# Viral Genetics Core

> **NIH NIH P01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2020 · $169,182

## Abstract

Viral rebound from latent HIV-1 reservoirs is the major threat for HIV-positive patients. One major hurdle in 
defining viral rebound is the inability of current technology to accurately quantify the latent HIV-1 viral pool and 
track the reactivation and viral expansion events that contribute to the rebound process. The overall goal of this 
program project is to develop a better understanding of HIV rebound using the humanized BLT (bone marrowliver- 
thymus) mouse model for HIV infection and latency. To improve this model, we have developed a barcode 
approach to track the HIV infection during initial acute infection, ART suppression (latency) and rebound with 
Drs. Matt Marsden and Jerry Zack. We have also developed highly sensitive sequencing approach with Dr. 
Otto Yang to define viral quasi-species in HIV patient samples, which will be applied to our analysis of viral 
sequences in this project. In pursuit of the goals of the P01, Core B will provide novel viral genetic technology. 
The rationale for this technology is to enable more precise measurements of HIV-1 latently infected cells that 
are induced to express in vivo, and to more effectively monitor the viral strains that emerge and predominate in 
the plasma and tissues during rebound. Our innovative strategy involves barcoding individual HIV-1 viruses 
and then using them for tracking infection, thereby enabling the marking of each latently infected cell with a 
unique barcode identifier, and thereafter progeny viruses. The barcoded HIV-1 latent pool will then allow us to 
track the viral activity (transcription and virion production) in each latently infected cell as well as the fate of 
these latently infected cells by sequence analysis of the barcodes present in samples harvested from in vitro 
and in vivo experiments. The objective of this Viral Genetic Core is to provide technical support for tracking HIV 
during acute infection, latency and rebound with the following specific aims: 
Specific Aim 1. Construction and characterization of barcoded HIV virus libraries. 
Specific Aim 2. Sequencing-analyses the barcoded libraries during acute infection, latency and rebound. 
We will provide barcode technology to understand the tissue location of latent reservoirs, how tissue/cellular 
environment and immune responses impact reactivation potentials, and subsequent expansion/elimination of 
the viral pool by various treatment and immune responses.

## Key facts

- **NIH application ID:** 10057931
- **Project number:** 5P01AI131294-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** YUSHENG du
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $169,182
- **Award type:** 5
- **Project period:** 2017-08-10 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10057931

## Citation

> US National Institutes of Health, RePORTER application 10057931, Viral Genetics Core (5P01AI131294-04). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10057931. Licensed CC0.

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