Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
Public Health England, London, United Kingdom.
J Infect Dis. 2021 Sep 17;224(6):1048-1059. doi: 10.1093/infdis/jiab060.
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.
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.
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.
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.
为推进“90-90-90”的“治疗所有”目标，精准且具有成本效益的人类免疫缺陷病毒（HIV）发病率和耐药性监测工作非常重要。
我们开发了用于 HIV 发病率和耐药性检测的微滴 HIV 测序（HIDA），这是一种用于发病率和耐药性突变（DRM）检测的单次采血监测工具。我们在微滴内扩增全长 HIV 包膜和 pol 基因序列，这种分区扩增与长读高通量测序相结合，使我们能够恢复多个独特的序列。
与当前的发病率检测相比，我们在确定感染阶段方面的精确度更高，83 名新近感染和 81 名慢性感染个体的错误近期感染率（分类为慢性感染的比例）为 1.2%，近期感染平均持续时间（近期感染分类的平均时间跨度）为 262 天。微滴 HIV 测序显示出更高的检测少数变体和关联 DRM 的能力。通过筛查所有 93 种世界卫生组织监测 DRM，我们检测到 6 种预处理耐药突变，其流行率为 2.6%-13.2%，并关联了突变。
微滴 HIV 测序的 HIDA 可能通过作为一种精确和高通量的横断面调查工具来促进全球 HIV 实时监测，该工具可推广用于其他病原体的监测。
