NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b

• Published in: PloS one 2017-07, Vol.12 (7), p.e0182193-e0182193
• Main Authors: Neukam, Karin, Martínez, Alfredo P, Culasso, Andrés C A, Ridruejo, Ezequiel, García, Gabriel, Di Lello, Federico A
• Format: Article
• Language: English
• Subjects: Argentina; Biology and life sciences; Cladistic analysis; Computer and Information Sciences; Cross-Sectional Studies; Datasets; Genome, Viral - genetics; Genomes; Genotype; Genotype & phenotype; Genotyping; Hepacivirus - classification; Hepacivirus - genetics; Hepatitis; Hepatitis C; Hepatitis C - virology; Hepatitis C virus; Hybridization; Infections; Infectious diseases; Medicine and health sciences; Methods; Nucleic acids; Patients; Phylogenetics; Phylogeny; Protease inhibitors; Proteinase inhibitors; Research and Analysis Methods; Viral Nonstructural Proteins - genetics; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0182193

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.