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Article: Variation of the hepatitis C virus 5' non-coding region: Implications for secondary structure, virus detection and typing

TitleVariation of the hepatitis C virus 5' non-coding region: Implications for secondary structure, virus detection and typing
Authors
Issue Date1995
PublisherSociety for General Microbiology. The Journal's web site is located at http://vir.sgmjournals.org
Citation
Journal Of General Virology, 1995, v. 76 n. 7, p. 1749-1761 How to Cite?
AbstractVariation in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) was investigated in detail by comparing 314 5'NCR sequences of viruses of genotypes 1 to 6. Evidence was obtained for the existence of associations between particular 5'NCR sequence motifs and virus types and subtypes. No recombination was observed between the 5'NCR and coding regions of different genotypes, implying that the sequence of subgenomic regions such as the 5'NCR can be used to deduce virus genotype. The distribution of polymorphic sites within the 5'NCR is used to propose improved oligonucleotide primers for virus detection and quantification that would be equally efficient in detecting RNA of different virus genotypes. The accuracy of two different genotyping methods (RFLP and the line probe assay) based on analysis of sequence polymorphisms in the 5'NCR is predicted from the sequences surveyed to be 97% and 83% respectively for types 1 to 6, with higher accuracies for distinguishing between subtypes 1a/1b, 2a/2b or 3a/3b. Several sites of genotype-specific polymorphism were covariant and maintained the base pairings required for a secondary structure model of the 5'NCR. Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5'NCR.
Persistent Identifierhttp://hdl.handle.net/10722/162088
ISSN
2015 Impact Factor: 3.192
2015 SCImago Journal Rankings: 1.741
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorSmith, DBen_US
dc.contributor.authorMellor, Jen_US
dc.contributor.authorJarvis, LMen_US
dc.contributor.authorDavidson, Fen_US
dc.contributor.authorKolberg, Jen_US
dc.contributor.authorUrdea, Men_US
dc.contributor.authorYap, PLen_US
dc.contributor.authorSimmonds, Pen_US
dc.contributor.authorConradie, JDen_US
dc.contributor.authorNeill, AGSen_US
dc.contributor.authorDusheiko, GMen_US
dc.contributor.authorKew, MCen_US
dc.contributor.authorCrookes, Ren_US
dc.contributor.authorKoshy, Aen_US
dc.contributor.authorLin, CKen_US
dc.contributor.authorLai, Cen_US
dc.contributor.authorMurrayLyon, IMen_US
dc.contributor.authorElGuneid, Aen_US
dc.contributor.authorGunaid, AAen_US
dc.date.accessioned2012-09-05T05:17:13Z-
dc.date.available2012-09-05T05:17:13Z-
dc.date.issued1995en_US
dc.identifier.citationJournal Of General Virology, 1995, v. 76 n. 7, p. 1749-1761en_US
dc.identifier.issn0022-1317en_US
dc.identifier.urihttp://hdl.handle.net/10722/162088-
dc.description.abstractVariation in the 5' non-coding region (5'NCR) of hepatitis C virus (HCV) was investigated in detail by comparing 314 5'NCR sequences of viruses of genotypes 1 to 6. Evidence was obtained for the existence of associations between particular 5'NCR sequence motifs and virus types and subtypes. No recombination was observed between the 5'NCR and coding regions of different genotypes, implying that the sequence of subgenomic regions such as the 5'NCR can be used to deduce virus genotype. The distribution of polymorphic sites within the 5'NCR is used to propose improved oligonucleotide primers for virus detection and quantification that would be equally efficient in detecting RNA of different virus genotypes. The accuracy of two different genotyping methods (RFLP and the line probe assay) based on analysis of sequence polymorphisms in the 5'NCR is predicted from the sequences surveyed to be 97% and 83% respectively for types 1 to 6, with higher accuracies for distinguishing between subtypes 1a/1b, 2a/2b or 3a/3b. Several sites of genotype-specific polymorphism were covariant and maintained the base pairings required for a secondary structure model of the 5'NCR. Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5'NCR.en_US
dc.languageengen_US
dc.publisherSociety for General Microbiology. The Journal's web site is located at http://vir.sgmjournals.orgen_US
dc.relation.ispartofJournal of General Virologyen_US
dc.subject.meshBase Compositionen_US
dc.subject.meshBase Sequenceen_US
dc.subject.meshCodonen_US
dc.subject.meshGenetic Variationen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHepacivirus - Classification - Genetics - Isolation & Purificationen_US
dc.subject.meshHumansen_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshNucleic Acid Conformationen_US
dc.subject.meshPolymorphism, Geneticen_US
dc.subject.meshRna, Viral - Analysisen_US
dc.subject.meshRecombination, Geneticen_US
dc.titleVariation of the hepatitis C virus 5' non-coding region: Implications for secondary structure, virus detection and typingen_US
dc.typeArticleen_US
dc.identifier.emailLai, C:hrmelcl@hku.hken_US
dc.identifier.authorityLai, C=rp00314en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1099/0022-1317-76-7-1749-
dc.identifier.pmid9049380en_US
dc.identifier.scopuseid_2-s2.0-0029027606en_US
dc.identifier.volume76en_US
dc.identifier.issue7en_US
dc.identifier.spage1749en_US
dc.identifier.epage1761en_US
dc.identifier.isiWOS:A1995RH28000020-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridSmith, DB=7410361795en_US
dc.identifier.scopusauthoridMellor, J=7103106842en_US
dc.identifier.scopusauthoridJarvis, LM=7101946900en_US
dc.identifier.scopusauthoridDavidson, F=7101716792en_US
dc.identifier.scopusauthoridKolberg, J=35952908200en_US
dc.identifier.scopusauthoridUrdea, M=7005511490en_US
dc.identifier.scopusauthoridYap, PL=16938057500en_US
dc.identifier.scopusauthoridSimmonds, P=7102203090en_US
dc.identifier.scopusauthoridConradie, JD=7004072675en_US
dc.identifier.scopusauthoridNeill, AGS=7005311730en_US
dc.identifier.scopusauthoridDusheiko, GM=7006885162en_US
dc.identifier.scopusauthoridKew, MC=7102927763en_US
dc.identifier.scopusauthoridCrookes, R=12143173900en_US
dc.identifier.scopusauthoridKoshy, A=7005478544en_US
dc.identifier.scopusauthoridLin, CK=15034856400en_US
dc.identifier.scopusauthoridLai, C=7403086396en_US
dc.identifier.scopusauthoridMurrayLyon, IM=35460136700en_US
dc.identifier.scopusauthoridElGuneid, A=6506985041en_US
dc.identifier.scopusauthoridGunaid, AA=6603878455en_US

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