Next Generation Sequencing Reveals a High Prevalence of HIV-1 Minority Variants and an Expanded Drug Resistance Profile Among Individuals Initiated to Antiretroviral Therapy in a Resource-constrained Setting

Abstract Introduction Because next-generation sequencing (NGS) can detect minority mutations that have been linked to treatment failure but are missed by population Sanger sequencing, it has the potential to enhance HIV treatment monitoring. Comparing NGS based on the Illumina platform to Sanger sequencing, we assessed the clinical importance of NGS in HIV-1 medication resistance testing. Methods In this retrospective case-control study, 167 people with matched Sanger sequencing data underwent HIV genotypic analysis using an Illumina-Miseq. These included 122 time-matched controls from the same cohort who had viral suppression at 12 months, and 45 patients with virologic failure at 12 months. Results NGS identified all major HIV drug resistance mutations detected by Sanger sequencing and revealed additional major mutations M184V and K65R that increased the resistance profile to antiretroviral therapy used in this cohort. Abacavir's HIV drug resistance score increased 60-fold, Zidovudine's by 25-fold and to Emtricitabine/Lamivudine by 90-fold. Overall, 108/167 (64.7%) of our subjects had minority DRMs at baseline. K70E, M184V, Y115F, and K70R were among the NRTI minority SDRMs discovered, whereas K103N, Y181C, and K101E were NNRTI minority SDRMs. PI minority SDRMs were also detected in 4 individuals. Being female ( p = 0.005 ) and having a CD4 < 250 cells/mL ( p = 0.029 ) were associated with minority mutations. Minority surveillance DRMs expanded the HIV drug resistance profiles of individuals. A higher frequency of baseline minority mutations correlated with a higher viral load count at end point ( p < 0.005 ). Conclusions NGS identified pre-treatment minority variants linked to increased viral load count and enhanced resistance to NNRTIs and NRTIs, and it detected more major mutations than Sanger sequencing. Being female and having low CD4 count were associated with presence of minority mutations. NGS could be used to create drug resistance profiles for people receiving HIV-1 ART, allowing clinicians to use both major and minor mutation profiles to inform treatment choices and so increase the effectiveness of the currently available antiretroviral medication. This may be crucial if the UNAIDS 95-95-95 targets are to be met and if we are to eliminate HIV/AIDS as a public health issue by 2030.