Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context
Open Access
- 8 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Scientific Reports
- Vol. 11 (1), 1-10
- https://doi.org/10.1038/s41598-021-82673-8
Abstract
This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010–2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.Funding Information
- National Institutes of Health (1R01MH100021, K01AI110181, R01AI136056)
- Centers for Disease Control and Prevention (5 NU62PS924515-03-00, 1 NU62PS924572-01-00)
This publication has 43 references indexed in Scilit:
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesBioinformatics, 2014
- Influenza A Virus Migration and Persistence in North American Wild BirdsPLoS Pathogens, 2013
- Phylogenetic insights into regional HIV transmissionAIDS, 2012
- Characterizing HIV Transmission Networks Across the United StatesClinical Infectious Diseases, 2012
- Ancient Hybridization and an Irish Origin for the Modern Polar Bear MatrilineCurrent Biology, 2011
- Longitudinal Phylogenetic Surveillance Identifies Distinct Patterns of Cluster DynamicsJAIDS Journal of Acquired Immune Deficiency Syndromes, 2010
- Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approachAIDS, 2010
- Bayesian Phylogeography Finds Its RootsPLoS Computational Biology, 2009
- An exploratory study on the social and genotypic clustering of HIV infection in men having sex with menAIDS, 2009
- A public health model for the molecular surveillance of HIV transmission in San Diego, CaliforniaAIDS, 2009