HIV Reservoir Quantification Using Cross-subtype Multiplex DdPCR

Overview

Journal iScience

Publisher Cell Press

Date 2022 Feb 2

PMID 35106463

Authors

Noah A J Cassidy

Carolyn S Fish

Claire N Levy

Pavitra Roychoudhury

Daniel B Reeves

Sean M Hughes

Joshua T Schiffer

Sarah Benki-Nugent

Grace John-Stewart

Dalton Wamalwa

Keith R Jerome

Julie Overbaugh

Florian Hladik

Dara A Lehman

Affiliations

Soon will be listed here.

Abstract

A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%-33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.

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