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 identifying cells that harbor latent proviruses. We devised a single-round viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and make it possible to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses are found in more than 50% of infected cells. The latently infected cells harbor proviruses but lack evidence for multiple spliced transcripts. LTR-silent integrations occurred to variable degrees in all CD4+ T subsets examined, with CD4+ TEM and CD4+ TREG displaying the highest frequency of latent infections. This viral vector permits the interrogation of HIV latency at single-cell resolution, revealing mechanisms of latency establishment and allowing the characterization of effective latency-reversing agents.

Original languageEnglish
Article number100238
JournalCell Reports Methods
Issue number6
StatePublished - 20 Jun 2022


  • CD4 T cell subsets
  • CD4+ T memory cells
  • CD4+ T stem cells
  • HIV integration
  • HIV persistence
  • HIV reservoir
  • HIV-1
  • latency establishment
  • mass cytometry
  • reporter virus


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