title: Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection.
abstract: To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24 gag were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (r = 0.43; P = 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack.
  
  
  OBJECTIVE
  Rapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens.
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors.forename: Justine E
authors.initials: JE
authors.lastname: Sunshine
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Brendan B
authors.initials: BB
authors.lastname: Larsen
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Brandon
authors.initials: B
authors.lastname: Maust
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Ellie
authors.initials: E
authors.lastname: Casey
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Wenje
authors.initials: W
authors.lastname: Deng
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Lennie
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Dylan H
authors.initials: DH
authors.lastname: Westfall
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Moon
authors.initials: M
authors.lastname: Kim
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Suvankar
authors.initials: S
authors.lastname: Ghorai
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.
authors.forename: Erinn
authors.initials: E
authors.lastname: Lanxon-Cookson
authors.affiliation: U.S. Military HIV Research Program, Silver Spring, Maryland, USA, and The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA.
authors.forename: Morgane
authors.initials: M
authors.lastname: Rolland
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Ann C
authors.initials: AC
authors.lastname: Collier
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Janine
authors.initials: J
authors.lastname: Maenza
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Department of Global Health, University of Washington, Seattle, Washington, USA nfrahm@fredhutch.org.
authors.forename: Nicole
authors.initials: N
authors.lastname: Frahm
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019277:Entropy; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D018703:Founder Effect; D056084:Genetic Fitness; D006679:HIV Seropositivity / Q000175:diagnosis / Q000276:immunology / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D057131:Immune Evasion / Q000235:genetics*; D007371:Interferon-gamma / Q000494:pharmacology; D007376:Interleukin-2 / Q000494:pharmacology; D008969:Molecular Sequence Data; D009154:Mutation; D061251:Primary Cell Culture; D012641:Selection, Genetic; D013602:T-Lymphocytes, Cytotoxic / Q000187:drug effects / Q000276:immunology / Q000821:virology; D019562:Viral Load; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics* / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D007376:Interleukin-2; D054301:gag Gene Products, Human Immunodeficiency Virus; D007371:Interferon-gamma