Detecting Sources of Immune Activation and Viral Rebound in HIV Infection

Stephen W. Wietgrefe, Lijie Duan, Jodi Anderson, Guillermo Marques, Mark Sanders, Nathan W. Cummins, Andrew D. Badley, Curtis Dobrowolski, Jonathan Karn, Amelie Pagliuzza, Nicolas Chomont, Geremy Sannier, Mathieu Dube, Daniel E. Kaufmann, Paul Zuck, Guoxin Wu, Bonnie J. Howell, Cavan Reilly, Alon Herschhorn, Timothy W. SchackerAshley T. Haase

Research output: Contribution to journalArticlepeer-review


Anti-retroviral therapy (ART) generally suppresses HIV replication to undetectable levels in peripheral blood, but immune activation associated with increased morbidity and mortality is sustained during ART, and infection rebounds when treatment is interrupted. To identify drivers of immune activation and potential sources of viral rebound, we modified RNAscope in situ hybridization to visualize HIV-producing cells as a standard against which to compare the following assays of potential sources of immune activation and virus rebound following treatment interruption: (i) envelope detection by induced transcription-based sequencing (EDITS) assay; (ii) HIVFlow; (iii) Flow-FISH assays that can scan tissues and cell suspensions to detect rare cells expressing env mRNA, gag mRNA/Gag protein and p24; and (iv) an ultrasensitive immunoassay that detects p24 in cell/tissue lysates at subfemtomolar levels. We show that the sensitivities of these assays are sufficient to detect one rare HIVproducing/ env mRNA1/p241 cell in one million uninfected cells. These high-throughput technologies provide contemporary tools to detect and characterize rare cells producing virus and viral antigens as potential sources of immune activation and viral rebound.

Original languageEnglish (US)
JournalJournal of virology
Issue number15
StatePublished - Aug 2022


  • HIV
  • immune activation
  • viral rebound

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology


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