title: Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification.
abstract: Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences.
  
  
  OBJECTIVE
  Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains.
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Stoddard
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Shuyi
authors.initials: S
authors.lastname: Wang
authors.affiliation: T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Elena E
authors.initials: EE
authors.lastname: Giorgi
authors.affiliation: T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Department of Biology, Stanford University, Stanford, California, USA.
authors.forename: Lily M
authors.initials: LM
authors.lastname: Blair
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Gerald H
authors.initials: GH
authors.lastname: Learn
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.affiliation: Department of Transfusion Medicine, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: Harvey J
authors.initials: HJ
authors.lastname: Alter
authors.affiliation: Blood Systems Research Institute, University of California San Francisco, San Francisco, California, USA.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Busch
authors.affiliation: Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Fierer
authors.affiliation: T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Ruy M
authors.initials: RM
authors.lastname: Ribeiro
authors.affiliation: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Alan S
authors.initials: AS
authors.lastname: Perelson
authors.affiliation: T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Santa Fe Institute, Santa Fe, New Mexico, USA.
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Bhattacharya
authors.affiliation: Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA shawg@upenn.edu.
authors.forename: George M
authors.initials: GM
authors.lastname: Shaw
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D060005:Genotyping Techniques; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000635:transmission* / Q000662:veterinary / Q000821:virology; D006801:Humans; D016031:Liver Transplantation / Q000009:adverse effects*; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D002679:Pan troglodytes; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014019:Tissue Donors; D066027:Transplant Recipients