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PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity
Chris Wymant1,2, Matthew Hall1,2, Oliver Ratmann2,3
1Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, United Kingdom.
Molecular Biology and Evolution
|November 30, 2017
Summary
This study introduces phyloscanner, a novel software tool for pathogen genomics. It enhances understanding of pathogen transmission and diversity within and between hosts using sequence data.
Area of Science:
- Genomics
- Epidemiology
- Bioinformatics
Background:
- Pathogen populations within a single host can be genetically diverse.
- Understanding within-host evolution and transmission dynamics is crucial for controlling infectious diseases.
Purpose of the Study:
- To introduce phyloscanner, a new software tool for analyzing pathogen genetic diversity.
- To enable high-resolution inference of transmission routes and identify multiply infected individuals.
Main Methods:
- Development of the phyloscanner software tool.
- Analysis of pathogen sequence data from viral (HIV-1, HCV) and bacterial (Streptococcus pneumoniae) pathogens.
- Application to data from various sequencing platforms (Illumina, Roche 454, Oxford Nanopore MinION).
Main Results:
- phyloscanner accurately infers transmission direction from sequence data alone.
- The tool identifies multiply infected individuals by detecting distinct, unconnected subpopulations.
- Low-level contamination is effectively flagged and removed, improving data quality.
Conclusions:
- phyloscanner offers unprecedented resolution into pathogen transmission processes.
- The software is versatile, applicable to diverse pathogens and sequencing technologies.
- This tool advances the field of pathogen genomics and outbreak investigation.
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