Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium

Abstract

HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21–22 February, 2018), a second “Winnipeg Consensus” symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium’s goals and highlights.

Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays

“…NGS-based HIVDR assays have been shown to outperform their Sanger counterparts on numerous metrics, including sensitivity; however, their transition from a research tool to a clinical test has been slow. There are many reasons for this, which have been summarized well by Ji et al [31]. Multiple studies have done excellent work evaluating NGS-based HIVDR pipelines, including previous multi-laboratory collaborations [32,33].…”

HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies

“…There is currently only one commercially available NGS assay approved by the FDA in November 2019 for clinical HIVDR genotyping, known as the Sentosa SQ HIV-1 Genotyping Assay [12,50]. This is a standardized, semi-automated and novel deep in vitro sequencing assay developed by Vela Diagnostics (Vela-Diagnostics, Humburg, Germany) for sequencing the combined HIV-1 PR, RT and integrase (IN) genes with minimal expertise [51].…”

“…This could be achieved through internal and external quality assurance programs [11], and validating in-house assays against those that are FDA approved, such as the Sentosa SQ HIV-1 Genotyping Assay. Moreover, validation of commonly used data analysis pipelines for HIVDR mutation calling, such as HyDRA, PASeq and MiCall, is required to address challenges with bioinformatics and data quality [12]. These data analysis pipelines commonly comprise filtering of low-quality data, detection and quantification of amino acid variants at known mutation positions.…”

“…Despite that, 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]. On the other hand, NGS is more sensitive, having the ability to detect LA-DRVs (i.e., viral variants at <20%) [11], and enabling quantitative detection of HIVDR mutations [12]. However, there remains a dearth of knowledge around the clinical significance of LA-DRVs on ART effectiveness [13], although a high concordance with Sanger sequencing has been shown in detection of mutations at ≥20% frequency [6].…”

Next Generation Sequencing for HIV-1 Drug Resistance Testing—A Special Issue Walkthrough

“…Ji et al [ 19 ] and Avila-Rios et al [ 20 ] provide an overview to the theme of the Special Issue. Ji et al introduce the Second Winnipeg Symposium and highlight existing technical and knowledge gaps related to the adoption of NGS for HIV-1 drug resistance testing in clinical care, public health, and research.…”