# A method for accurate and sensitive detection of HIV drug-resistant minority variants

> **NIH NIH R42** · MEDOSOME BIOTEC, LLC · 2022 · $999,999

## Abstract

PROJECT SUMMARY / ABSTRACT
Drug resistance to HIV is a major threat to achieving long-term viral suppression in HIV+ individuals. Up to
16% of newly infected individuals acquire HIV with resistance to at least one of the major antiretroviral classes,
and incomplete viral suppression and virologic failure are often associated with drug resistance. Therefore,
current DHHS guideline recommends drug resistance testing before beginning or changing antiretroviral
therapy. Genotypic assay based on population or bulk sequencing is the most commonly used method to
determine HIV drug resistance mutations. However, because HIV circulates as quasispecies in vivo, current
commercial assays are not sensitive in detecting minority drug resistant variants, which are known to
compromise clinical response to antiretroviral therapy. Therefore, an accurate and sensitive assay that is
capable of detecting drug resistant minority populations is urgently needed to guide rational selection of
optimal antiretroviral therapy. In Phase I STTR studies, we have developed a Single Variant Sequencing (SVS)
approach, which takes advantage of the speed and accuracy of the high-throughput MiSeq technology, and a
random sequencing tags strategy that removes biases and technical artifacts known to obscure true
representations of minority variants. We successfully optimized the primers, amplification and sequencing
conditions for the PR and RT regions of subtype B HIV-1, and determined the sensitivity, specificity and
precision of the assay. We showed that authentic minority variants present at 1% of quasispecies were
detected accurately and reproducibly with minimal variations between technical replicates. Building on our
success, this Phase II STTR application will complete the development of the assay by expanding to drug
resistant loci in the integrase gene and subtype C viruses, and then experimentally validate and commercialize
the SVS assay via four Specific Aims: 1) Complete the development of an optimized SVS assay for sensitive
quantification of HIV-1 subtype B and C drug resistance minority variants in RT, PR and IN genes, 2)
Experimentally validate the SVS assay using well characterized molecular clones and viruses, 3) Conduct pre-
market evaluation using real-world clinical samples, and 4) Validate the SVS assay in Medosome’s CLIA
certified and CAP accredited Florida licensed clinical genetic testing laboratory. An accurate and sensitive low
cost SVS assay will have tremendous commercialization potential, given the global burden of HIV with more
than 35 million HIV+ individuals requiring resistance testing at least once.

## Key facts

- **NIH application ID:** 10384312
- **Project number:** 2R42AI122855-02A1
- **Recipient organization:** MEDOSOME BIOTEC, LLC
- **Principal Investigator:** GARY P. WANG
- **Activity code:** R42 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $999,999
- **Award type:** 2
- **Project period:** 2016-03-15 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10384312

## Citation

> US National Institutes of Health, RePORTER application 10384312, A method for accurate and sensitive detection of HIV drug-resistant minority variants (2R42AI122855-02A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10384312. Licensed CC0.

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