Background:
Two children, P1 and P2, living with HIV have persistent low-level viremia (LLV) despite adherence to ART documented by directly-observed-therapy and/or therapeutic drug monitoring. We hypothesized that their persistent viremia was due to clones of HIV-infected cells harboring HIV epitopes that escaped immune surveillance.
Methods:
Plasma HIV RNA was monitored. Blood RNA and DNA from P1 over 7 years and P2 over 6 years was used to generate HIV sequences (env, pol, HIV 5′ and 3′-half and 3Kb central region genomes), to determine HIV integration sites (HIVIS), and to evaluate immunologic biomarkers and HIV-specific immune responses.
Results:
Plasma HIV RNA levels ranged from 79-9176c/mL in P1 and 440-15600c/mL in P2; with levels decreasing over time although neither had specimens with undetectable viral loads. No drug resistance was detected in P1, and no novel mutations were detected in 73 single-genome-sequences (SGS) from P2 after immigration to the USA. C2V5 env SGS from P1 and P2 revealed no evidence of HIV evolution over time. P1’s 448 sequences and P2’s 816 sequences revealed 69 and 175 unique indels in the vpr and/or tat1 sequences, with 447/448 (99.8%) and 809/816 (99.1%) genomes having defects in one or both genes. In contrast, 0% of vpr and 0.5% of tat1 genes were defective in 394 DNA sequences from 4 individuals matched for ART-suppression. Elevated immune biomarkers included C-reactive protein and myeloid-derived-suppressor-cells in P1. The largest HIV cell clones comprised 5% of P1’s 235 and 3% of P2’s 287 HIVIS. Interferon-gamma ELISpots with (1) non-escaped predicted HIV HLA-binding peptides (76 for P1 and 25 for P2), (2) HIV Gag, Pol, and Nef potential T-cell epitope peptide pools from the NIH and (3) control antigens, detected reactive T cells to control antigens, but no reactive T cells to HIV (1) or (2) in P1 or P2 across multiple timepoints.
Conclusions:
Our data suggest that the persistent LLV in these two individuals is unlikely to have originated from proliferating HIV-infected clones or from ongoing HIV replication. Rather, their lack of HIV-specific T cell responses suggests that immune tolerance to HIV causes a failure to eliminate infected cells expressing HIV proteins. Furthermore, the near absence of intact vpr or tat1 and the high frequency of unique inactivating mutations in these genes suggests that ongoing selection maintains the cells with vpr- and tat1-deleted viruses, possibly by conferring resistance to apoptosis.