Establishment and implementation of an external quality assurance program for next-generation sequencing-based HIV drug resistance typing

Funding period: 2023–2025
Lead: Hezhao Ji
Total GRDI funding: $186,800

Effective monitoring of HIV drug resistance (HIVDR) is required at both individual and population levels for improved containment of HIV/AIDS. With previous GRDI support, NML scientists from the National Laboratory for HIV Genetics (NLHG) and the Bioinformatics Core developed a MiSeq-HyDRA platform for enhanced HIVDR surveillance by integrating next-generation sequencing into HIVDR typing. Similar technologies were also developed in other institutes worldwide recently. With proven sensitivity for minority variants, high cost-effectiveness and data throughput, NGS is a trending new standard for HIVDR test, replacing the conventional Sanger sequencing approach.

Notably, all existing NGS HIVDR methodologies were developed by varied independent groups with little coordination and no pre-existing guidelines to reference. This lack of convention leads to uncertainties in data reliability and makes comparing outputs from different protocols or labs unnecessarily challenging. Moreover, it impedes regulatory agencies’ ability to benchmark such assays for accreditation purposes. A well-developed external quality assurance (EQA) program that objectively assesses the lab capacity in performing NGS HIVDR assays and the data quality from such assays is urgently needed, yet to be developed, to facilitate the general adoption of such technology.

In September 2019, our NML project team hosted the 2nd international symposium on NGS HIVDR in Winnipeg, explicitly themed for the EQA strategies for such assays. A series of articles was published as the symposium proceedings, highlighting the requirement for an EQA program for NGS HIVDR assays and the challenges one may face setting it up. Unfortunately, the subsequent COVID-19 pandemic disrupted the international follow-up effort to establish such a program, which was a unanimous recommendation from this 2nd “Winnipeg Consensus” symposium[8].

By continuing to collaborate with our national and international counterparts, we propose to resume our actions on building and implementing an innovative EQA program to support the general adoption of NGS HIVDR technology in Canada and beyond. This proposal comprises proficiency test (PT) material preparation, NGS data assessment and scoring algorithm establishment, EQA web portal development, and the launch of an inaugural EQA program for NGS HIVDR typing. The project team includes NML staff from NLHG and the Bioinformatics Core. It also involves external partners from academia (Duke University & Stanford University), government (NIAID/USA) and non-government (WHO Global HIV Drug Resistance Network, and PAHO) programs for ensured success. The immediate output from this project is an international EQA program that enables an objective assessment of data quality from NGS HIVDR assays or the performance of a lab in conducting such assays. It will be equipped with a repository of well-characterized PT materials, a fully validated NGS HIVDR data scoring algorithm, and a web portal that automates EQA data submission, data assessment and scoring, and EQA reporting.

This new R&D effort will improve the mandated service from NLHG and further strengthen the international leadership of NML in the field. It also promotes NML international collaboration in addressing public health needs, especially within the WHO/PAHO framework. This prospective international EQA program will place NML/PHAC at the centre of genotypic HIVDR reference service internationally, and it may serve as a new portal for sharing NML expertise with the world.