Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans
Identifieur interne : 000498 ( PascalFrancis/Corpus ); précédent : 000497; suivant : 000499Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans
Auteurs : Irshad M. Sulaiman ; XIN LIU ; Michael Frace ; Nikhat Sulaiman ; Melissa Olsen-Rasmussen ; Elizabeth Neuhaus ; Paul A. Rota ; Robert M. WohlhueterSource :
- Applied and environmental microbiology : (Print) [ 0099-2240 ] ; 2006.
Descripteurs français
- Pascal (Inist)
English descriptors
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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Format Inist (serveur)
NO : | PASCAL 06-0260043 INIST |
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ET : | Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans |
AU : | SULAIMAN (Irshad M.); XIN LIU; FRACE (Michael); SULAIMAN (Nikhat); OLSEN-RASMUSSEN (Melissa); NEUHAUS (Elizabeth); ROTA (Paul A.); WOHLHUETER (Robert M.) |
AF : | Biotechnology Core Facility Branch, Scientific Resources Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention/Atlanta, Georgia 30333/Etats-Unis (1 aut., 3 aut., 4 aut., 5 aut., 6 aut., 8 aut.); Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention/Atlanta, Georgia 30333/Etats-Unis (2 aut., 7 aut.) |
DT : | Publication en série; Niveau analytique |
SO : | Applied and environmental microbiology : (Print); ISSN 0099-2240; Coden AEMIDF; Etats-Unis; Da. 2006; Vol. 72; No. 1; Pp. 207-211; Bibl. 15 ref. |
LA : | Anglais |
EA : | 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. |
CC : | 002A05 |
FD : | Caractérisation; Génome; Homme; Coronavirus; Syndrome respiratoire aigu sévère |
FG : | Coronaviridae; Nidovirales; Virus; Virose; Infection |
ED : | Characterization; Genome; Human; Coronavirus; Severe acute respiratory syndrome |
EG : | Coronaviridae; Nidovirales; Virus; Viral disease; Infection |
SD : | Caracterización; Genoma; Hombre; Coronavirus; Síndrome respiratorio agudo severo |
LO : | INIST-7195.354000133228220250 |
ID : | 06-0260043 |
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Pascal:06-0260043Le 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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<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>
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<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>
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<fC07 i1="04" i2="X" l="SPA"><s0>Virosis</s0>
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<fC07 i1="05" i2="X" l="FRE"><s0>Infection</s0>
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<fC07 i1="05" i2="X" l="ENG"><s0>Infection</s0>
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<fC07 i1="05" i2="X" l="SPA"><s0>Infección</s0>
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<fN21><s1>163</s1>
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<server><NO>PASCAL 06-0260043 INIST</NO>
<ET>Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans</ET>
<AU>SULAIMAN (Irshad M.); XIN LIU; FRACE (Michael); SULAIMAN (Nikhat); OLSEN-RASMUSSEN (Melissa); NEUHAUS (Elizabeth); ROTA (Paul A.); WOHLHUETER (Robert M.)</AU>
<AF>Biotechnology Core Facility Branch, Scientific Resources Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention/Atlanta, Georgia 30333/Etats-Unis (1 aut., 3 aut., 4 aut., 5 aut., 6 aut., 8 aut.); Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention/Atlanta, Georgia 30333/Etats-Unis (2 aut., 7 aut.)</AF>
<DT>Publication en série; Niveau analytique</DT>
<SO>Applied and environmental microbiology : (Print); ISSN 0099-2240; Coden AEMIDF; Etats-Unis; Da. 2006; Vol. 72; No. 1; Pp. 207-211; Bibl. 15 ref.</SO>
<LA>Anglais</LA>
<EA>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.</EA>
<CC>002A05</CC>
<FD>Caractérisation; Génome; Homme; Coronavirus; Syndrome respiratoire aigu sévère</FD>
<FG>Coronaviridae; Nidovirales; Virus; Virose; Infection</FG>
<ED>Characterization; Genome; Human; Coronavirus; Severe acute respiratory syndrome</ED>
<EG>Coronaviridae; Nidovirales; Virus; Viral disease; Infection</EG>
<SD>Caracterización; Genoma; Hombre; Coronavirus; Síndrome respiratorio agudo severo</SD>
<LO>INIST-7195.354000133228220250</LO>
<ID>06-0260043</ID>
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