In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Nat Commun. 2021 Jun 17;12(1):3727. doi: 10.1038/s41467-021-24080-1.


Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution from cell clones that harbor inducible proviruses to plasma viremia is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5'-end of the genome, often involving the major splice donor site. TCR and integration site sequencing reveal that cell clones with predicted pathogen-specificity can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we find several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, suggesting that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Retroviral Agents / therapeutic use*
  • CD4-Positive T-Lymphocytes / virology
  • DNA, Viral / blood
  • HIV Infections / blood*
  • HIV Infections / drug therapy*
  • HIV Infections / virology
  • HIV-1 / genetics
  • HIV-1 / metabolism*
  • HIV-1 / pathogenicity
  • Humans
  • Ionomycin / pharmacology
  • Male
  • Middle Aged
  • Phylogeny
  • Proviruses / genetics*
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Sequence Deletion
  • Single-Cell Analysis / methods*
  • Viral Load / genetics
  • Viremia / virology*


  • Anti-Retroviral Agents
  • DNA, Viral
  • Receptors, Antigen, T-Cell
  • Receptors, Antigen, T-Cell, alpha-beta
  • Ionomycin