title: Hypervariable region 1 sequence stability during hepatitis C virus replication in chimpanzees.
abstract: The putative envelope 2 (E2) gene of hepatitis C virus (HCV) contains a highly variable region referred to as hypervariable region 1 (HVR1). We hypothesized that this genetic variability is driven by immune selection pressure, rather than representing the accumulation of random mutations in a region with relatively little functional constraint. To test this hypothesis, we examined the E2 sequence of a human inoculum that was passaged through eight chimpanzees, which appear to have a replicative rate (opportunity for chance mutation) similar to that of humans. Acute-phase plasma samples from a human (the inoculum) and six of eight serially infected chimpanzees were studied. For each, 33 cloned cDNAs were examined by a combined heteroduplex-single-stranded conformational polymorphism assay to assess quasispecies complexity and optimize selection of clones with unique gel shift patterns (clonotypes) for sequencing. The sequence diversity of HCV was significantly lower in the chimpanzees than in the humans, and during eight serial passages there was no change in the sequence of the majority clonotype from each animal examined. Similarly, the rates of protein sequence altering (nonsynonymous) substitution were lower in the chimpanzees than in the humans. These findings demonstrate that nonsynonymous mutations indicate selection pressure rather than being an incidental result of HCV replication.
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. sray@jhmi.edu
authors.forename: S C
authors.initials: SC
authors.lastname: Ray
authors.forename: Q
authors.initials: Q
authors.lastname: Mao
authors.forename: R E
authors.initials: RE
authors.lastname: Lanford
authors.forename: S
authors.initials: S
authors.lastname: Bassett
authors.forename: O
authors.initials: O
authors.lastname: Laeyendecker
authors.forename: Y M
authors.initials: YM
authors.lastname: Wang
authors.forename: D L
authors.initials: DL
authors.lastname: Thomas
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D016174:Hepacivirus / Q000502:physiology*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D002679:Pan troglodytes; D010802:Phylogeny; D018807:Polymorphism, Single-Stranded Conformational; D017386:Sequence Homology, Amino Acid; D012692:Serial Passage; D014759:Viral Envelope Proteins / Q000235:genetics*; D014779:Virus Replication / Q000235:genetics*
chemical_list: D017931:DNA Primers; D014759:Viral Envelope Proteins; C091015:glycoprotein E2, Hepatitis C virus