Related Experiment Video
Updated: Dec 29, 2025
11:10
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
12.7K
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing
Keylie M Gibson1, Kamwing Jair2, Amanda D Castel2
1Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA. kmgibson@gwu.edu.
Scientific Reports
|February 8, 2020
Summary
Washington, DC
Area of Science:
- Epidemiology
- Virology
- Genetics
Background:
- Washington, DC faces a widespread HIV-1 epidemic.
- Understanding local HIV-1 transmission dynamics is crucial for public health interventions.
Purpose of the Study:
- To characterize the phylodynamics of the HIV-1 epidemic in Washington, DC.
- To analyze viral diversity, drug resistance mutations, and transmission clusters using next-generation sequencing (NGS).
Main Methods:
- Sequencing of viral samples from 68 participants (2016-2017) and integration with epidemiological data.
- Phylogenetic and network analyses of HIV-1 polymerase (pol) and envelope (env) genes.
- Haplotype reconstruction and HIV-TRACE analysis to infer transmission clusters.
Main Results:
- Higher HIV-1 diversity observed in men who have sex with men, heterosexual, and male participants.
- 54.0% of participants carried at least one drug-resistant mutation (DRM), with highest prevalence in the 40-49 age group (22.9%).
- Phylogenetic analysis identified transmission clusters, with haplotype reconstruction providing deeper insights and linking more participants.
Conclusions:
- NGS data coupled with epidemiological information provides a comprehensive understanding of the HIV-1 epidemic in DC.
- Haplotype reconstruction offers novel insights into HIV-1 phylodynamics and transmission networks.
- This study expands the understanding of HIV-1 diversity, drug resistance, and transmission dynamics in the DC epidemic.
