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Updated: May 14, 2026
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods
Tanja Stadler1, Sebastian Bonhoeffer
1Institut für Integrative Biologie, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland. tanja.stadler@env.ethz.ch
Summary
This study introduces a novel phylogenetic method to quantify host population structure for disease transmission. The approach accurately estimates population dynamics, aiding in understanding sexually transmitted disease (STD) spread.
Area of Science:
- Epidemiology
- Phylogenetics
- Population Genetics
Background:
- Host population structure significantly impacts disease spread, especially for sexually transmitted diseases (STDs).
- Obtaining quantitative data on contact structures for STDs is challenging.
- Phylogenetic trees from pathogen genetic data offer insights into transmission dynamics.
Purpose of the Study:
- To develop a novel computational method for quantifying host population structure using phylogenetic trees.
- To estimate epidemiological parameters and understand disease transmission patterns.
- To assess the influence of different subpopulations on overall disease dynamics.
Main Methods:
- Developed a maximum-likelihood framework utilizing a multi-type branching process.
- Assigned hosts to distinct types (subpopulations) within the model.
- Applied the method to simulated phylogenetic trees and a real-world HIV-1 dataset from Latvia.
Main Results:
- The method accurately estimates population structure parameters from phylogenetic trees, even with unknown tip states.
- Quantified the impact of the intravenous drug user (IDU) epidemic on the heterosexual HIV-1 epidemic in Latvia.
- Identified superspreader dynamics within the men-having-sex-with-men (MSM) HIV-1 epidemic.
Conclusions:
- The new phylogenetic method provides a robust tool for quantifying host population structure in epidemiological studies.
- This approach enhances our understanding of disease transmission, particularly for STDs.
- The findings highlight the importance of subpopulation dynamics and superspreading in HIV-1 transmission.
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