Abstract
Purpose: Despite ART initiation in the acute phase of HIV infection (AHI), the viral reservoir persists. In the NOVA study, the viral reservoir declined between 24 and 156 weeks after ART initiation in individuals treated during AHI and correlated with the presence of HIV-specific CD8+ T-cell responses at 24 weeks. Now we further explore the effect of selective CD8+ T-cell pressure on viral integration sites.
Method: Two individuals participating in the Netherlands Cohort Study on Acute HIV Infection (NOVA study) (P1 and P2) were selected for an in-depth study (clinical characteristics shown in Fig. 1). HIV-specific CD8+ T-cell proliferative responses upon HIV peptide stimulation were determined by flow cytometry. Viral isolates were sequenced and analyzed for the presence of CD8+ T-cell epitopes using a HLA-I class binding prediction tool. HIV proviral structure and integration sites were characterized using a modified Integrated Proviral Sequencing Assay (IPSA).
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Results: In P1, strong, broad HIV-specific proliferative CD8+ T-cell responses were observed at 24 weeks, which corresponded with a substantial number of viral escape mutations in HLA-A*02:01:01, HLA-B*13:02:01, HLA-B*15:01:01 (Gag), HLA-B*13:02:01 and HLA-B*15:01:01 (Nef) restricted epitopes. In P2, low frequencies of proliferating CD8+ T-cells were observed at 24 weeks, which is reflected by a relatively low number of escape mutations at that time point. In P2 viral escape was mostly observed in HLA-B*40:01:02 (Gag) restricted epitopes and in HLA-A*01:01 and HLA-A*02:01:01 (Nef and Pol) restricted epitopes (Fig. 2). IPSA demonstrated a strong decrease in intact HIV DNA between 24 and 156 weeks in both participants. Interestingly, 65-77% of intact proviruses were located in a genic site, of which 33-66% in antisense region implying selection for transcriptionally latent proviruses.
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Conclusions: This study found that broad HIV-specific CD8+ T-cell responses drive viral escape mutations and associates with proviral loss and propensity of antisense (silent) integration.