NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b.
To evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes.A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5533332?pdf=render |
| _version_ | 1818520047752052736 |
|---|---|
| author | Karin Neukam Alfredo P Martínez Andrés C A Culasso Ezequiel Ridruejo Gabriel García Federico A Di Lello |
| author_facet | Karin Neukam Alfredo P Martínez Andrés C A Culasso Ezequiel Ridruejo Gabriel García Federico A Di Lello |
| author_sort | Karin Neukam |
| collection | DOAJ |
| description | To evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes.A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a cross-sectional study conducted in patients seen from January 2012 to June 2016 at an outpatient clinic in Buenos Aires, Argentina.The samples were included within well supported subtype clades: 64 with HCV-1b and 39 with HCV-1a infection. Twenty of the HCV-1a infected patientes were included in a supported sub-clade "1" and 19 individuals were among the basal sub-clade "2". LiPA 2.0 failed to subtype HCV-1 in 20 (19.2%) individuals. Subtype classification determined by NS3 direct sequencing showed that 2/18 (11.1%) of the HCV-1a-infected patients as determined by LiPA 2.0 were in fact infected by HCV-1b. Of the HCV-1b-infected according to LiPA 2.0, 10/66 (15.2%) patients showed HCV-1a infection according to NS3 sequencing. Overall misclassification was 14.3% (κ-index for the concordance with NS3 sequencing = 0.635). One (1%) patient was erroneously genotyped as HCV-1 and was revealed as HCV genotype 4 infection.Genomic sequencing of the HCV NS3 region represents an adequate alternative since it provides reliable genetic information. It even distinguishes between HCV-1a clades related to resistance-associated substitutions to HCV protease inhibitors, it provides reliable genetic information for genotyping/subgenotyping and simultaneously allows to determine the presence of resistance-associated substitutions to currently recommended DAAs. |
| first_indexed | 2024-12-11T01:32:11Z |
| format | Article |
| id | doaj.art-e4c88dc3c0124f7bbc4b7d4a9f85f500 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T01:32:11Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-e4c88dc3c0124f7bbc4b7d4a9f85f5002022-12-22T01:25:20ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01127e018219310.1371/journal.pone.0182193NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b.Karin NeukamAlfredo P MartínezAndrés C A CulassoEzequiel RidruejoGabriel GarcíaFederico A Di LelloTo evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes.A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a cross-sectional study conducted in patients seen from January 2012 to June 2016 at an outpatient clinic in Buenos Aires, Argentina.The samples were included within well supported subtype clades: 64 with HCV-1b and 39 with HCV-1a infection. Twenty of the HCV-1a infected patientes were included in a supported sub-clade "1" and 19 individuals were among the basal sub-clade "2". LiPA 2.0 failed to subtype HCV-1 in 20 (19.2%) individuals. Subtype classification determined by NS3 direct sequencing showed that 2/18 (11.1%) of the HCV-1a-infected patients as determined by LiPA 2.0 were in fact infected by HCV-1b. Of the HCV-1b-infected according to LiPA 2.0, 10/66 (15.2%) patients showed HCV-1a infection according to NS3 sequencing. Overall misclassification was 14.3% (κ-index for the concordance with NS3 sequencing = 0.635). One (1%) patient was erroneously genotyped as HCV-1 and was revealed as HCV genotype 4 infection.Genomic sequencing of the HCV NS3 region represents an adequate alternative since it provides reliable genetic information. It even distinguishes between HCV-1a clades related to resistance-associated substitutions to HCV protease inhibitors, it provides reliable genetic information for genotyping/subgenotyping and simultaneously allows to determine the presence of resistance-associated substitutions to currently recommended DAAs.http://europepmc.org/articles/PMC5533332?pdf=render |
| spellingShingle | Karin Neukam Alfredo P Martínez Andrés C A Culasso Ezequiel Ridruejo Gabriel García Federico A Di Lello NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. PLoS ONE |
| title | NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. |
| title_full | NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. |
| title_fullStr | NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. |
| title_full_unstemmed | NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. |
| title_short | NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. |
| title_sort | ns3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis c virus subtypes 1a and 1b |
| url | http://europepmc.org/articles/PMC5533332?pdf=render |
| work_keys_str_mv | AT karinneukam ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b AT alfredopmartinez ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b AT andrescaculasso ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b AT ezequielridruejo ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b AT gabrielgarcia ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b AT federicoadilello ns3genomicsequencingandphylogeneticanalysisasalternativetoacommerciallyavailableassaytoreliablydeterminehepatitiscvirussubtypes1aand1b |