# Evolution  of  antiviral  resistance  mutations  and  their  biological  and  biophysical  implications

> **NIH NIH U54** · SEATTLE CHILDREN'S HOSPITAL · 2021 · $1,175,609

## Abstract

ABSTRACT
HIV-1 under antiretroviral treatment selects for genetically-linked mutations that are correlated due to
constraints on protein structural stability and function, which contribute to fitness. Project 5 studies are
concerned with analyzing pairs (or higher-order) patterns of antiretroviral resistance mutations and their
combined biophysical, biochemical, and structural effects on drug-resistance and viral fitness. During the past
funding period, new statistical methods were developed to identify correlative mutational patterns present in
genetically unlinked Gag and protease deep sequencing data. Potts Hamiltonian probabilistic models were
constructed from protease sequence alignments to identify mutational patterns that lead to drug-resistance.
To extend the past findings, it is proposed to identify genetically-linked patterns of antiretroviral resistance
mutations from full-length, individual viruses from clade B or non-clade B HIV-infected patients during
antiretroviral treatment. To investigate structural constraints in HIV proteins that influence selection of
resistance mutations, Potts models of protein sequence covariation will be developed utilizing sequence and
structural data. The combination of a novel full-length sequencing approach and virology expertise by Torbett
will be complemented by bioinformatics and modeling expertise of Levy to serve the following specific aims:
1) Identify genetically-linked drug-resistance mutations (pairs or higher order) from HIV in longitudinal patient
samples utilizing Multi-read Barcode-Assisted Single Molecule Sequencing (MrBASMS). Covariant
mutations will be functionally and structurally characterized using previously described biochemical,
biophysical and virological assays to validate their role in the rise of drug resistance.
2) Both full-length, from 1), and HIV sequence data from databases and structural information will be utilized to
construct Potts models of drug naïve and drug-experienced protease, reverse transcriptase, integrase and
Gag. Potts models will be used to investigate the effects of epistatic mutational combinations on fitness, as
well as predict HIV protein residues at risk for drug-resistance mutation development. These studies will
provide critical insight into HIV genetic barriers that must be overcome to develop resistance to multiple
inhibitor combinations.
The MrBASMS sequencing of HIV quasispecies from longitudinal patient samples will be led by Torbett and
Sarafianos, along with outside collaborator Routh (UTMB). The biochemical, structural and virological
validation of mutational covariants will be led by Torbett, Sarafianos and Levy, along with assistance from
Core 2. Levy will develop Potts models from HIV sequence data and protein structural information obtained
from Projects 1, 2, and Core 1.

## Key facts

- **NIH application ID:** 10242909
- **Project number:** 5U54AI150472-11
- **Recipient organization:** SEATTLE CHILDREN'S HOSPITAL
- **Principal Investigator:** Ronald Levy
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,175,609
- **Award type:** 5
- **Project period:** 2012-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10242909

## Citation

> US National Institutes of Health, RePORTER application 10242909, Evolution  of  antiviral  resistance  mutations  and  their  biological  and  biophysical  implications (5U54AI150472-11). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10242909. Licensed CC0.

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