Assessing the Suitability of Next-Generation Viral Outgrowth Assays to Measure Human Immunodeficiency Virus 1 Latent Reservoir Size

Mars Stone; Daniel I S Rosenbloom; Peter Bacchetti; Xutao Deng; Melanie Dimapasoc; Sheila Keating; Sonia Bakkour; Douglas D Richman; John W Mellors; Steven G Deeks; Jun Lai; Subul Beg; Janet D Siliciano; Amélie Pagliuzza; Nicolas Chomont; Carol Lackman-Smith; Roger G Ptak; Michael P Busch

doi:10.1093/infdis/jiaa089

Assessing the Suitability of Next-Generation Viral Outgrowth Assays to Measure Human Immunodeficiency Virus 1 Latent Reservoir Size

J Infect Dis. 2021 Oct 13;224(7):1209-1218. doi: 10.1093/infdis/jiaa089.

Authors

Mars Stone^{1

2}, Daniel I S Rosenbloom³, Peter Bacchetti⁴, Xutao Deng^{1

2}, Melanie Dimapasoc¹, Sheila Keating^{1

2}, Sonia Bakkour^{1

2}, Douglas D Richman^{5

6}, John W Mellors⁷, Steven G Deeks⁸, Jun Lai⁹, Subul Beg⁹, Janet D Siliciano⁹, Amélie Pagliuzza¹⁰, Nicolas Chomont¹⁰, Carol Lackman-Smith¹¹, Roger G Ptak¹¹, Michael P Busch^{1

2}

Affiliations

¹ Vitalant Research Institute, San Francisco, California, USA.
² Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
³ Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, New York, USA.
⁴ Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.
⁵ VA San Diego Healthcare System, San Diego, California, USA.
⁶ Center for AIDS Research, University of California, San Diego, La Jolla, California, USA.
⁷ Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
⁸ Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA.
⁹ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
¹⁰ Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada.
¹¹ Southern Research, Frederick, Maryland, USA.

Abstract

Background: Evaluations of human immunodeficiency virus (HIV) curative interventions require reliable and efficient quantification of replication-competent latent reservoirs. The "classic" quantitative viral outgrowth assay (QVOA) has been regarded as the reference standard, although prohibitively resource and labor intensive. We compared 6 "next-generation" viral outgrowth assays, using polymerase chain reaction or ultrasensitive p24 to assess their suitability as scalable proxies for QVOA.

Methods: Next-generation QVOAs were compared with classic QVOA using single leukapheresis-derived samples from 5 antiretroviral therapy-suppressed HIV-infected participants and 1 HIV-uninfected control; each laboratory tested blinded batches of 3 frozen and 1 fresh sample. Markov chain Monte Carlo methods estimated extra-Poisson variation at aliquot, batch, and laboratory levels. Models also estimated the effect of testing frozen versus fresh samples.

Results: Next-generation QVOAs had similar estimates of variation to QVOA. Assays with ultrasensitive readout reported higher infectious units per million values than classic QVOA. Within-batch testing had 2.5-fold extra-Poisson variation (95% credible interval [CI], 2.1-3.5-fold) for next-generation assays. Between-laboratory variation increased extra-Poisson variation to 3.4-fold (95% CI, 2.6-5.4-fold). Frozen storage did not substantially alter infectious units per million values (-18%; 95% CI, -52% to 39%).

Conclusions: The data offer cautious support for use of next-generation QVOAs as proxies for more laborious QVOA, while providing greater sensitivities and dynamic ranges. Measurement of latent reservoirs in eradication strategies would benefit from high throughput and scalable assays.

Keywords: HIV cure; HIV reservoir; IUPM; Inducible HIV RNA; assay comparison; latency; leukapheresis; quantitative viral out growth assay (QVOA).

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Antiretroviral Therapy, Highly Active
CD4-Positive T-Lymphocytes
Case-Control Studies
HIV Infections* / drug therapy
HIV Infections* / virology
HIV Reverse Transcriptase
HIV-1 / genetics*
HIV-1 / isolation & purification
High-Throughput Nucleotide Sequencing / methods*
Humans
Leukapheresis
Viral Load
Virus Latency*
Virus Replication* / physiology

Substances

HIV Reverse Transcriptase

Abstract

Publication types

MeSH terms

Substances

Grants and funding