@article{7ed3d25070944557877d4755d7299062,
title = "HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA)",
abstract = "The Intact Proviral DNA Assay (IPDA) was developed to address the critical need for a scalable method for intact HIV-1 reservoir quantification. This droplet digital PCR-based assay simultaneously targets two HIV-1 regions to distinguish genomically intact proviruses against a large background of defective ones, and its application has yielded insights into HIV-1 persistence. Reports of assay failures however, attributed to HIV-1 polymorphism, have recently emerged. Here, we describe a diverse North American cohort of people with HIV-1 subtype B, where the IPDA yielded a failure rate of 28% due to viral polymorphism. We further demonstrate that within-host HIV-1 diversity can lead the IPDA to underestimate intact reservoir size, and provide examples of how this phenomenon could lead to erroneous interpretation of clinical trial data. While the IPDA represents a major methodological advance, HIV-1 diversity should be addressed before its widespread adoption as a principal readout in HIV-1 remission trials.",
author = "Kinloch, {Natalie N.} and Yanqin Ren and {Conce Alberto}, {Winiffer D.} and Winnie Dong and Pragya Khadka and Huang, {Szu Han} and Mota, {Talia M.} and Andrew Wilson and Aniqa Shahid and Don Kirkby and Marianne Harris and Colin Kovacs and Erika Benko and Ostrowski, {Mario A.} and {Del Rio Estrada}, {Perla M.} and Avery Wimpelberg and Christopher Cannon and Hardy, {W. David} and Lynsay MacLaren and Harris Goldstein and Brumme, {Chanson J.} and Lee, {Guinevere Q.} and Lynch, {Rebecca M.} and Brumme, {Zabrina L.} and Jones, {R. Brad}",
note = "Funding Information: This work was supported by the Martin Delaney {\textquoteleft}BELIEVE{\textquoteright} Collaboratory (NIH grant 1UM1AI26617), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, and OAR. It was also supported in part by the NIH funded R01 grants AI31798 and AI147845 (to R.B.J.) and Canadian Institutes of Health Research (CIHR) project grant PJT-159625 (to Z.L.B.) and HB1-164063 (to Z.L.B. and M.A.O.). N.N.K. is supported by a CIHR Vanier Doctoral Award. A.S. is supported by a CIHR Doctoral Award. Z.L.B. is supported by a Scholar Award from the Michael Smith Foundation for Health Research. We thank the National Cancer Institute (NCI) Biological Research Branch for provision of IL-15 and IL-2, the NCI{\textquoteright}s AIDS and Cancer Virus Program for provision of HIV-1 p24 ELISA reagents, and the NIH AIDS Research and Reference Reagent Program for provision of the CCR5+ MOLT-4 cells. We thank Marina Caskey for providing dei-dentified samples from ART-na{\"i}ve donors used in this study. We thank the BC Centre for Excellence in HIV/AIDS for support. We thank the Massachusetts General Hospital Center for Computational & Integrative Biology DNA Core, specifically Nicole Stange-Thomann, Amy Avery, Kristina Belanger, and Huajun Wang for providing us with the Illumina MiSeq deep sequencing service used in this manuscript. We thank Bruce Ganase, Jeff Knaggs, Daniel MacMillan, Hanwei Sudderuddin and James Nakagawa for research and bioinformatics support and Gursev Anmole, Mark Brockman and Robert Holt for helpful discussions. We thank Michel Nussenzweig, Christian Gaebler and Yotam Bar-On for provision of materials and helpful discussions. We gratefully acknowledge the contributions of the study participants, without whom this work would not be possible. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
doi = "10.1038/s41467-020-20442-3",
language = "English (US)",
volume = "12",
journal = "Nature communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}
