Polymorphism of SARS-CoV Genomes
Identifieur interne : 001620 ( Pmc/Corpus ); précédent : 001619; suivant : 001621Polymorphism of SARS-CoV Genomes
Auteurs : Lei Shang ; Yan Qi ; Qi-Yu Bao ; Wei Tian ; Jian-Cheng Xu ; Ming-Guang Feng ; Huan-Ming YangSource :
- Yi Chuan Xue Bao = Acta Genetica Sinica [ 0379-4172 ] ; 2006.
Abstract
In this work, severe acute respiratory syndrome associated
Url:
DOI: 10.1016/S0379-4172(06)60061-9
PubMed: 16625834
PubMed Central: 7131822
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Polymorphism of SARS-CoV Genomes</title><author><name sortKey="Shang, Lei" sort="Shang, Lei" uniqKey="Shang L" first="Lei" last="Shang">Lei Shang</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute of Microbiology, Zhejiang University, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Qi, Yan" sort="Qi, Yan" uniqKey="Qi Y" first="Yan" last="Qi">Yan Qi</name><affiliation><nlm:aff id="aff2">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation><nlm:aff id="aff2">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author><author><name sortKey="Tian, Wei" sort="Tian, Wei" uniqKey="Tian W" first="Wei" last="Tian">Wei Tian</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Jian Cheng" sort="Xu, Jian Cheng" uniqKey="Xu J" first="Jian-Cheng" last="Xu">Jian-Cheng Xu</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Feng, Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name><affiliation><nlm:aff id="aff3">Institute of Microbiology, Zhejiang University, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Huan Ming" sort="Yang, Huan Ming" uniqKey="Yang H" first="Huan-Ming" last="Yang">Huan-Ming Yang</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">16625834</idno><idno type="pmc">7131822</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131822</idno><idno type="RBID">PMC:7131822</idno><idno type="doi">10.1016/S0379-4172(06)60061-9</idno><date when="2006">2006</date><idno type="wicri:Area/Pmc/Corpus">001620</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001620</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Polymorphism of SARS-CoV Genomes</title><author><name sortKey="Shang, Lei" sort="Shang, Lei" uniqKey="Shang L" first="Lei" last="Shang">Lei Shang</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute of Microbiology, Zhejiang University, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Qi, Yan" sort="Qi, Yan" uniqKey="Qi Y" first="Yan" last="Qi">Yan Qi</name><affiliation><nlm:aff id="aff2">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation><nlm:aff id="aff2">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author><author><name sortKey="Tian, Wei" sort="Tian, Wei" uniqKey="Tian W" first="Wei" last="Tian">Wei Tian</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Jian Cheng" sort="Xu, Jian Cheng" uniqKey="Xu J" first="Jian-Cheng" last="Xu">Jian-Cheng Xu</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Feng, Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name><affiliation><nlm:aff id="aff3">Institute of Microbiology, Zhejiang University, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Huan Ming" sort="Yang, Huan Ming" uniqKey="Yang H" first="Huan-Ming" last="Yang">Huan-Ming Yang</name><affiliation><nlm:aff id="aff1">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff></affiliation></author></analytic><series><title level="j">Yi Chuan Xue Bao = Acta Genetica Sinica</title><idno type="ISSN">0379-4172</idno><idno type="eISSN">0379-4172</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In this work, severe acute respiratory syndrome associated <italic>coronavirus</italic> (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI Gen-Bank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3′ end (19.0 kb-29.7 kb). Regions encoding Orf10–11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27 700–28 000) which encodes parts of the putative ORF9 and ORF10–11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Yi Chuan Xue Bao</journal-id><journal-id journal-id-type="iso-abbrev">Yi Chuan Xue Bao</journal-id><journal-title-group><journal-title>Yi Chuan Xue Bao = Acta Genetica Sinica</journal-title></journal-title-group><issn pub-type="ppub">0379-4172</issn><issn pub-type="epub">0379-4172</issn><publisher><publisher-name>Institute of Genetics and Developmental Biology & The Genetics Society of China. Published by Elsevier Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">16625834</article-id><article-id pub-id-type="pmc">7131822</article-id><article-id pub-id-type="publisher-id">S0379-4172(06)60061-9</article-id><article-id pub-id-type="doi">10.1016/S0379-4172(06)60061-9</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Polymorphism of SARS-CoV Genomes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>SHANG</surname><given-names>Lei</given-names></name><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff3" ref-type="aff">c</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>QI</surname><given-names>Yan</given-names></name><xref rid="aff2" ref-type="aff">b</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>BAO</surname><given-names>Qi-Yu</given-names></name><email>baoqy@genomics.org.cn</email><xref rid="aff2" ref-type="aff">b</xref><xref rid="cor1" ref-type="corresp">*</xref></contrib><contrib contrib-type="author"><name><surname>TIAN</surname><given-names>Wei</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>XU</surname><given-names>Jian-Cheng</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>FENG</surname><given-names>Ming-Guang</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>YANG</surname><given-names>Huan-Ming</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib></contrib-group><aff id="aff1"><label>a</label>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</aff><aff id="aff2"><label>b</label>Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</aff><aff id="aff3"><label>c</label>Institute of Microbiology, Zhejiang University, Hangzhou 310029, China</aff><author-notes><corresp id="cor1"><label>*</label>Corresponding author Tel: +86-577-8889 2799 <email>baoqy@genomics.org.cn</email></corresp><fn id="fn1"><label>1</label><p>Contributed equally to this study</p></fn></author-notes><pub-date pub-type="pmc-release"><day>25</day><month>4</month><year>2006</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>4</month><year>2006</year></pub-date><pub-date pub-type="epub"><day>25</day><month>4</month><year>2006</year></pub-date><volume>33</volume><issue>4</issue><fpage>354</fpage><lpage>364</lpage><history><date date-type="received"><day>16</day><month>4</month><year>2005</year></date><date date-type="accepted"><day>1</day><month>9</month><year>2005</year></date></history><permissions><copyright-statement>Copyright © 2006 Institute of Genetics and Developmental Biology & The Genetics Society of China. Published by Elsevier Ltd All rights reserved.</copyright-statement><copyright-year>2006</copyright-year><copyright-holder>Institute of Genetics and Developmental Biology & The Genetics Society of China</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>In this work, severe acute respiratory syndrome associated <italic>coronavirus</italic> (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI Gen-Bank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3′ end (19.0 kb-29.7 kb). Regions encoding Orf10–11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27 700–28 000) which encodes parts of the putative ORF9 and ORF10–11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. 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SARS <italic>coronavirus</italic> in cell culture and human populations isolated in 2003</article-title><source>BMC Infect Dis</source><volume>4</volume><issue>1</issue><year>2004</year><fpage>32</fpage><lpage>40</lpage><pub-id pub-id-type="pmid">15347429</pub-id></element-citation></ref></ref-list><fn-group><fn id="d32e281"><p>This work was supported by the Science Foundation of Wenzhou City(No. Y2003A005) and Zhejiang University (No. 181130–544301).</p></fn></fn-group></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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