# Unveiling the chromosomal address of intact HIV clones to provide insights into persistence

> **NIH NIH R21** · UNIVERSITY OF PENNSYLVANIA · 2020 · $205,069

## Abstract

The advent of antiviral therapy (ART) revealed a treatment-resistant reservoir in CD4+ T cells
capable of refueling HIV viremia when treatment is stopped. This reservoir is a major barrier to
achieving a cure for HIV infection. Recent work suggests reservoir decay on ART is slower in
some individuals due to proliferation of T cells containing intact proviruses since identical intact
sequences are predominant after many years on ART in roughly half of subjects. These
identical sequences likely represent clones of cells that have proliferated. The driving forces
behind proviral clonal expansion remain mysterious, but integration into introns of oncogenes
likely plays a role. To study this question, we combine proviral sequencing with integration site
sequencing. Our innovation is recognizing that to properly assign proviruses we need longer
stretches of HIV DNA than typically provided by current methodologies. We propose a new
method to clone integration sites that is based on long-range PCR techniques previously utilized
by our group. In Aim 1 we propose to develop a method that will capture unique junctions that
are created in proviruses with large deletions. These deleted proviruses retain splicing ability
and fall into two broad categories, those with strong and those with weak potential to express
HIV proteins. In Aim 2, we propose a method to clone the integration site of intact proviruses
which requires amplifying longer stretches of HIV DNA that are contiguous with the human
DNA. With this in mind, we describe a systematic approach to identify the chromosomal address
of the intact proviruses including intact proviral clones. We hypothesize that intact proviral
clones are generally in introns and that this placement within the intron plays an important role
in clonal expansion as it permits splicing of HIV to downstream exons of oncogenes. This in turn
provides a new target for HIV eradication strategies. The premise of our proposal is largely
based on preliminary data from our group showing that there are two counterbalancing forces
that cause (1) proviral contraction through immune clearance and (2) proviral expansion through
clonal proliferation after splicing to a downstream oncogene. We ask in this proposal if the same
two forces act on both defective and intact replication-competent proviruses. The significance of
our proposal include that it may contribute to growing evidence that the reservoir is more visible
than previously realized. Our work suggests that perturbing these two forces by either
enhancing immune clearance or targeting splicing or downstream exons of splicing may reduce
reservoir size. We envision this work could lead to a larger study to understand if dysfunctional
cytotoxic T cells have a role in intact proviral clonal expansion.

## Key facts

- **NIH application ID:** 9889887
- **Project number:** 5R21AI143564-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Una T O'Doherty
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $205,069
- **Award type:** 5
- **Project period:** 2019-03-08 → 2022-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9889887

## Citation

> US National Institutes of Health, RePORTER application 9889887, Unveiling the chromosomal address of intact HIV clones to provide insights into persistence (5R21AI143564-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/9889887. Licensed CC0.

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