A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing

• Published in: Scientific reports Vol. 10; no. 1; p. 1989
• Main Authors: Gibson, Keylie M., Jair, Kamwing, Castel, Amanda D., Bendall, Matthew L., Wilbourn, Brittany, Jordan, Jeanne A., Crandall, Keith A., Pérez-Losada, Marcos
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.02.2020; Nature Publishing Group
• Subjects: 45; 45/23; 45/77; 631/114/2785; 692/699/255/1901; Adult; Aged; Anti-HIV Agents - pharmacology; Anti-HIV Agents - therapeutic use; Cross-Sectional Studies; District of Columbia - epidemiology; Drug resistance; Drug Resistance, Viral - genetics; env Gene Products, Human Immunodeficiency Virus - genetics; Epidemics; Epidemics - statistics & numerical data; Epidemiology; Female; Genetic Variation; Haplotypes; Heterosexuality - statistics & numerical data; HIV; HIV Infections - drug therapy; HIV Infections - epidemiology; HIV Infections - transmission; HIV Infections - virology; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus; Humanities and Social Sciences; Humans; Male; Middle Aged; Molecular Epidemiology; multidisciplinary; Mutation Rate; Next-generation sequencing; Phylogenetics; Phylogeny; pol Gene Products, Human Immunodeficiency Virus - genetics; Science; Science (multidisciplinary); Sex Factors; Sexual and Gender Minorities - statistics & numerical data; Transgender Persons - statistics & numerical data; Young Adult; District of Columbia
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-58410-y

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.