RT Journal Article SR Electronic T1 Development of an HIV reporter virus that identifies latently infected CD4+ T cells JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.01.17.476679 DO 10.1101/2022.01.17.476679 A1 Kim, Eun Hye A1 Manganaro, Lara A1 Schotsaert, Michael A1 Brown, Brian D. A1 Mulder, Lubbertus C.F. A1 Simon, Viviana YR 2022 UL http://biorxiv.org/content/early/2022/01/18/2022.01.17.476679.abstract AB There is no cure for HIV infection as the virus establishes a latent reservoir, which escapes highly active antiretroviral treatments. One major obstacle is the difficulty to identify cells that harbor latent proviruses. We devised a novel viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and allows to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses make up over 50% of all infected cells. These latently infected cells harbor proviruses, but lack evidence for viral transcription. LTR silent integrations occurred to variable degrees in all CD4+ T-subsets examined with CD4+ TEM and CD4+ Treg displaying the highest frequency. Viral vectors such as the one described here, permit interrogation HIV latency at a single-cell resolution, revealing mechanisms of latency establishment and allowing for the characterization of effective latency reversing agents.Competing Interest StatementThe authors have declared no competing interest.