title: Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons.
abstract: Hepatitis C virus (HCV) exists as a swarm of genetically distinct but related variants, or a quasispecies, whose complexity and sequence evolution are critical to studies of viral pathogenesis. Because most studies of the HCV quasispecies have focused on a relatively small genomic segment, the first hypervariable region of the E2 gene, it is possible that viral complexity is occasionally underestimated (due to primer mismatch) and that sequence evolution is misperceived due to unrecognized covariation. This report describes a sensitive and reproducible method to amplify most of the HCV genome as a single 5.2-kb amplicon by using primers directed at relatively conserved genomic segments. Using 52 specimens obtained during acute infection over a range of viral RNA concentrations, the overall rate of successful amplification was 94% and varied in a concentration-dependent manner, with successful amplification in 26 of 26 (100%) specimens at greater than 10(5) IU/ml, 15 of 16 (94%) at 10(4) to 10(5) IU/ml, 6 of 7 (86%) at 10(3) to 10(4) IU/ml, and 2 of 3 (67%) at less than 10(3) IU/ml. Quasispecies complexity, determined by using this novel long-amplicon method followed by heteroduplex mobility assay combined with single-stranded conformational polymorphism (HDA+SSCP) analysis, was very high, even during acute HCV infection, when 10 to 21 (median, 16) different HDA+SSCP patterns were detected among 33 cDNA clones examined. Replicate analyses indicate that this diversity is not dominated by random errors generated during amplification. Therefore, the HCV quasispecies is highly complex even during acute infection and is accurately represented in amplicons representing more than half of the viral genome.
authors.affiliation: Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liu
authors.forename: Dale M
authors.initials: DM
authors.lastname: Netski
authors.forename: Qing
authors.initials: Q
authors.lastname: Mao
authors.forename: Oliver
authors.initials: O
authors.lastname: Laeyendecker
authors.forename: John R
authors.initials: JR
authors.lastname: Ticehurst
authors.forename: Xiao-Hong
authors.initials: XH
authors.lastname: Wang
authors.forename: David L
authors.initials: DL
authors.lastname: Thomas
authors.forename: Stuart C
authors.initials: SC
authors.lastname: Ray
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D017931:DNA Primers; D005784:Gene Amplification; D014644:Genetic Variation; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D018807:Polymorphism, Single-Stranded Conformational; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D017931:DNA Primers