# Phylodynamic Analysis of HIV Transmission Clusters in Kazakhstan for Targeted Interventions

> **NIH NIH R03** · YALE UNIVERSITY · 2021 · $63,996

## Abstract

PROJECT SUMMARY
The HIV epidemic in Central Asia, including Kazakhstan was originally confined largely to persons who inject
drugs (PWID), but is now spreading through sexual- and migrant-associated transmissions. Central Asia
represents the world's most rapidly growing HIV epidemic region. Phylogenetic transmission clusters,
composed of genetically similar HIV sequences (<1.5% diversity), represent recently-acquired/rapidly-
transmitting infections (transmission “hotspots”). Our objective is to identify PWID-associated currently at-risk
populations, sothey may be linked to services expeditiously.Our specific aims are: 1. Obtain sequences
from well-characterized Kazakhstani HIV-infected blood samples from PWID and other high risk
persons for phylodynamic and statistical modeling of HIV transmission clusters: To achieve this we will:
a) Analyze previously generated 800 HIV pol sequences, and prospectively collect 400 blood samples, from
consenting HIV-positive PWID and other high-risk groups, including men who have sex with men (MSM),
heterosexuals, and male/female sexual partners; b) Administer a validated questionnaire to 400 consenting
participants to characterize gender, sexual/social contacts, travel history, and risk behaviors; c) Include the
same data for the above-mentioned 800 HIV historic samples collected and previously characterized by our
collaborators; d) Extract HIV RNA/DNA from the prospective blood samples to carry out amplification and
sequencing of the HIV pol gene. 2. We will use these HIV DNA sequences and linked questionnaire data
to identify PWID-associated HIV transmission clusters and common clinical, sociodemographic and
behavioral characteristics to focus resources towards the most relevant settings/high-risk behaviors. These
clusters will be elucidated by: a) Using phylogenetic analysis to identify HIV subtypes/recombinant forms; b)
Determining profiles of drug resistance and trends of its spatiotemporal transmission; c) Using genetic
distance to the closest sequence as a measure of clustering and questionnaire data to identify subpopulations
exhibiting rapid transmission; d) Using our prospectively generated 400 HIV sequences along with historic 800
Kazakhstani (and central Asian sequences obtained from open-access databases) to determine whether
identified transmission clusters are newly emerging and/or rapidly expanding, and e) Inferring intra-Kazakhstan
and Central Asian movements of HIV-1 by applying structured coalescent phylogenetic models. These
analyses will be cross-confirmed using the open-source near real-time tracking platform, nextHIV, that
performs automated alignment, subtyping, genotypic resistance determination, phylogenetic reconstruction and
genetic distance clustering. The ultimate goal of our R03 small grant is to provide evidence regarding
transmission hotspots that will help target emerging/expanding transmission clusters, stimulating both HIV
control and prevention, and HIV molecular virology r...

## Key facts

- **NIH application ID:** 10212364
- **Project number:** 5R03DA052179-02
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Syed Ali
- **Activity code:** R03 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $63,996
- **Award type:** 5
- **Project period:** 2020-07-15 → 2022-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10212364

## Citation

> US National Institutes of Health, RePORTER application 10212364, Phylodynamic Analysis of HIV Transmission Clusters in Kazakhstan for Targeted Interventions (5R03DA052179-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10212364. Licensed CC0.

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