title: Comparative analysis of nearly full-length hepatitis C virus quasispecies from patients experiencing viral breakthrough during antiviral therapy: clustered mutations in three functional genes, E2, NS2, and NS5a.
abstract: Viral breakthrough is a recognized response pattern to interferon-based antiviral therapy in patients with chronic hepatitis C virus (HCV) infection. The emergence of drug-resistant HCV quasispecies variants is assumed to be a major mechanism responsible for viral breakthrough. By using a long reverse transcription-PCR protocol recently developed in our lab, multiple nearly full-length HCV quasispecies variants were generated from 9.1-kb amplicons at both the baseline and breakthrough points in two patients experiencing viral breakthrough. Comparative analyses of consensus dominant quasispecies variants revealed that most mutations, occurring at the time of breakthrough, involved three functional viral genes, E2, NS2, and NS5a. Interestingly, similar mutation patterns were also observed in minor quasispecies variants at baseline. These three genes had the highest values of average amino acid complexity at the HCV 1a population level. No single amino acids were identified to be associated with viral breakthrough. Taken together, at the near-full-length HCV genome level, our data suggested that viral breakthrough might be attributed to the selection of minor quasispecies variants at the baseline with or without additional mutations during antiviral therapy. Furthermore, the pattern for mutation clustering indicated potential mutation linkage among E2, NS2, and NS5a due to structural or functional relatedness in HCV replication.
authors.affiliation: Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, 3635 Vista Avenue, St. Louis, MO 63110, USA. fanx@slu.edu
authors.forename: Zekuan
authors.initials: Z
authors.lastname: Xu
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Fan
authors.forename: Yanjuan
authors.initials: Y
authors.lastname: Xu
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Di Bisceglie
mesh_terms: D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000494:pharmacology*; D016679:Genome, Viral; D016174:Hepacivirus / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012254:Ribavirin / Q000494:pharmacology; D017386:Sequence Homology, Amino Acid; D014759:Viral Envelope Proteins / Q000235:genetics*; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D000998:Antiviral Agents; D012254:Ribavirin; D014759:Viral Envelope Proteins; D017361:Viral Nonstructural Proteins; C097010:NS2 protein, Hepatitis C virus; C091015:glycoprotein E2, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase