HIV-1 genetic diversity to estimate time of infection and infer adherence to preexposure prophylaxis

Abstract

Objective: To estimate time of HIV infection in participants from the Bangkok Tenofovir Study (BTS) with daily oral tenofovir disoproxil fumarate (TDF) for preexposure prophylaxis (PrEP) and relate infection with adherence patterns.

Design: We used the diversity structure of the virus population at the first HIV RNA-positive sample to estimate the date of infection, and mapped these estimates to medication diaries obtained under daily directly observed therapy (DOT).

Methods: HIV genetic diversity was investigated in all 17 PrEP breakthrough infections and in 16 placebo recipients. We generated 10-25 HIV env sequences from each participant by single genome amplification, and calculated time since infection (and 95% confidence interval) using Poisson models of early virus evolution. Study medication diaries obtained under daily DOT were then used to compute the number of missed TDF doses at the approximate date of infection.

Results: Fifteen of the 17 PrEP breakthrough infections were successfully amplified. Of these, 13 were initiated by a single genetic variant and generated reliable estimates of time since infection (median = 47 [IQR = 35] days). Eleven of these 13 were under daily DOT at the estimated time of infection. Analysis of medication diaries in these 11 participants showed 100% adherence in five, 90-95% adherence in two, 55% adherence in one, and nonadherence in three.

Conclusion: We estimated time of infection in participants from BTS and found several infections when high levels of adherence to TDF were reported. Our results suggest that the biological efficacy of daily TDF against parenteral HIV exposure is not 100%.

Fig. 1.. Computation of number of tenofovir disoproxil fumarate doses taken within the estimated date of infection.

The diversity structure of the virus population (highlighter plot) defined at the first nucleic acid testing positive (NAT+) sample using single genome amplification and sequence analysis is used to estimate date of infection using the Poisson Fitter or Shifted Poisson Mixture Model (SPMM). Estimates of date of infection are then integrated with adherence maps generated under daily directly observed therapy to compute the number of TDF doses taken within this period of time. One square represents 1 day (red = missed TDF dose; blue = TDF dose taken). Orange circle denotes the last negative EIA or NAT specimen. The estimated time of infection (and 95% CI) is indicated with a green line. The highlighter plot illustrates the changes observed in each individual sequence relative to the consensus (A: green, T: red, G: orange, C: light blue, IUPAC: dark blue, gaps: gray, circle: APOBEC signatures, diamond: G to A conversions). EIA, enzyme immunoassay; NAT, nucleic acid testing; TDF, tenofovir disoproxil fumarate.

Fig. 2.. HIV env diversity in incident infections from the Bangkok Tenofovir Study (BTS) with daily tenofovir disoproxil fumarate.

Diversity was measured when HIV RNA was detected in plasma for the first time. This visit coincided with the seroconversion visit in 14 of the 17 infections in the TDF group, and in 15 of the 16 infections in the placebo group. Estimates of diversity were determined by measuring mean pairwise distances between individual sequences from each participant. Results are expressed as number of nucleotide substitutions per site. Horizontal lines denote median values for each group.

Fig. 3.. Analysis of pill taking behavior at the estimated time of infection.

The estimated infection time (and 95% CI) is indicated with a green line. Adherence diaries obtained under daily directly observed therapy (horizontal lines) were used to manually count the number of missed TDF doses within this period of time. One square represents 1 day (red = missed TDF dose; blue = TDF dose taken). Each block represents 1 month. Orange circle denotes the last negative EIA or NAT specimen. CI, confidence interval; TDF, tenofovir disoproxil fumarate.

Fig. 4.. Effect of preexposure prophylaxis with tenofovir disoproxil fumarate or emtricitabine/tenofovir disoproxil fumarate on the length of the virus eclipse phase in macaques infected with simian HIV.

These macaques were part of studies assessing how high virus doses affect PrEP efficacy, and received placebo or daily PrEP with TDF [26] or FTC/TDF. Animals were exposed to a single high (1000 TCID50) dose of a SHIV162p3 isolate containing the HIV-1 envelope, and received clinically equivalent doses of TDF (22 mg/kg) or a combination of TDF (22 mg/kg) and FTC (20 mg/kg). Treatment was initiated 7 days prior to SHIV exposure and stopped 28 days after virus inoculation. (a) Time for SHIV RNA detection in plasma. (b) Impact of TDF or FTC/TDF on the length of the virus eclipse phase as defined by RNA detection in plasma. Time of RNA detection increased from 7 days in untreated animals (n = 10), to 11.7 in animals receiving daily TDF (n = 3) and 21 days in animals receiving daily FTC/TDF ([26] and unpublished observation). FTC, emtricitabine; PrEP, preexposure prophylaxis; SHIV, simian HIV; TDF, tenofovir disoproxil fumarate.