name>
</author>
<author><name sortKey="Jebbink, Maarten F" sort="Jebbink, Maarten F" uniqKey="Jebbink M" first="Maarten F" last="Jebbink">Maarten F. Jebbink</name>
</author>
<author><name sortKey="Ross, Howard A" sort="Ross, Howard A" uniqKey="Ross H" first="Howard A" last="Ross">Howard A. Ross</name>
</author>
<author><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name>
</author>
<author><name sortKey="Van Der Hoek, Lia" sort="Van Der Hoek, Lia" uniqKey="Van Der Hoek L" first="Lia" last="Van Der Hoek">Lia Van Der Hoek</name>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Mosaic structure of human coronavirus NL63, one thousand years of evolution.</title>
<author><name sortKey="Pyrc, Krzysztof" sort="Pyrc, Krzysztof" uniqKey="Pyrc K" first="Krzysztof" last="Pyrc">Krzysztof Pyrc</name>
<affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands. k.a.pyrc@amc.uva.nl</nlm:affiliation>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam</wicri:regionArea>
<placeName><settlement type="city">Amsterdam</settlement>
<region nuts="2" type="province">Hollande-Septentrionale</region>
</placeName>
<orgName type="university">Université d'Amsterdam</orgName>
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</author>
<author><name sortKey="Dijkman, Ronald" sort="Dijkman, Ronald" uniqKey="Dijkman R" first="Ronald" last="Dijkman">Ronald Dijkman</name>
</author>
<author><name sortKey="Deng, Lea" sort="Deng, Lea" uniqKey="Deng L" first="Lea" last="Deng">Lea Deng</name>
</author>
<author><name sortKey="Jebbink, Maarten F" sort="Jebbink, Maarten F" uniqKey="Jebbink M" first="Maarten F" last="Jebbink">Maarten F. Jebbink</name>
</author>
<author><name sortKey="Ross, Howard A" sort="Ross, Howard A" uniqKey="Ross H" first="Howard A" last="Ross">Howard A. Ross</name>
</author>
<author><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name>
</author>
<author><name sortKey="Van Der Hoek, Lia" sort="Van Der Hoek, Lia" uniqKey="Van Der Hoek L" first="Lia" last="Van Der Hoek">Lia Van Der Hoek</name>
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</analytic>
<series><title level="j">Journal of molecular biology</title>
<idno type="ISSN">0022-2836</idno>
<imprint><date when="2006" type="published">2006</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Biological Evolution</term>
<term>Coronavirus (classification)</term>
<term>Coronavirus (genetics)</term>
<term>Coronavirus Infections (virology)</term>
<term>Croup</term>
<term>Genome, Viral</term>
<term>Humans</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Reverse Transcriptase Polymerase Chain Reaction</term>
<term>Sequence Homology, Nucleic Acid</term>
<term>Species Specificity</term>
<term>Time Factors</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Coronavirus ()</term>
<term>Coronavirus (génétique)</term>
<term>Données de séquences moléculaires</term>
<term>Facteurs temps</term>
<term>Génome viral</term>
<term>Humains</term>
<term>Infections à coronavirus (virologie)</term>
<term>Laryngite diphtérique</term>
<term>Phylogénie</term>
<term>RT-PCR</term>
<term>Similitude de séquences d'acides nucléiques</term>
<term>Spécificité d'espèce</term>
<term>Séquence nucléotidique</term>
<term>Évolution biologique</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Biological Evolution</term>
<term>Croup</term>
<term>Genome, Viral</term>
<term>Humans</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Reverse Transcriptase Polymerase Chain Reaction</term>
<term>Sequence Homology, Nucleic Acid</term>
<term>Species Specificity</term>
<term>Time Factors</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Coronavirus</term>
<term>Données de séquences moléculaires</term>
<term>Facteurs temps</term>
<term>Génome viral</term>
<term>Humains</term>
<term>Laryngite diphtérique</term>
<term>Phylogénie</term>
<term>RT-PCR</term>
<term>Similitude de séquences d'acides nucléiques</term>
<term>Spécificité d'espèce</term>
<term>Séquence nucléotidique</term>
<term>Évolution biologique</term>
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<front><div type="abstract" xml:lang="en">Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be approximately 3 x 10(-4) substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.</div>
</front>
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