HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA)

• Published in: Nature communications Vol. 12; no. 1; pp. 165 - 10
• Main Authors: Kinloch, Natalie N., Ren, Yanqin, Conce Alberto, Winiffer D., Dong, Winnie, Khadka, Pragya, Huang, Szu Han, Mota, Talia M., Wilson, Andrew, Shahid, Aniqa, Kirkby, Don, Harris, Marianne, Kovacs, Colin, Benko, Erika, Ostrowski, Mario A., Del Rio Estrada, Perla M., Wimpelberg, Avery, Cannon, Christopher, Hardy, W. David, MacLaren, Lynsay, Goldstein, Harris, Brumme, Chanson J., Lee, Guinevere Q., Lynch, Rebecca M., Brumme, Zabrina L., Jones, R. Brad
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.01.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 13/1; 13/31; 38/77; 45; 45/23; 45/62; 631/1647/2234; 631/208/514; 692/308/575; 692/699/255/1901; Assaying; Base Sequence; Biodiversity; CD4-Positive T-Lymphocytes - virology; Clinical trials; Deoxyribonucleic acid; DNA; DNA, Viral - analysis; DNA, Viral - genetics; Failure; Failure rates; HIV; HIV Infections - virology; HIV-1 - genetics; Human immunodeficiency virus; Humanities and Social Sciences; Humans; multidisciplinary; Phylogeny; Polymerase Chain Reaction - methods; Polymorphism; Proviruses; Proviruses - genetics; Remission; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20442-3

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. The intact proviral DNA assay quantifies the genomically intact HIV reservoir, but assay failure due to HIV-1 polymorphism has been observed. Here, the authors report a 28% failure rate in a cohort of people with HIV-1, and note within-host HIV-1 diversity as a further challenge to IPDA accuracy.