Performance of HIV-1 drug resistance testing at low-level viremia and its ability to predict future virologic outcomes and viral evolution in treatment-naive individuals

Abstract

Background: Low-level viremia (LLV; human immunodeficiency virus [HIV-1] RNA 50-999 copies/mL) occurs frequently in patients receiving antiretroviral therapy (ART), but there are few or no data available demonstrating that HIV-1 drug resistance testing at a plasma viral load (pVL) <1000 copies/mL provides potentially clinically useful information. Here, we assess the ability to perform resistance testing by genotyping at LLV and whether it is predictive of future virologic outcomes in patients beginning ART.

Methods: Resistance testing by genotyping at LLV was attempted on 4915 plasma samples from 2492 patients. A subset of previously ART-naive patients was analyzed who achieved undetectable pVL and subsequently rebounded with LLV (n = 212). A genotypic sensitivity score (GSS) was calculated based on therapy and resistance testing results by genotyping, and stratified according to number of active drugs.

Results: Eighty-eight percent of LLV resistance assays produced useable sequences, with higher success at higher pVL. Overall, 16 of 212 (8%) patients had pretherapy resistance. Thirty-eight of 196 (19%) patients without pretherapy resistance evolved resistance to 1 or more drug classes, primarily the nucleoside reverse transcriptase (14%) and/or nonnucleoside reverse transcriptase (9%) inhibitors. Patients with resistance at LLV (GSS <3) had a 2.1-fold higher risk of virologic failure (95% confidence interval, 1.2- to 3.7-fold) than those without resistance (P = .007). Progressively lower GSS scores at LLV were associated with a higher increase in pVL over time (P < .001). Acquisition of additional resistance mutations to a new class of antiretroviral drugs during LLV was not found in a subset of patients.

Conclusions: Routine HIV-1 genotyping of LLV samples can be performed with a reasonably high success rate, and the results appear predictive of future virologic outcomes.

Keywords: ART; HIV-1; low-level viremia; outcome; resistance.

Figure 1.

A, Success at testing depending on the viral load of the sample and polymerase chain reaction (PCR) attempted. Successful results were obtained in approximately 90% in samples with viral loads >250 copies/mL and decreased to 79% and 62% in samples with viral loads of 200–249 copies/mL or 50–99 copies/mL. Backup PCR (repetition of amplification with different primers when first attempt was unsuccessful) products were more commonly used at lower viral loads. B, Effect of duration of storage on successful PCR and sequencing. The samples with a longer age (time from collection to testing) had marginally lower success at testing. Samples <12 months old stored at −20°C had slightly greater testing success compared with those older than this; however, success in testing remained around 70%–90% in all samples.

Figure 2.

A, Time to virologic failure was more rapid in patients with resistance during low-level viremia (LLV). Kaplan-Meier curve of time to virologic failure >1000 copies/mL while remaining on constant therapy, as a function of whether patients had resistance at LLV (genotypic sensitivity score [GSS] <3) or not (GSS ≥3). Patients with resistance at LLV had a more rapid rate of virologic failure (P = .007). B, More extensive resistance at LLV leads to higher viral load rebounds. Progressively lower GSS scores at LLV were significantly associated with a higher increase in median plasma viral load over time in patients while remaining on constant therapy (overall P < .001).

Figure 3.

A, Time to virologic failure (patients with >1 viral input copies amplified, and sequence mixtures). B, Time to virologic failure (patients with 1 viral species amplified, and no sequence mixtures). Time to virologic failure curves are different between patients with resistance and no resistance whether virologic mixtures were observed in the sequence chromatograms (A) or not (B) (P = .007).