# Cellular and viral determinants of the persistent HIV reservoir

> **NIH VA I01** · VA SAN DIEGO HEALTHCARE SYSTEM · 2024 · —

## Abstract

Eradication of the latent HIV reservoir remains the major stumbling block to achieving cure. To eliminate this
reservoir, accurate definition (a biomarker) of latently infected cells of different types and within different
tissues is highly needed. Several biomarkers proposed previously were able to very modestly enrich (~10-fold)
for latently infected cells, but failed to capture the substantial portion of the latent reservoir. Without the
detailed characterization of latently infected cells, identification of a suitable biomarker to capture the majority
of the reservoir cells will remain challenging. Our long-term goal is to identify a biomarker of HIV latency that
can be translated into strategies to target latently infected cells for elimination. The overall objectives of this
application are to identify cellular and viral determinants of the persistent HIV reservoir and to test selected
biomarkers for their ability to capture latently infected cells in vitro and ex vivo. Our central hypothesis is that a
successful biomarker will be represented by reservoir determinants identified individually for cells of different
phenotypes and states. The term “phenotype” refers to the canonical phenotypic subsets defined with widely
used surface protein markers (for example, maturation phenotype – central memory; functional phenotype – T
helper 17). The term “state” refers to a cell state more broadly defined by the cell's total transcriptomic
signature: gene sets and pathways that are actively expressed. The rationale of the proposed research is the
expected improvement in the efficiency of the reservoir capture when heterogeneity of the reservoir cells is
taken into account. We will test our central hypothesis by pursuing the following specific aims: (1) Identify
cellular determinants of different reservoir subsets and test selected biomarkers for cell enrichment in vitro; (2)
Identify viral determinants of different reservoir subsets in vitro; (3) Validate the reservoir determinants and
selected biomarkers using samples from people with HIV. To identify cellular and viral determinants of the
persistent reservoir, latest innovations in RNA sequencing (RNA-Seq) technologies will be used. Single cell
RNA-Seq coupled with immunophenotyping will be used to characterize the phenotypes and states of cells that
can be infected with either CXCR4- or CCR5-tropic virus. Genes that can discriminate between latently
infected and uninfected cells will be identified individually within each cell type. To inform on how the identified
cellular determinants of the persistent reservoir relate to the type of provirus that they define, proviral activity in
different cell types will be characterized using single cell RNA-Seq data, full length sequencing of HIV
transcripts, and the PrimeFlow assay to quantify responsiveness of provirus to reactivation stimuli. Biomarkers
will be selected from sets of cellular determinants of the HIV reservoir in different cell subsets. Anti...

## Key facts

- **NIH application ID:** 10726613
- **Project number:** 5I01BX005285-03
- **Recipient organization:** VA SAN DIEGO HEALTHCARE SYSTEM
- **Principal Investigator:** Nadejda S Beliakova-Bethell
- **Activity code:** I01 (R01, R21, SBIR, etc.)
- **Funding institute:** VA
- **Fiscal year:** 2024
- **Award amount:** —
- **Award type:** 5
- **Project period:** 2021-10-01 → 2025-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10726613

## Citation

> US National Institutes of Health, RePORTER application 10726613, Cellular and viral determinants of the persistent HIV reservoir (5I01BX005285-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10726613. Licensed CC0.

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