Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context

Kayo Fujimoto,Lu-Yu Hwang,Richa Lavingia,Lambodhar Damodaran,Michelle Carr,Marlene Mcneese,John A Schneider,Joseph T Hicks,Natascha Del Vecchio,Justin Bahl,Ricardo Mora,Joel O Wertheim,Camden J Hallmark,Biru Yang

doi: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.

Highlights

The rate of diagnosis of human immunodeficiency virus (HIV) in the United States (U.S.) decreased between 2011 and 2015, certain subpopulations bear an excess burden of new HIV d iagnoses[1]
HIV-1 phylogenetic clusters in Houston/Harris County are characterized by subpopulations who are members of racial/ethnic minority groups
Hispanic and Latino populations are vulnerable to HIV viral transmission dynamics, increasing the HIV infection disparities due to structural drivers (e.g., HIV stigma in Hispanic/Latino communities, treatment accessibility/availability) that underlie the increase in new HIV infections among these populations[28]

Summary

Introduction

The rate of diagnosis of human immunodeficiency virus (HIV) in the United States (U.S.) decreased between 2011 and 2015, certain subpopulations bear an excess burden of new HIV d iagnoses[1]. A number of HIV-1 molecular epidemiological studies have identified subpopulations in transmission networks that were characterized in terms of cluster membership, cluster size, and the degree of connectivity within a cluster. Previous studies have identified and characterized emerging local transmission clusters and associated them with certain epidemiological profiles of co-clustered individuals in HIV-1 transmission networks. Our primary goal was to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations who act as sources and recipients of HIV-1 infection in the culturally and racially/ethnically diverse context of Houston/Harris County, TX. Our approach enabled us to reconstruct HIV-1 transmission clusters; infer demographic and risk parameters of HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and assess the effects of network mixing patterns based on racial/ethnic and age characteristics of the index person and partners on the degree of network connectivity.

Methods

Results

Conclusion