Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients

Abstract

Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/founder (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.

Figure 1. Plasma viral load and CD4 count in the two recipients during the first year of infection.

Plasma viral load in RNA copies/ml is plotted on a log₁₀ scale along the left vertical axis, while the CD4 T cell count in cells/µl is plotted along the right vertical axis. Time is indicated along the horizontal axis as days post-Fiebig Stage I/II in each recipient. The solid circles represent the longitudinal CD4 counts; the open circles represent plasma viral load. (A) HIV-1 elite controller R880F (B) HIV-1 rapid progressor R463F.

Figure 2. Kinetics of in vitro replication of viruses recovered from the earliest-available plasma samples from R880F and R463F and IMCs corresponding to each subject's deduced T/F virus sequence.

(A and B). Infection with virus isolates (A) or PBMC stocks derived from IMCs (B) was performed in either pools of human CD8 depleted PBMC isolated from 3 individual donors (A) or single individuals (B), and the data is representative of at least 3 independent experiments for each. Reverse transcriptase activity (measured in digital light units (DLU) or p24 antigen is plotted on a log₁₀ scale on the vertical axis against days following infection of cells in in vitro culture. HIV-1 NL4.3 is shown in (A) as a positive control for in vitro replication. (C). Analysis of the in vitro growth rates of viruses R880 and R463 from each of 9 experiments. The growth rate of each was calculated as the slope of increase in the logarithms of p24 or RT activity over the times when this increase was linear. A Wilcoxon signed-rank test was used to compare the ratios obtained in the experiments. (D). A competition growth assay was performed in triplicate as described in Methods with approximately equal input copies of R880F and R463F viral stocks. Relative amounts of each virus at days 2, 4, 6, 8, and 10 were determined by qPCR. (E). An amino acid sequence alignment of the B*5703 Gag CD8 T cell epitopes for the R880 transmission pair is shown.

Figure 3. T cell response kinetics during acute and early HIV-1 infection.

For both R880F (A) and R463F(B), individual peptide response magnitudes in an IFNγ ELISpot assay are shown as a percentage of the overall response. The insert shows the number of peptide responses detected and the total response magnitude (SFC/10⁶ PBMCs) at each of the time points tested. The sequences of the peptides are shown in Table 2.

Figure 4. Longitudinal autologous neutralizing antibody IC50 titer during the first year of infection.

(A). The IC50 neutralizing titer (plasma dilution) against the T/F virus Env-pseudotyped HIV-1 derived from either R463F or R880F is plotted on the vertical axis on a log scale. R463F is depicted by open triangles; R880F is depicted by open squares. These experiments were replicated independently at least 3 times. (B). Heat map showing autologous neutralizing Ab activity versus Envs sampled during the first year of infection. Upper Panel R880F, Lower Panel R463F. Plasma sample dates (post-Fiebig I/II) are shown across the top, and Env clones used as pseudotypes from each time point are shown on the left. Green indicates IC50 Ab titers less than 1∶100; yellow indicates IC50s between 1∶100–1∶1000; orange indicates IC50s between 1∶1000–1∶10,000; red indicates IC50s>1∶10,000.