title: Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.
abstract: Selecting human immunodeficiency virus (HIV) sequences for inclusion within vaccines has been a difficult problem, as circulating HIV strains evolve relentlessly and become increasingly divergent over time. We report an assessment of this divergence from three perspectives: (i) across different hosts as a function of time of infection, (ii) between donors and recipients in known transmission pairs, and (iii) within individual hosts over time in relation to the initially replicating virus and to the deduced ancestral sequence of the intrahost viral population. Surprisingly, we consistently found less divergence between viruses from different individuals sampled in primary infection than in individuals sampled at more advanced stages of illness. Furthermore, longitudinal analysis of intrahost divergence revealed a 2- to 3-year period of evolution toward a common ancestral sequence at the start of infection, indicating that HIV recovers certain ancestral features when infecting a new host. These results have important implications for the study of HIV population genetics and rational vaccine design, including favoring the inclusion of viral gene sequences taken early in infection.
authors.affiliation: Department of Microbiology, SC 42, University of Washington, Seattle, WA 98195, USA.
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Herbeck
authors.forename: David C
authors.initials: DC
authors.lastname: Nickle
authors.forename: Gerald H
authors.initials: GH
authors.lastname: Learn
authors.forename: Geoffrey S
authors.initials: GS
authors.lastname: Gottlieb
authors.forename: Marcel E
authors.initials: ME
authors.lastname: Curlin
authors.forename: Laura
authors.initials: L
authors.lastname: Heath
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
mesh_terms: D019143:Evolution, Molecular; D015686:Gene Products, env / Q000235:genetics; D015752:Genes, env; D014644:Genetic Variation; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D015686:Gene Products, env