Journal article
New Assay Reveals Vast Excess of Defective over Intact HIV-1 Transcripts in Antiretroviral Therapy-Suppressed Individuals
HA Martin, GN Kadiyala, S Telwatte, A Wedrychowski, TH Chen, S Moron-Lopez, D Arneson, R Hoh, S Deeks, J Wong, SA Yukl
Journal of Virology | AMER SOC MICROBIOLOGY | Published : 2022
DOI: 10.1128/jvi.01605-22
Abstract
Most of the HIV DNA in infected individuals is noninfectious because of deleterious mutations. However, it is unclear how much of the transcribed HIV RNA is potentially infectious or defective. To address this question, we developed and validated a novel intact viral RNA assay (IVRA) that uses droplet digital reverse transcriptase PCR (dd-RT-PCR) for the commonly mutated packaging signal (Psi) and Rev response element (RRE) regions (from the intact proviral DNA assay [IPDA]) to quantify likely intact (Psi1 RRE1), 39 defective (Psi1 RRE2), and 59 defective (Psi2 RRE1) HIV RNA. We then applied the IPDA and IVRA to quantify intact and defective HIV DNA and RNA from peripheral CD41 T cells from ..
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Awarded by National Institute of Allergy and Infectious Diseases
Funding Acknowledgements
We thank the study participants for their generous donation of samples and the SCOPE project staff at Zuckerberg San Francisco General Hospital. This work was supported by the National Institute of Allergy and Infectious Diseases (R01AI132128 [S.Y./J.W.], P01AI169606 [S.Y.]) and the National Institute of Diabetes and Digestive and Kidney Diseases (R01DK108349 [S.Y.], R01DK120387 [S.Y.]). S.T. is supported by a CFAR Mentored Scientist in HIV Award (grant no. P30 AI027763, award no. A120163, principal investigator [PI] Paul Volberding) and the California HIV/AIDS Research Program (award no. BB19-SF-009/A135087). We declare that we have no competing interests. S.Y. designed the study; R.H., S.D., and J.W. provided samples; H.A.M., G.N.K., S.T., A.W., T.-H.C., and S.M.-L. designed experiments; H.A.M., G.N.K., S.T., A.W., T.-H.C., and S.M.-L. conducted experiments; H.A.M., G.N.K., D.A., and S.Y. analyzed data; S.Y. wrote the original draft; all authors reviewed and edited the manuscript; S.Y. and J.W. provided supervision and funding.