title: Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals.
abstract: Studies on human immunodeficiency virus type 1 (HIV-1) diversity are critical for understanding viral pathogenesis and the emergence of immune escape variants and for design of vaccine strategies. To investigate HIV-1 population genetics, we used single-genome sequencing to obtain pro-pol and env sequences from longitudinal samples (n = 93) from 14 acutely or recently infected patients. The first available sample after infection for 12/14 patients revealed HIV-1 populations with low genetic diversity, consistent with transmission or outgrowth of a single variant. In contrast, two patients showed high diversity and coexistence of distinct virus populations in samples collected days after a nonreactive enzyme-linked immunosorbent assay or indeterminate Western blot, consistent with transmission or outgrowth of multiple variants. Comparison of PR and RT sequences from the first sample for all patients with the consensus subgroup B sequence revealed that nearly all nonsynonymous differences were confined to identified cytotoxic T-lymphocyte (CTL) epitopes. For HLA-typed patients, mutations compared to the consensus in transmitted variants were found in epitopes that would not be recognized by the patient's major histocompatibility complex type. Reversion of transmitted mutations was rarely seen over the study interval (up to 5 years). These data indicate that acute subtype B HIV-1 infection usually results from transmission or outgrowth of single viral variants carrying mutations in CTL epitopes that were selected prior to transmission either in the donor or in a previous donor and that reversion of these mutations can be very slow. These results have important implications for vaccine strategies because they imply that some HLA alleles could be compromised in newly acquired HIV infections.
authors.affiliation: HIV Drug Resistance Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD 21702-1201, USA. kearneym@ncifcrf.gov
authors.forename: M
authors.initials: M
authors.lastname: Kearney
authors.forename: F
authors.initials: F
authors.lastname: Maldarelli
authors.forename: W
authors.initials: W
authors.lastname: Shao
authors.forename: J B
authors.initials: JB
authors.lastname: Margolick
authors.forename: E S
authors.initials: ES
authors.lastname: Daar
authors.forename: J W
authors.initials: JW
authors.lastname: Mellors
authors.forename: V
authors.initials: V
authors.lastname: Rao
authors.forename: J M
authors.initials: JM
authors.lastname: Coffin
authors.forename: S
authors.initials: S
authors.lastname: Palmer
mesh_terms: D000328:Adult; D019943:Amino Acid Substitution / Q000235:genetics; D018984:Epitopes, T-Lymphocyte / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008137:Longitudinal Studies; D008297:Male; D008875:Middle Aged; D020125:Mutation, Missense; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018984:Epitopes, T-Lymphocyte; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1