Selection on the human immunodeficiency virus type 1 proteome following primary infection

Abstract

Typically during human immunodeficiency virus type 1 (HIV-1) infection, a nearly homogeneous viral population first emerges and then diversifies over time due to selective forces that are poorly understood. To identify these forces, we conducted an intensive longitudinal study of viral genetic changes and T-cell immunity in one subject at < or =17 time points during his first 3 years of infection, and in his infecting partner near the time of transmission. Autologous peptides covering amino acid sites inferred to be under positive selection were powerful for identifying HIV-1-specific cytotoxic-T-lymphocyte (CTL) epitopes. Positive selection and mutations resulting in escape from CTLs occurred across the viral proteome. We detected 25 CTL epitopes, including 14 previously unreported. Seven new epitopes mapped to the viral Env protein, emphasizing Env as a major target of CTLs. One-third of the selected sites were associated with epitopic mutational escapes from CTLs. Most of these resulted from replacement with amino acids found at low database frequency. Another one-third represented acquisition of amino acids found at high database frequency, suggesting potential reversions of CTL epitopic sites recognized by the immune system of the transmitting partner and mutation toward improved viral fitness in the absence of immune targeting within the recipient. A majority of the remaining selected sites occurred in the envelope protein and may have been subjected to humoral immune selection. Hence, a majority of the amino acids undergoing selection in this subject appeared to result from fitness-balanced CTL selection, confirming CTLs as a dominant selective force in HIV-1 infection.

FIG. 1.

Clinical progression, venipuncture time points, and positive selection following acute HIV-1 infection in PIC1362. (A) Longitudinal viral load and CD4⁺ and CD8⁺ T-cell counts. The arrow indicates the single treatment of interleukin 2 (IL-2) taken by the subject. (B) Time points of IFN-γ ELISPOT analysis (row 1) and full-length (row 2) as well as subgenomic (row 3) sequencing, indicated by X's. Open circles indicate additional time points at which Gag p17 and p24 coding regions were sequenced. (C) Coding elements of the viral genome encompassed by targeted gene sequencing. (D) Codon positions of amino acids potentially under positive selection in the HIV-1 genome and their relationships to CTL responses and other potential selective forces. Reference epitopes were identified using peptides derived from HIV-1 subtype B lab strains or consensus sequences. Autologous epitopes were identified using peptides whose amino acid sequences were derived from the viral gene sequences of the subject. The numbers in parentheses correspond to the numbers of epitopes or amino acid sites within each category. Arrows pointing downward show sites mutated to a lower database (db) frequency, meaning the amino acid at a particular position had a database frequency of >50% during the initial infection and later mutated to a state with a database frequency of less than 50% and less than half of the database frequency of the initial state. Arrows pointing upward show sites mutated to a higher database frequency, meaning the amino acid at a particular position had a database frequency of <50% during the initial infection and later mutated to a state with a database frequency of more than 50% and at least twofold higher than the database frequency of the initial state. NGLS, N-linked glycosylation site.

FIG. 2.

Two major positive-selection forces hypothesized to act on HIV-1 during the natural course of infection: escape from CTL responses and increasing replication fitness. Dark-gray bars indicate immune escape mutations that are balanced by a partial loss in replication fitness. Light-gray bars indicate immune escape mutations that have little or no replication fitness cost. Thick vertical lines indicate sequence differences from the theoretically most replication-fit virus that have no or little effect on viral fitness.