Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
Highlights
In an effort to end the HIV epidemic by 2030, the UNAIDS 95-95-95 goals aim to ensure that 95% of all people living with HIV know their status, 95% of all people diagnosed receive sustained antiretroviral treatment (ART), and 95% of all people receiving ART have sustainable viral suppression [1,2]
HIV-1 drug resistance (HIVDR) mutations detected by Sanger sequencing have been shown to predict treatment response, making it a reliable method for use in making clinical decisions [10]
There remains a dearth of knowledge around the clinical significance of low-abundance drug-resistant variants (LA-DRVs) on ART effectiveness [13], a high concordance with Sanger sequencing has been shown in detection of mutations at ≥20% frequency [6]
Summary
In an effort to end the HIV epidemic by 2030, the UNAIDS 95-95-95 goals aim to ensure that 95% of all people living with HIV know their status, 95% of all people diagnosed receive sustained antiretroviral treatment (ART), and 95% of all people receiving ART have sustainable viral suppression [1,2]. Sanger sequencing remains the preferred clinical diagnostic method for HIVDR genotyping, generation sequencing (NGS) methods are becoming more affordable but their use in the therapeutic management of patients on ART is yet to be established [6]. This, means that Sanger sequencing does not reliably detect mutations that are less represented within the viral pool, known as low-abundance drug-resistant variants (LA-DRVs) [8,9]. HIVDR mutations detected by Sanger sequencing have been shown to predict treatment response, making it a reliable method for use in making clinical decisions [10]. Given its highthroughput and cost-efficiency through parallel sequencing and sample pooling, NGS is becoming a more common method for HIVDR genotyping [14,15]. We discuss the available and emerging Sanger sequencing and NGS methods for HIVDR genotyping, highlighting challenges for their use in RLS and for clinical diagnostics
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