ArticlePLoS medicine2013
HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis.
Article in PLoS medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 2 of them syntheses that pooled it.
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Who cites it
85 citing papers in PubMed, 2 syntheses or guidelines pooled it, 132 citations in OpenAlex.
- Pooled it
- Sexually transmitted hepatitis C virus infections: current trends, and recent advances in understanding the spread in men who have sex with men.Journal of the International AIDS Society · 2019Pooled it
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- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
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- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- A deep learning approach to real-time HIV outbreak detection using genetic data.PLoS computational biology · 2022Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- Markov genealogy processes.Theoretical population biology · 2022Article
- Evaluating whole HIV-1 genome sequence for estimation of incidence and migration in a rural South African community.Wellcome open research · 2022Article
- Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study.Virus evolution · 2022Article
- Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya.Frontiers in microbiology · 2022Article
- 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
- Article
- The Role of Dendritic Cells in TB and HIV Infection.Journal of clinical medicine · 2020Review
- Number of HIV-1 founder variants is determined by the recency of the source partner infection.Science (New York, N.Y.) · 2020Article
- Understanding the HIV Epidemic Among MSM in Baltimore: A Modeling Study Estimating the Impact of Past HIV Interventions and Who Acquired and Contributed to Infections.Journal of acquired immune deficiency syndromes (1999) · 2020Article
- Vaccines and Broadly Neutralizing Antibodies for HIV-1 Prevention.Annual review of immunology · 2020Review
25 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundConventional epidemiological surveillance of infectious diseases is focused on characterization of incident infections and estimation of the number of prevalent infections. Advances in methods for the analysis of the population-level genetic variation of viruses can potentially provide information about donors, not just recipients, of infection. Genetic sequences from many viruses are increasingly abundant, especially HIV, which is routinely sequenced for surveillance of drug resistance mutations. We conducted a phylodynamic analysis of HIV genetic sequence data and surveillance data from a US population of men who have sex with men (MSM) and estimated incidence and transmission rates by stage of infection. METHODS AND
findingsWe analyzed 662 HIV-1 subtype B sequences collected between October 14, 2004, and February 24, 2012, from MSM in the Detroit metropolitan area, Michigan. These sequences were cross-referenced with a database of 30,200 patients diagnosed with HIV infection in the state of Michigan, which includes clinical information that is informative about the recency of infection at the time of diagnosis. These data were analyzed using recently developed population genetic methods that have enabled the estimation of transmission rates from the population-level genetic diversity of the virus. We found that genetic data are highly informative about HIV donors in ways that standard surveillance data are not. Genetic data are especially informative about the stage of infection of donors at the point of transmission. We estimate that 44.7% (95% CI, 42.2%-46.4%) of transmissions occur during the first year of infection.
conclusionsIn this study, almost half of transmissions occurred within the first year of HIV infection in MSM. Our conclusions may be sensitive to un-modeled intra-host evolutionary dynamics, un-modeled sexual risk behavior, and uncertainty in the stage of infected hosts at the time of sampling. The intensity of transmission during early infection may have significance for public health interventions based on early treatment of newly diagnosed individuals.
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