Little is known about the establishment of HIV reservoir at the earliest stages of infection. Here, we analyzed clade C HIV-1 reservoir seeding in women identified with hyperacute infections in Durban, South Africa through twice-weekly screening of high-risk individuals.
PBMC were available from two patients detected at Fiebig II: (1) peak viremia 2.6×10[sup]6[/sup] HIV-1 RNA copies/mL, treated same day, (2) peak 7.7×10[sup]5[/sup], remained untreated, and two patients detected at Fiebig V: (3) peak 130, on-treatment for 7 days, (4) peak 5.7×10[sup]7[/sup], remained untreated. Longitudinal samples were available at 1, 6, and 12-month post-detection. Total PBMC DNA was extracted, diluted for single-template full-HIV-genome PCR, and Illumina deep-sequenced. ‘Intact’ proviral genomes were defined as the absence of deleterious mutations (out-of-frame indels, premature stop codons, large deletions).
Immediately post-detection at study baseline, HIV reservoir sizes in patients at Fiebig II was lower than those at Fiebig V (0.8, 2.2 versus 3.4, 31.1 genome-intact HIV per million PBMC), and relative contribution of intact genomes to the total pool of HIV DNA were higher in Fiebig II than V (82%, 100% versus 14%, 35%, Figure1). Also at baseline, no APOBEC3G/3F-hypermutated HIV DNA was detected at Fiebig II, in contrast to 5% and 4% at V. In all four patients, HIV reservoir sizes decreased over a year by ~1-10 fold. Among all 87 genome-intact proviruses detected in all patients over one year, 87-100% of genetic variations were single-base substitutions distributed evenly across the viral genome, suggesting that single-base substitution errors during reverse transcription was the predominant driver leading to early reservoir diversity. This diversity increased over time in untreated patients (median pairwise single-base differences within-sample increased from 0 to 18 and 4 to 39) but decreased in treated patients (from 3 to undetectable, and from 3 to 6 to 0). Of interest, a genome-intact provirus that had a single-base substitution that translated into Y143H, an integrase inhibitor resistance associated mutation, was detected 1-month post-detection from patient 1, whose regimen contained raltegravir since day-zero, indicating early-seeding of a drug-resistant variant.
Early HIV reservoirs in PBMC were small and had high levels of sequence homogeneity. Single-base substitutions were the major source of genetic diversity, and early treatment limited diversification.