The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39).
Identifieur interne : 005D47 ( Main/Exploration ); précédent : 005D46; suivant : 005D48The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39).
Auteurs : F Y Zeng ; C W M. Chan ; M N Chan ; J D Chen ; K Y C. Chow ; C C Hon ; K H Hui ; J. Li ; V Y Y. Li ; C Y Wang ; P Y Wang ; Y. Guan ; B. Zheng ; L L M. Poon ; K H Chan ; K Y Yuen ; J S M. Peiris ; F C LeungSource :
- Experimental biology and medicine (Maywood, N.J.) [ 1535-3702 ] ; 2003.
Descripteurs français
- KwdFr :
- ADN complémentaire (génétique), ARN viral (génétique), Analyse de séquence d'ADN, Cadres ouverts de lecture, Données de séquences moléculaires, Génome viral, Phylogénie, Protéines virales (), Protéines virales (génétique), Régions 3' non traduites (génétique), Régions 5' non traduites (génétique), Similitude de séquences d'acides aminés, Syndrome respiratoire aigu sévère (virologie), Séquence conservée, Séquence d'acides aminés, Séquence nucléotidique, Techniques d'amplification d'acides nucléiques (), Transcription génétique, Virus du SRAS (), Virus du SRAS (génétique).
- MESH :
- génétique : ADN complémentaire, ARN viral, Protéines virales, Régions 3' non traduites, Régions 5' non traduites, Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- Analyse de séquence d'ADN, Cadres ouverts de lecture, Données de séquences moléculaires, Génome viral, Phylogénie, Protéines virales, Similitude de séquences d'acides aminés, Séquence conservée, Séquence d'acides aminés, Séquence nucléotidique, Techniques d'amplification d'acides nucléiques, Transcription génétique, Virus du SRAS.
English descriptors
- KwdEn :
- 3' Untranslated Regions (genetics), 5' Untranslated Regions (genetics), Amino Acid Sequence, Base Sequence, Conserved Sequence, DNA, Complementary (genetics), Genome, Viral, Molecular Sequence Data, Nucleic Acid Amplification Techniques (methods), Open Reading Frames, Phylogeny, RNA, Viral (genetics), SARS Virus (classification), SARS Virus (genetics), Sequence Analysis, DNA, Sequence Homology, Amino Acid, Severe Acute Respiratory Syndrome (virology), Transcription, Genetic, Viral Proteins (chemistry), Viral Proteins (genetics).
- MESH :
- chemical , chemistry : Viral Proteins.
- chemical , genetics : 3' Untranslated Regions, 5' Untranslated Regions, DNA, Complementary, RNA, Viral, Viral Proteins.
- classification : SARS Virus.
- genetics : SARS Virus.
- methods : Nucleic Acid Amplification Techniques.
- virology : Severe Acute Respiratory Syndrome.
- Amino Acid Sequence, Base Sequence, Conserved Sequence, Genome, Viral, Molecular Sequence Data, Open Reading Frames, Phylogeny, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription, Genetic.
Abstract
The complete genomic nucleotide sequence (29.7kb) of a Hong Kong severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) strain HK-39 is determined. Phylogenetic analysis of the genomic sequence reveals it to be a distinct member of the Coronaviridae family. 5' RACE assay confirms the presence of at least six subgenomic transcripts all containing the predicted intergenic sequences. Five open reading frames (ORFs), namely ORF1a, 1b, S, M, and N, are found to be homologues to other CoV members, and three more unknown ORFs (X1, X2, and X3) are unparalleled in all other known CoV species. Optimal alignment and computer analysis of the homologous ORFs has predicted the characteristic structural and functional domains on the putative genes. The overall nucleotides conservation of the homologous ORFs is low (<5%) compared with other known CoVs, implying that HK-39 is a newly emergent SARS-CoV phylogenetically distant from other known members. SimPlot analysis supports this finding, and also suggests that this novel virus is not a product of a recent recombinant from any of the known characterized CoVs. Together, these results confirm that HK-39 is a novel and distinct member of the Coronaviridae family, with unknown origin. The completion of the genomic sequence of the virus will assist in tracing its origin.
DOI: 10.1177/15353702-0322807-13
PubMed: 12876307
Affiliations:
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Le document en format XML
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Chan</name></author><author><name sortKey="Chan, M N" sort="Chan, M N" uniqKey="Chan M" first="M N" last="Chan">M N Chan</name></author><author><name sortKey="Chen, J D" sort="Chen, J D" uniqKey="Chen J" first="J D" last="Chen">J D Chen</name></author><author><name sortKey="Chow, K Y C" sort="Chow, K Y C" uniqKey="Chow K" first="K Y C" last="Chow">K Y C. Chow</name></author><author><name sortKey="Hon, C C" sort="Hon, C C" uniqKey="Hon C" first="C C" last="Hon">C C Hon</name></author><author><name sortKey="Hui, K H" sort="Hui, K H" uniqKey="Hui K" first="K H" last="Hui">K H Hui</name></author><author><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name></author><author><name sortKey="Li, V Y Y" sort="Li, V Y Y" uniqKey="Li V" first="V Y Y" last="Li">V Y Y. Li</name></author><author><name sortKey="Wang, C Y" sort="Wang, C Y" uniqKey="Wang C" first="C Y" last="Wang">C Y Wang</name></author><author><name sortKey="Wang, P Y" sort="Wang, P Y" uniqKey="Wang P" first="P Y" last="Wang">P Y Wang</name></author><author><name sortKey="Guan, Y" sort="Guan, Y" uniqKey="Guan Y" first="Y" last="Guan">Y. Guan</name></author><author><name sortKey="Zheng, B" sort="Zheng, B" uniqKey="Zheng B" first="B" last="Zheng">B. Zheng</name></author><author><name sortKey="Poon, L L M" sort="Poon, L L M" uniqKey="Poon L" first="L L M" last="Poon">L L M. Poon</name></author><author><name sortKey="Chan, K H" sort="Chan, K H" uniqKey="Chan K" first="K H" last="Chan">K H Chan</name></author><author><name sortKey="Yuen, K Y" sort="Yuen, K Y" uniqKey="Yuen K" first="K Y" last="Yuen">K Y Yuen</name></author><author><name sortKey="Peiris, J S M" sort="Peiris, J S M" uniqKey="Peiris J" first="J S M" last="Peiris">J S M. Peiris</name></author><author><name sortKey="Leung, F C" sort="Leung, F C" uniqKey="Leung F" first="F C" last="Leung">F C Leung</name></author></analytic><series><title level="j">Experimental biology and medicine (Maywood, N.J.)</title><idno type="ISSN">1535-3702</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>3' Untranslated Regions (genetics)</term><term>5' Untranslated Regions (genetics)</term><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Conserved Sequence</term><term>DNA, Complementary (genetics)</term><term>Genome, Viral</term><term>Molecular Sequence Data</term><term>Nucleic Acid Amplification Techniques (methods)</term><term>Open Reading Frames</term><term>Phylogeny</term><term>RNA, Viral (genetics)</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>Sequence Analysis, DNA</term><term>Sequence Homology, Amino Acid</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Transcription, Genetic</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (génétique)</term><term>ARN viral (génétique)</term><term>Analyse de séquence d'ADN</term><term>Cadres ouverts de lecture</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Phylogénie</term><term>Protéines virales ()</term><term>Protéines virales (génétique)</term><term>Régions 3' non traduites (génétique)</term><term>Régions 5' non traduites (génétique)</term><term>Similitude de séquences d'acides aminés</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Séquence conservée</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Techniques d'amplification d'acides nucléiques ()</term><term>Transcription génétique</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>3' Untranslated Regions</term><term>5' Untranslated Regions</term><term>DNA, Complementary</term><term>RNA, Viral</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term><term>ARN viral</term><term>Protéines virales</term><term>Régions 3' non traduites</term><term>Régions 5' non traduites</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Nucleic Acid Amplification Techniques</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Conserved Sequence</term><term>Genome, Viral</term><term>Molecular Sequence Data</term><term>Open Reading Frames</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Sequence Homology, Amino Acid</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cadres ouverts de lecture</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Phylogénie</term><term>Protéines virales</term><term>Similitude de séquences d'acides aminés</term><term>Séquence conservée</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Techniques d'amplification d'acides nucléiques</term><term>Transcription génétique</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The complete genomic nucleotide sequence (29.7kb) of a Hong Kong severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) strain HK-39 is determined. Phylogenetic analysis of the genomic sequence reveals it to be a distinct member of the Coronaviridae family. 5' RACE assay confirms the presence of at least six subgenomic transcripts all containing the predicted intergenic sequences. Five open reading frames (ORFs), namely ORF1a, 1b, S, M, and N, are found to be homologues to other CoV members, and three more unknown ORFs (X1, X2, and X3) are unparalleled in all other known CoV species. Optimal alignment and computer analysis of the homologous ORFs has predicted the characteristic structural and functional domains on the putative genes. The overall nucleotides conservation of the homologous ORFs is low (<5%) compared with other known CoVs, implying that HK-39 is a newly emergent SARS-CoV phylogenetically distant from other known members. SimPlot analysis supports this finding, and also suggests that this novel virus is not a product of a recent recombinant from any of the known characterized CoVs. Together, these results confirm that HK-39 is a novel and distinct member of the Coronaviridae family, with unknown origin. The completion of the genomic sequence of the virus will assist in tracing its origin.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Chan, C W M" sort="Chan, C W M" uniqKey="Chan C" first="C W M" last="Chan">C W M. Chan</name><name sortKey="Chan, K H" sort="Chan, K H" uniqKey="Chan K" first="K H" last="Chan">K H Chan</name><name sortKey="Chan, M N" sort="Chan, M N" uniqKey="Chan M" first="M N" last="Chan">M N Chan</name><name sortKey="Chen, J D" sort="Chen, J D" uniqKey="Chen J" first="J D" last="Chen">J D Chen</name><name sortKey="Chow, K Y C" sort="Chow, K Y C" uniqKey="Chow K" first="K Y C" last="Chow">K Y C. Chow</name><name sortKey="Guan, Y" sort="Guan, Y" uniqKey="Guan Y" first="Y" last="Guan">Y. Guan</name><name sortKey="Hon, C C" sort="Hon, C C" uniqKey="Hon C" first="C C" last="Hon">C C Hon</name><name sortKey="Hui, K H" sort="Hui, K H" uniqKey="Hui K" first="K H" last="Hui">K H Hui</name><name sortKey="Leung, F C" sort="Leung, F C" uniqKey="Leung F" first="F C" last="Leung">F C Leung</name><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name><name sortKey="Li, V Y Y" sort="Li, V Y Y" uniqKey="Li V" first="V Y Y" last="Li">V Y Y. Li</name><name sortKey="Peiris, J S M" sort="Peiris, J S M" uniqKey="Peiris J" first="J S M" last="Peiris">J S M. Peiris</name><name sortKey="Poon, L L M" sort="Poon, L L M" uniqKey="Poon L" first="L L M" last="Poon">L L M. Poon</name><name sortKey="Wang, C Y" sort="Wang, C Y" uniqKey="Wang C" first="C Y" last="Wang">C Y Wang</name><name sortKey="Wang, P Y" sort="Wang, P Y" uniqKey="Wang P" first="P Y" last="Wang">P Y Wang</name><name sortKey="Yuen, K Y" sort="Yuen, K Y" uniqKey="Yuen K" first="K Y" last="Yuen">K Y Yuen</name><name sortKey="Zeng, F Y" sort="Zeng, F Y" uniqKey="Zeng F" first="F Y" last="Zeng">F Y Zeng</name><name sortKey="Zheng, B" sort="Zheng, B" uniqKey="Zheng B" first="B" last="Zheng">B. Zheng</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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