SrasV1, PascalFrancis, Curation, bibRecord, 000492

Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans

Identifieur interne : 000492 ( PascalFrancis/Curation ); précédent : 000491; suivant : 000493

Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans

Auteurs : Irshad M. Sulaiman [États-Unis] ; XIN LIU [États-Unis] ; Michael Frace [États-Unis] ; Nikhat Sulaiman [États-Unis] ; Melissa Olsen-Rasmussen [États-Unis] ; Elizabeth Neuhaus [États-Unis] ; Paul A. Rota [États-Unis] ; Robert M. Wohlhueter [États-Unis]

Source :

Applied and environmental microbiology : (Print) [ 0099-2240 ] ; 2006.

RBID : Pascal:06-0260043

Descripteurs français

Pascal (Inist)
- Caractérisation, Génome, Homme, Coronavirus, Syndrome respiratoire aigu sévère.
Wicri :
- topic : Homme.

English descriptors

KwdEn :
- Characterization, Coronavirus, Genome, Human, Severe acute respiratory syndrome.

Abstract

Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Aflymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.

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A11	`01`	`1`		`@1 SULAIMAN (Irshad M.)`
A11	`02`	`1`		`@1 XIN LIU`
A11	`03`	`1`		`@1 FRACE (Michael)`
A11	`04`	`1`		`@1 SULAIMAN (Nikhat)`
A11	`05`	`1`		`@1 OLSEN-RASMUSSEN (Melissa)`
A11	`06`	`1`		`@1 NEUHAUS (Elizabeth)`
A11	`07`	`1`		`@1 ROTA (Paul A.)`
A11	`08`	`1`		`@1 WOHLHUETER (Robert M.)`
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C01	`01`		`ENG`	@0 Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Aflymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.
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C03	`01`	`X`	`FRE`	`@0 Caractérisation @5 10`
C03	`01`	`X`	`ENG`	`@0 Characterization @5 10`
C03	`01`	`X`	`SPA`	`@0 Caracterización @5 10`
C03	`02`	`X`	`FRE`	`@0 Génome @5 11`
C03	`02`	`X`	`ENG`	`@0 Genome @5 11`
C03	`02`	`X`	`SPA`	`@0 Genoma @5 11`
C03	`03`	`X`	`FRE`	`@0 Homme @5 12`
C03	`03`	`X`	`ENG`	`@0 Human @5 12`
C03	`03`	`X`	`SPA`	`@0 Hombre @5 12`
C03	`04`	`X`	`FRE`	`@0 Coronavirus @2 NW @5 13`
C03	`04`	`X`	`ENG`	`@0 Coronavirus @2 NW @5 13`
C03	`04`	`X`	`SPA`	`@0 Coronavirus @2 NW @5 13`
C03	`05`	`X`	`FRE`	`@0 Syndrome respiratoire aigu sévère @2 NM @5 19`
C03	`05`	`X`	`ENG`	`@0 Severe acute respiratory syndrome @2 NM @5 19`
C03	`05`	`X`	`SPA`	`@0 Síndrome respiratorio agudo severo @2 NM @5 19`
C07	`01`	`X`	`FRE`	`@0 Coronaviridae @2 NW`
C07	`01`	`X`	`ENG`	`@0 Coronaviridae @2 NW`
C07	`01`	`X`	`SPA`	`@0 Coronaviridae @2 NW`
C07	`02`	`X`	`FRE`	`@0 Nidovirales @2 NW`
C07	`02`	`X`	`ENG`	`@0 Nidovirales @2 NW`
C07	`02`	`X`	`SPA`	`@0 Nidovirales @2 NW`
C07	`03`	`X`	`FRE`	`@0 Virus @2 NW`
C07	`03`	`X`	`ENG`	`@0 Virus @2 NW`
C07	`03`	`X`	`SPA`	`@0 Virus @2 NW`
C07	`04`	`X`	`FRE`	`@0 Virose`
C07	`04`	`X`	`ENG`	`@0 Viral disease`
C07	`04`	`X`	`SPA`	`@0 Virosis`
C07	`05`	`X`	`FRE`	`@0 Infection`
C07	`05`	`X`	`ENG`	`@0 Infection`
C07	`05`	`X`	`SPA`	`@0 Infección`
N21				`@1 163`

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Le document en format XML

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<front><div type="abstract" xml:lang="en">Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Aflymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.</div>
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<s1>© 2006 INIST-CNRS. All rights reserved.</s1>
</fA44>
<fA45><s0>15 ref.</s0>
</fA45>
<fA47 i1="01" i2="1"><s0>06-0260043</s0>
</fA47>
<fA60><s1>P</s1>
</fA60>
<fA61><s0>A</s0>
</fA61>
<fA64 i1="01" i2="1"><s0>Applied and environmental microbiology : (Print)</s0>
</fA64>
<fA66 i1="01"><s0>USA</s0>
</fA66>
<fC01 i1="01" l="ENG"><s0>Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Aflymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.</s0>
</fC01>
<fC02 i1="01" i2="X"><s0>002A05</s0>
</fC02>
<fC03 i1="01" i2="X" l="FRE"><s0>Caractérisation</s0>
<s5>10</s5>
</fC03>
<fC03 i1="01" i2="X" l="ENG"><s0>Characterization</s0>
<s5>10</s5>
</fC03>
<fC03 i1="01" i2="X" l="SPA"><s0>Caracterización</s0>
<s5>10</s5>
</fC03>
<fC03 i1="02" i2="X" l="FRE"><s0>Génome</s0>
<s5>11</s5>
</fC03>
<fC03 i1="02" i2="X" l="ENG"><s0>Genome</s0>
<s5>11</s5>
</fC03>
<fC03 i1="02" i2="X" l="SPA"><s0>Genoma</s0>
<s5>11</s5>
</fC03>
<fC03 i1="03" i2="X" l="FRE"><s0>Homme</s0>
<s5>12</s5>
</fC03>
<fC03 i1="03" i2="X" l="ENG"><s0>Human</s0>
<s5>12</s5>
</fC03>
<fC03 i1="03" i2="X" l="SPA"><s0>Hombre</s0>
<s5>12</s5>
</fC03>
<fC03 i1="04" i2="X" l="FRE"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>13</s5>
</fC03>
<fC03 i1="04" i2="X" l="ENG"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>13</s5>
</fC03>
<fC03 i1="04" i2="X" l="SPA"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>13</s5>
</fC03>
<fC03 i1="05" i2="X" l="FRE"><s0>Syndrome respiratoire aigu sévère</s0>
<s2>NM</s2>
<s5>19</s5>
</fC03>
<fC03 i1="05" i2="X" l="ENG"><s0>Severe acute respiratory syndrome</s0>
<s2>NM</s2>
<s5>19</s5>
</fC03>
<fC03 i1="05" i2="X" l="SPA"><s0>Síndrome respiratorio agudo severo</s0>
<s2>NM</s2>
<s5>19</s5>
</fC03>
<fC07 i1="01" i2="X" l="FRE"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="01" i2="X" l="ENG"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="01" i2="X" l="SPA"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="FRE"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="ENG"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="SPA"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="FRE"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="ENG"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="SPA"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="04" i2="X" l="FRE"><s0>Virose</s0>
</fC07>
<fC07 i1="04" i2="X" l="ENG"><s0>Viral disease</s0>
</fC07>
<fC07 i1="04" i2="X" l="SPA"><s0>Virosis</s0>
</fC07>
<fC07 i1="05" i2="X" l="FRE"><s0>Infection</s0>
</fC07>
<fC07 i1="05" i2="X" l="ENG"><s0>Infection</s0>
</fC07>
<fC07 i1="05" i2="X" l="SPA"><s0>Infección</s0>
</fC07>
<fN21><s1>163</s1>
</fN21>
</pA>
</standard>
</inist>
</record>

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Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans

Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans

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