ArticleScientific reports2020
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 10 citations in OpenAlex.
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States.Viruses · 2022Article
- Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1.Frontiers in microbiology · 2022Article
- HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations.Molecular biology and evolution · 2021Article
- Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020.Viruses · 2021Article
- Persistence of HIV transmission clusters among people who inject drugs.AIDS (London, England) · 2020Article
- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
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Corrections and comments
- Erratum issued
Authors and funding
9 authors at 14 institutions in 2 countries.
Funding
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.
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