PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity. Molecular Biology and Evolution
A central feature of pathogen genomics is that different infectious particles (virions and bacterial cells) within an infected individual may be genetically distinct, with patterns of relatedness among infectious particles being the result of both within-host evolution and transmission from one host to the next.
In the current work, Wymant and colleagues on behalf of the BEEHIVE Collaboration present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. The show that phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. In addition, phyloscanner allows to identify multiply infected individuals, as they harbor subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed.
The authors illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, Hepatitis C virus sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual.
In conclusion, phyloscanner aims to simplify identification of transmission, multiple infection, recombination, and contamination across pathogen genomics by providing a tool for automatic phylogenetic analysis of next generation sequencing deep sequencing data, or multiple genotypes per host generated by other means. Phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner.