ArticleJournal of acquired immune deficiency syndromes (1999)2015
Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns.
Article in Journal of acquired immune deficiency syndromes (1999), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Defining HIV-1 transmission clusters based on sequence data.AIDS (London, England) · 2017Pooled it
- Dynamics of clustering rates in the Rhode Island HIV-1 epidemic.AIDS (London, England) · 2025Article
- Predictors of HIV Molecular Cluster Membership and Implications for Partner Services.AIDS research and human retroviruses · 2023Article
- Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States.Viruses · 2022Article
- Evaluating the sensitivity of jurisdictional heterogeneity and jurisdictional mixing in national level HIV prevention analyses: context of the U.S. ending the HIV epidemic plan.BMC medical research methodology · 2022Article
- Molecular epidemiology of HIV-1 in Oryol Oblast, Russia.Virus evolution · 2022Article
- Detection of SARS-CoV-2 infection clusters: The useful combination of spatiotemporal clustering and genomic analyses.Frontiers in public health · 2022Article
- Characterization of HIV Risk Behaviors and Clusters Using HIV-Transmission Cluster Engine Among a Cohort of Persons Living with HIV in Washington, DC.AIDS research and human retroviruses · 2021Article
- Interplay Between Geography and HIV Transmission Clusters in Los Angeles County.Open forum infectious diseases · 2021Article
- Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context.Scientific reports · 2021Article
- Genetic clustering analysis for HIV infection among MSM in Nigeria: implications for intervention.AIDS (London, England) · 2020Observational
- Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes.Frontiers in microbiology · 2020Article
- Nation-Wide Viral Sequence Analysis of HIV-1 Subtype B Epidemic in 2003-2012 Revealed a Contribution of Men Who Have Sex With Men to the Transmission Cluster Formation and Growth in Japan.Frontiers in reproductive health · 2020Article
- Natural selection favoring more transmissible HIV detected in United States molecular transmission network.Nature communications · 2019Article
- Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing.Viruses · 2019Article
- A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses.AIDS research and human retroviruses · 2019Article
- Transmission patterns of HIV-1 non-R5 strains in Poland.Scientific reports · 2019Article
- Article
- Sexual, Social, and Genetic Network Overlap: A Socio-Molecular Approach Toward Public Health Intervention of HIV.American journal of public health · 2018Article
- HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men.AIDS research and human retroviruses · 2018Article
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6 authors.
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Abstract
introductionHIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago.
methodsWe performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients.
resultsWe compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. DISCUSSION: Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.
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