Next generation sequencing reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Background: The emergence and spread of antiretroviral drug resistant HIV-1 variants is one of the major factors responsible for therapeutic failure in persons living with HIV (PLWH) as it jeopardises the efforts to reduce the progression of AIDS. While Sanger sequencing is the conventional method for HIV drug resistance testing, it is unable to detect low-abundance variants. This study assessed the impact of next-generation sequencing (NGS) on drug resistance testing before switching of therapy.

Methods: Blood samples were collected from 60 PLWH to detect for the presence of low-abundance drug resistance variants using NGS of HIV protease and reverse transcriptase genes. Sanger sequencing was performed for all the samples for validation purpose. We used the HyDRA bioinformatics pipeline was used to analyse for the drug resistance mutations and Stanford HIV drug resistance database for interpretations of the variants.

Results: Out of the 60 samples, 58 had complete sequence data and were considered for analysis. Low-abundance HIV drug resistance variants were identified in 38 out of the 58 samples (65.5%). Overall, we found 757 variants from the NGS data where the most prevalent minority variants were K65R (65.5%), K14R, K45R, L63P and I64V identified in 63.79% of the samples and I15V, K70R, V77I and L283I identified in 60.3% of the samples.

Conclusion: Findings from the study reveal that more than half (65.5%) of the sampled population harboured low-abundance HIV-1 variants, most of which were previously reported to cause virological failure and consequently antiviral drug resistance.