Direct sequencing of SARS-coronavirus S and N genes from clinical specimens shows limited variation.
Identifieur interne : 002C09 ( PubMed/Curation ); précédent : 002C08; suivant : 002C10Direct sequencing of SARS-coronavirus S and N genes from clinical specimens shows limited variation.
Auteurs : Suxiang Tong [États-Unis] ; Jairam R. Lingappa ; Qi Chen ; Bo Shu ; Ashley C. Lamonte ; Byron T. Cook ; Charryse Birge ; Shur-Wern Wang Chern ; Xin Liu ; Renee Galloway ; Le Quynh Mai ; Wai Fu Ng ; Jyh-Yuan Yang ; Jagdish Butany ; James A. Comer ; Stephan S. Monroe ; Suzanne R. Beard ; Thomas G. Ksiazek ; Dean Erdman ; Paul A. Rota ; Mark A. Pallansch ; Larry J. AndersonSource :
- The Journal of infectious diseases [ 0022-1899 ] ; 2004.
Descripteurs français
- KwdFr :
- ARN viral (génétique), ARN viral (isolement et purification), Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires (génétique), Génome viral, Humains, Mutation faux-sens, Mutation ponctuelle, Polymorphisme génétique, Protéines de l'enveloppe virale (génétique), Protéines nucléocapside (génétique), Substitution d'acide aminé (génétique), Syndrome respiratoire aigu sévère (virologie), Virus du SRAS (génétique), Virus du SRAS (isolement et purification).
- MESH :
- génétique : ARN viral, Glycoprotéines membranaires, Protéines de l'enveloppe virale, Protéines nucléocapside, Substitution d'acide aminé, Virus du SRAS.
- isolement et purification : ARN viral, Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- Glycoprotéine de spicule des coronavirus, Génome viral, Humains, Mutation faux-sens, Mutation ponctuelle, Polymorphisme génétique.
English descriptors
- KwdEn :
- Amino Acid Substitution (genetics), Genome, Viral, Humans, Membrane Glycoproteins (genetics), Mutation, Missense, Nucleocapsid Proteins (genetics), Point Mutation, Polymorphism, Genetic, RNA, Viral (genetics), RNA, Viral (isolation & purification), SARS Virus (genetics), SARS Virus (isolation & purification), Severe Acute Respiratory Syndrome (virology), Spike Glycoprotein, Coronavirus, Viral Envelope Proteins (genetics).
- MESH :
- chemical , genetics : Membrane Glycoproteins, Nucleocapsid Proteins, RNA, Viral, Viral Envelope Proteins.
- genetics : Amino Acid Substitution, SARS Virus.
- chemical , isolation & purification : RNA, Viral, SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Genome, Viral, Humans, Mutation, Missense, Point Mutation, Polymorphism, Genetic, Spike Glycoprotein, Coronavirus.
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.
DOI: 10.1086/422849
PubMed: 15319863
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pubmed:15319863Le document en format XML
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Lingappa</name></author><author><name sortKey="Chen, Qi" sort="Chen, Qi" uniqKey="Chen Q" first="Qi" last="Chen">Qi Chen</name></author><author><name sortKey="Shu, Bo" sort="Shu, Bo" uniqKey="Shu B" first="Bo" last="Shu">Bo Shu</name></author><author><name sortKey="Lamonte, Ashley C" sort="Lamonte, Ashley C" uniqKey="Lamonte A" first="Ashley C" last="Lamonte">Ashley C. Lamonte</name></author><author><name sortKey="Cook, Byron T" sort="Cook, Byron T" uniqKey="Cook B" first="Byron T" last="Cook">Byron T. Cook</name></author><author><name sortKey="Birge, Charryse" sort="Birge, Charryse" uniqKey="Birge C" first="Charryse" last="Birge">Charryse Birge</name></author><author><name sortKey="Chern, Shur Wern Wang" sort="Chern, Shur Wern Wang" uniqKey="Chern S" first="Shur-Wern Wang" last="Chern">Shur-Wern Wang Chern</name></author><author><name sortKey="Liu, Xin" sort="Liu, Xin" uniqKey="Liu X" first="Xin" last="Liu">Xin Liu</name></author><author><name sortKey="Galloway, Renee" sort="Galloway, Renee" uniqKey="Galloway R" first="Renee" last="Galloway">Renee Galloway</name></author><author><name sortKey="Mai, Le Quynh" sort="Mai, Le Quynh" uniqKey="Mai L" first="Le Quynh" last="Mai">Le Quynh Mai</name></author><author><name sortKey="Ng, Wai Fu" sort="Ng, Wai Fu" uniqKey="Ng W" first="Wai Fu" last="Ng">Wai Fu Ng</name></author><author><name sortKey="Yang, Jyh Yuan" sort="Yang, Jyh Yuan" uniqKey="Yang J" first="Jyh-Yuan" last="Yang">Jyh-Yuan Yang</name></author><author><name sortKey="Butany, Jagdish" sort="Butany, Jagdish" uniqKey="Butany J" first="Jagdish" last="Butany">Jagdish Butany</name></author><author><name sortKey="Comer, James A" sort="Comer, James A" uniqKey="Comer J" first="James A" last="Comer">James A. Comer</name></author><author><name sortKey="Monroe, Stephan S" sort="Monroe, Stephan S" uniqKey="Monroe S" first="Stephan S" last="Monroe">Stephan S. Monroe</name></author><author><name sortKey="Beard, Suzanne R" sort="Beard, Suzanne R" uniqKey="Beard S" first="Suzanne R" last="Beard">Suzanne R. Beard</name></author><author><name sortKey="Ksiazek, Thomas G" sort="Ksiazek, Thomas G" uniqKey="Ksiazek T" first="Thomas G" last="Ksiazek">Thomas G. Ksiazek</name></author><author><name sortKey="Erdman, Dean" sort="Erdman, Dean" uniqKey="Erdman D" first="Dean" last="Erdman">Dean Erdman</name></author><author><name sortKey="Rota, Paul A" sort="Rota, Paul A" uniqKey="Rota P" first="Paul A" last="Rota">Paul A. Rota</name></author><author><name sortKey="Pallansch, Mark A" sort="Pallansch, Mark A" uniqKey="Pallansch M" first="Mark A" last="Pallansch">Mark A. Pallansch</name></author><author><name sortKey="Anderson, Larry J" sort="Anderson, Larry J" uniqKey="Anderson L" first="Larry J" last="Anderson">Larry J. Anderson</name></author></analytic><series><title level="j">The Journal of infectious diseases</title><idno type="ISSN">0022-1899</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Substitution (genetics)</term><term>Genome, Viral</term><term>Humans</term><term>Membrane Glycoproteins (genetics)</term><term>Mutation, Missense</term><term>Nucleocapsid Proteins (genetics)</term><term>Point Mutation</term><term>Polymorphism, Genetic</term><term>RNA, Viral (genetics)</term><term>RNA, Viral (isolation & purification)</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>ARN viral (isolement et purification)</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires (génétique)</term><term>Génome viral</term><term>Humains</term><term>Mutation faux-sens</term><term>Mutation ponctuelle</term><term>Polymorphisme génétique</term><term>Protéines de l'enveloppe virale (génétique)</term><term>Protéines nucléocapside (génétique)</term><term>Substitution d'acide aminé (génétique)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>Nucleocapsid Proteins</term><term>RNA, Viral</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Amino Acid Substitution</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Glycoprotéines membranaires</term><term>Protéines de l'enveloppe virale</term><term>Protéines nucléocapside</term><term>Substitution d'acide aminé</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>RNA, Viral</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ARN viral</term><term>Virus du SRAS</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>Genome, Viral</term><term>Humans</term><term>Mutation, Missense</term><term>Point Mutation</term><term>Polymorphism, Genetic</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Glycoprotéine de spicule des coronavirus</term><term>Génome viral</term><term>Humains</term><term>Mutation faux-sens</term><term>Mutation ponctuelle</term><term>Polymorphisme génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15319863</PMID><DateCompleted><Year>2004</Year><Month>10</Month><Day>07</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0022-1899</ISSN><JournalIssue CitedMedium="Print"><Volume>190</Volume><Issue>6</Issue><PubDate><Year>2004</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>The Journal of infectious diseases</Title><ISOAbbreviation>J. Infect. Dis.</ISOAbbreviation></Journal><ArticleTitle>Direct sequencing of SARS-coronavirus S and N genes from clinical specimens shows limited variation.</ArticleTitle><Pagination><MedlinePgn>1127-31</MedlinePgn></Pagination><Abstract><AbstractText>Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Suxiang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-G17, Atlanta, GA 30333, USA. sot1@cdc.gov</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lingappa</LastName><ForeName>Jairam R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Qi</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Shu</LastName><ForeName>Bo</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>LaMonte</LastName><ForeName>Ashley C</ForeName><Initials>AC</Initials></Author><Author ValidYN="Y"><LastName>Cook</LastName><ForeName>Byron T</ForeName><Initials>BT</Initials></Author><Author ValidYN="Y"><LastName>Birge</LastName><ForeName>Charryse</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Chern</LastName><ForeName>Shur-wern Wang</ForeName><Initials>SW</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xin</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Galloway</LastName><ForeName>Renee</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Mai</LastName><ForeName>Le Quynh</ForeName><Initials>le Q</Initials></Author><Author ValidYN="Y"><LastName>Ng</LastName><ForeName>Wai Fu</ForeName><Initials>WF</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Jyh-Yuan</ForeName><Initials>JY</Initials></Author><Author ValidYN="Y"><LastName>Butany</LastName><ForeName>Jagdish</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Comer</LastName><ForeName>James A</ForeName><Initials>JA</Initials></Author><Author ValidYN="Y"><LastName>Monroe</LastName><ForeName>Stephan S</ForeName><Initials>SS</Initials></Author><Author ValidYN="Y"><LastName>Beard</LastName><ForeName>Suzanne R</ForeName><Initials>SR</Initials></Author><Author ValidYN="Y"><LastName>Ksiazek</LastName><ForeName>Thomas G</ForeName><Initials>TG</Initials></Author><Author ValidYN="Y"><LastName>Erdman</LastName><ForeName>Dean</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Rota</LastName><ForeName>Paul A</ForeName><Initials>PA</Initials></Author><Author ValidYN="Y"><LastName>Pallansch</LastName><ForeName>Mark A</ForeName><Initials>MA</Initials></Author><Author ValidYN="Y"><LastName>Anderson</LastName><ForeName>Larry J</ForeName><Initials>LJ</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2004</Year><Month>08</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Infect Dis</MedlineTA><NlmUniqueID>0413675</NlmUniqueID><ISSNLinking>0022-1899</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008562">Membrane Glycoproteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D019590">Nucleocapsid Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D064370">Spike Glycoprotein, Coronavirus</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014759">Viral Envelope Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C099602">nucleocapsid protein, Coronavirus</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C578557">spike glycoprotein, SARS-CoV</NameOfSubstance></Chemical></ChemicalList><CitationSubset>AIM</CitationSubset><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019943" MajorTopicYN="N">Amino Acid Substitution</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008562" MajorTopicYN="N">Membrane Glycoproteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020125" MajorTopicYN="N">Mutation, Missense</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019590" MajorTopicYN="N">Nucleocapsid Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017354" MajorTopicYN="N">Point Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D064370" MajorTopicYN="N">Spike Glycoprotein, Coronavirus</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014759" MajorTopicYN="N">Viral Envelope Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2004</Year><Month>01</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2004</Year><Month>03</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>8</Month><Day>21</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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