Quantifying the HIV reservoir with dilution assays and deep viral sequencing

TL;DR

This paper develops statistical methods to improve estimation of HIV reservoir size by combining dilution assays and deep viral sequencing data, even with missing or imperfect data, aiding HIV cure research.

Contribution

It introduces new inference methods and a bias-corrected estimator for IUPM using combined assay data, implemented in an open-source R package.

Findings

Methods perform well in simulations

Application to real data demonstrates utility

Improved accuracy over traditional estimates

Abstract

People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but "latent" HIV still persists in viral reservoirs. Eliminating these reservoirs is the goal of HIV cure research. The quantitative viral outgrowth assay (QVOA) is commonly used to estimate the reservoir size, i.e., the infectious units per million (IUPM) of HIV-persistent resting CD4+ T cells. A new variation of the QVOA, the Ultra Deep Sequencing Assay of the outgrowth virus (UDSA), was recently developed that further quantifies the number of viral lineages within a subset of infected wells. Performing the UDSA on a subset of wells provides additional information that can improve IUPM estimation. This paper considers statistical inference about the IUPM from combined dilution assay (QVOA) and deep viral sequencing (UDSA) data, even when some deep sequencing data are missing. Methods are proposed to accommodate assays with wells sequenced at multiple dilution levels and with imperfect sensitivity and specificity, and a novel bias-corrected estimator is included for small samples. The proposed methods are evaluated in a simulation study, applied to data from the University of North Carolina HIV Cure Center, and implemented in the open-source R package SLDeepAssay.