ArticleAIDS research and human retroviruses2014
Impact of sampling density on the extent of HIV clustering.
Article in AIDS research and human retroviruses, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 3 of them syntheses that pooled it.
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Who cites it
50 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Challenges in Elucidating HIV-1 Genetic Diversity in the Middle East and North Africa: A Review Based on a Systematic Search.Viruses · 2025Pooled it
- Pooled it
- Defining HIV-1 transmission clusters based on sequence data.AIDS (London, England) · 2017Pooled it
- Trial
- AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS.bioRxiv : the preprint server for biology · 2024Article
- Molecular epidemiology to aid virtual elimination of HIV transmission in Australia.Virus research · 2024Review
- Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics.Bioinformatics advances · 2024Article
- AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters.Frontiers in bioinformatics · 2024Article
- Modeling homophily in dynamic networks with application to HIV molecular surveillance.BMC infectious diseases · 2023Article
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.PLoS computational biology · 2022Article
- Identifying HIV-1 Transmission Clusters in Uzbekistan through Analysis of Molecular Surveillance Data.Viruses · 2022Article
- Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya.Frontiers in microbiology · 2022Article
- Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study.Virus evolution · 2022Article
- Sorting by Race/Ethnicity Across HIV Genetic Transmission Networks in Three Major Metropolitan Areas in the United States.AIDS research and human retroviruses · 2021Article
- Longitudinal typing of molecular HIV clusters in a statewide epidemic.AIDS (London, England) · 2021Article
- Human Immunodeficiency Virus (HIV) Drug Resistance, Phylogenetic Analysis, and Superinfection Among Men Who Have Sex with Men and Transgender Women in Sub-Saharan Africa: HIV Prevention Trials Network (HPTN) 075 Study.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Phylogenetic Cluster Analysis: Persons With Undiagnosed Infection Drive Human Immunodeficiency Virus Transmission in a Population With High Levels of Virologic Suppression.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Article
- High Prevalence of HIV-1 Drug Resistance and Dynamics of Transmission Among High-Risk Populations in Port-au-Prince, Haiti.Journal of acquired immune deficiency syndromes (1999) · 2020Article
- Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial.The Journal of infectious diseases · 2020Article
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5 authors.
Funding
Abstract
Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50-70% are suggested for HIV-1 V1C5 cluster analysis.
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