ArticleJournal of acquired immune deficiency syndromes (1999)2021
HIV Care Prioritization Using Phylogenetic Branch Length.
Article in Journal of acquired immune deficiency syndromes (1999), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics.GigaByte (Hong Kong, China) · 2025Article
- Scalable Epidemic Simulation Using FAVITES-Lite.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana.BMC infectious diseases · 2022Article
- The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.Scientific reports · 2022Article
- NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit.GigaByte (Hong Kong, China) · 2022Article
- Phylogenetic prioritization of HIV-1 transmission clusters with viral lineage-level diversification rates.Evolution, medicine, and public health · 2022Article
- SEPIA: simulation-based evaluation of prioritization algorithms.BMC medical informatics and decision making · 2021Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe structure of the HIV transmission networks can be dictated by just a few individuals. Public health intervention, such as ensuring people living with HIV adhere to antiretroviral therapy and remain virally suppressed, can help control the spread of the virus. However, such intervention requires using limited public health resource allocations. Determining which individuals are most at risk of transmitting HIV could allow public health officials to focus their limited resources on these individuals.
settingMolecular epidemiology can help prioritize people living with HIV by patterns of transmission inferred from their sampled viral sequences. Such prioritization has been previously suggested and performed by monitoring cluster growth. In this article, we introduce Prioritization using AnCesTral edge lengths (ProACT), a phylogenetic approach for prioritizing individuals living with HIV.
methodsProACT starts from a phylogeny inferred from sequence data and orders individuals according to their terminal branch length, breaking ties using ancestral branch lengths. We evaluated ProACT on a real data set of 926 HIV-1 subtype B pol data obtained in San Diego between 2005 and 2014 and a simulation data set modeling the same epidemic. Prioritization methods are compared by their ability to predict individuals who transmit most after the prioritization.
resultsAcross all simulation conditions and most real data sampling conditions, ProACT outperformed monitoring cluster growth for multiple metrics of prioritization efficacy.
conclusionThe simple strategy used by ProACT improves the effectiveness of prioritization compared with state-of-the-art methods that rely on monitoring the growth of transmission clusters defined based on genetic distance.
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