Ratnapriya, SnehaHarris, MirandaChov, AngelaVrbanac, VladimirDeruaz, MaudSodroski, JosephHerschhorn, Alon2023-05-182021-08-31Ratnapriya, Sneha, Miranda Harris, Angela Chov, Zachary T. Herbert, Vladimir Vrbanac, Maud Deruaz, Vasudevan Achuthan, Alan N. Engelman, Joseph Sodroski, and Alon Herschhorn. 2021. “Intra- and Extra-Cellular Environments Contribute to the Fate of HIV-1 Infection.” Cell Reports (Cambridge) 36 (9): 109622–109622. https://doi.org/10.1016/j.celrep.2021.109622.2211-1247https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37375234HIV-1 entry into host cells leads to one of the following three alternative fates: (1) HIV-1 elimination by restriction factors, (2) establishment of HIV-1 latency, or (3) active viral replication in target cells. Here, we report the development of an improved system for monitoring HIV-1 fate at single-cell and population levels and show the diverse applications of this system to study specific aspects of HIV-1 fate in different cell types and under different environments. An analysis of the transcriptome of infected, primary CD4+ T cells that support alternative fates of HIV-1 identifies differential gene expression signatures in these cells. Small molecules are able to selectively target cells that support viral replication with no significant effect on viral latency. In addition, HIV-1 fate varies in different tissues following infection of humanized mice in vivo. Altogether, these studies indicate that intra- and extra-cellular environments contribute to the fate of HIV-1 infection.en-USJournal Article2023-05-1810.1101/2020.07.22.195719