Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40–49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9–33.8% of the participants into clusters. HIV-TRACE grouped 2.9–12.8% of participants when using consensus sequences and 9.0–64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
Highlights
Washington, DC continues to experience a generalized HIV-1 epidemic
The number and size of transmission clusters may vary across HIV-1 gene regions[12,15,23,24,25], in this study we compared phylodynamic inferences based on the polymerase and envelope HIV-1 genes
The demographics of our subsample of DC Cohort participants reflects a similar composition of people living with HIV-1 (PLWH) in DC3,4 but includes slightly more participants infected through heterosexual contact and non-Hispanic Blacks, and a lower proportion of participants on ART than the overall Cohort sample
Summary
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. This study applies NGS to a subset of newly and previously diagnosed participants in the DC Cohort to characterize the recent (2016 and 2017) local phylodynamics of HIV-1 in Washington, DC. Towards this general aim, we 1) estimate the diversity of HIV-1 in Washington, DC, 2) determine the circulating drug resistant mutations, 3) identify and evaluate potential transmission clusters with consensus sequences and their association with epidemiologic and clinical factors, and 4) predict HIV-1 haplotypes for each sample and assess their potential for detecting transmission clusters. The number and size of transmission clusters may vary across HIV-1 gene regions[12,15,23,24,25], in this study we compared phylodynamic inferences based on the polymerase and envelope HIV-1 genes
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