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.

FIG. 1.

HIV-1 p6-rt diversity in acute and early infections. (a) Population structure and diversity (measured as percent APD per site) of the p6-rt region in single genome sequences. Sequences obtained from the first available plasma sample postseroconversion from all 14 patients are shown on a schematic neighbor-joining phylogenetic tree rooted on the HIV-1 consensus B sequence. (b) Population structure in acute infection after single-variant transmission. A neighbor-joining phylogenetic tree was constructed for the p6-rt fragment from the first available plasma sample from one single-variant-infected patient (1004). (c) Population structure in acute infection after multiple-variant transmission. A neighbor-joining phylogenetic tree was constructed for the p6-rt fragment from the first available plasma samples from the two multiple-variant-infected patients, 1003 and 1005.

FIG. 2.

Diversity of single genome sequences obtained from the first available plasma samples for all 14 patients. APD values for the first available samples from single-variant-infected patients are shown with circles, and those for multiple-variant-infected patients are shown with diamonds. Neutral accumulation of diversity predicted from the estimated mutation rate of HIV-1 (assumed to be 3 × 10⁻⁵ mutation per base per replication cycle and 1 replication cycle per day) is also shown.

FIG. 3.

Synonymous and nonsynonymous differences in pro compared to consensus subtype B sequence. The Highlighter plot shows the locations of amino acid changes (red) and synonymous mutations (green) in the pro gene relative to the consensus of the single genome sequences obtained from the first available sample after infection for each patient in the study and compared to the consensus B sequence. The shaded areas show the clustering of nonsynonymous changes. Locations of known CTL epitopes are shown above the plot.

FIG. 4.

Amino acid changes in protease compared to the consensus subtype B sequence. The bar graphs show the proportions of single genome sequences with amino acid changes at the indicated amino acid positions in pro compared to the consensus B sequence at early and late time points after infection, with different colors representing different times after infection, as shown. Horizontal boxes above the graphs represent known CTL epitopes in the subtype B consensus sequence. Red boxes designate CTL epitopes with probable escape mutations compared to the consensus. Yellow boxes designate epitopes expected to be recognized by each patient's MHC. Plots of CD4⁺ T-cell counts as a function of time are shown in the inset graphs. Downward arrows indicate CD4 counts of <200. (a) Typical patient (3024) infected with a single variant; (b) patient (1003) infected with multiple variants; (c) patient (1001) who was superinfected about 4 months after primary infection. Plots for all patients are shown in Fig. S1 (PR) and S2 (RT) in the supplemental material.

FIG. 5.

Amino acid changes in protease compared to the consensus subtype B sequence. An enlarged view of a portion of a graph like those in Fig. 4 (shown in full in Fig. S1 in the supplemental material) is shown for the indicated singly infected patients. Stars indicate mutant epitopes matching patient MHC types that were wild type in the earliest available sample after infection.

FIG. 6.

Diversity in p6-rt and env in longitudinal samples from early HIV infections. The time after infection, the virus load, and the percent diversity are shown graphically for those patients for whom the first available sample was collected within 3 months of seroconversion.

FIG. 7.

Evolution in p6-rt and env in single-variant-infected patient 3024. The left panels show neighbor-joining phylogenetic trees of single genome sequences obtained from longitudinal samples for both p6-rt and env from this single-variant-infected patient. The trees are rooted on the sequences obtained from the first available sample. The time after infection, the virus load, and the percent diversity and divergence in each sample are also listed and shown graphically on the right.