Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
Explore this paper's citation graph
Summary
It is shown that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa, and a community-wide methods comparison exercise revealed current limits and strengths in using HIV phylogenetics in challenging settings.
- Type
- article
- Published
- 2016-10-07
- Cited by
- 63
- References
- 64
- Access
- Open access
- OpenAlex
- https://openalex.org/W2528483098
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:4160889
Keywords
Phylogenetic tree, Biology, Coalescent theory, Phylogenetics, Human immunodeficiency virus (HIV)
References
- Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana
- Fast Dating Using Least-Squares Criteria and Algorithms
- Estimating the Rate of Intersubtype Recombination in Early HIV-1 Group M Strains
- Mapping the Shapes of Phylogenetic Trees from Human and Zoonotic RNA Viruses
- Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
- Modeling and analyzing HIV transmission: the effect of contact patterns
- Evolutionary analysis of the dynamics of viral infectious disease
- Incidence of HIV-1 infection in a rural region of Uganda
- The PANGEA-HIV Consortium: Phylogenetics and Networks for Generalised HIV Epidemics in Africa
- BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
- HPTN 071 (PopART): A Cluster-Randomized Trial of the Population Impact of an HIV Combination Prevention Intervention Including Universal Testing and Treatment: Mathematical Model
- Cost-effectiveness of HIV prevention for high-risk groups at scale: an economic evaluation of the Avahan programme in south India.
- The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models
- Phylogenetic insights into regional HIV transmission
- Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- Coalescent inference for infectious disease: meta-analysis of hepatitis C
- High Coverage of ART Associated with Decline in Risk of HIV Acquisition in Rural KwaZulu-Natal, South Africa
Cited by
- Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
- Biased phylodynamic inferences from analysing clusters of viral sequences
- Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic
- External introductions helped drive and sustain the high incidence of HIV-1 in rural KwaZulu-Natal, South Africa
- HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences
- Phylodynamique des infections virales.
- Phylogenetic Inference of HIV Transmission Clusters
- Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in “Real-World” Settings
- Phylodynamic Model Adequacy Using Posterior Predictive Simulations
- Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control
- Bayesian phylodynamic inference with complex models
- FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences
- HIV-1 diversity among young women in rural South Africa: HPTN 068
- A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
- HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men
- Ethical Considerations in Global HIV Phylogenetic Research
- Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study
- SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces
- Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa
- Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models
Related papers
- Reconciling Phylodynamics with Epidemiology: The Case of Dengue Virus in Southern Vietnam
- Phylodynamics on local sexual contact networks
- How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics?
- Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes
- Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches
- For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies
- A phylogenomics approach for selecting robust sets of phylogenetic markers
- Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs
- Prokaryotic phylogenies inferred from protein structural domains.