Background: Precise and cost-efficient human immunodeficiency virus (HIV) incidence and drug resistance surveillances are in high demand for the advancement of the 90-90-90 "treatment for all"target.
Methods: We developed microdrop HIV sequencing for the HIV incidence and drug resistance assay (HIDA), a single-blood-draw surveillance tool for incidence and drug resistance mutation (DRM) detection. We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences.
Results: We achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%-13.2% prevalence and cross-linked mutations.
Conclusions: HIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.
Bibliographical noteFunding Information: This work was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health (grant R01-AI095066) and the Bill & Melinda Gates Foundation (grants OPP1017716, OPP1062806, and OPP1115799 to CEPHIA).
Open Access: No Open Access licence.
Publisher Copyright: © 2021 The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved.
Citation: Sung Yong Park, Gina Faraci, Gary Murphy, Christopher Pilcher, Michael P Busch, Ha Youn Lee, Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance, The Journal of Infectious Diseases, Volume 224, Issue 6, 15 September 2021, Pages 1048–1059,
- Drug resistance mutations
- Genomic surveillance