TY - JOUR
T1 - PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity
AU - Wymant, Chris
AU - Hall, Matthew
AU - Ratmann, Oliver
AU - Bonsall, David
AU - Golubchik, Tanya
AU - de Cesare, Mariateresa
AU - Gall, Astrid
AU - Cornelissen, Marion
AU - Fraser, Christophe
PY - 2018
Y1 - 2018
N2 - A central feature of pathogen genomics is that different infectious particles (virions, bacterial cells, etc.) within an infected individual may be genetically distinct, with patterns of relatedness amongst infectious particles being the result of both within-host evolution and transmission from one host to the next. Here we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbour subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner
AB - A central feature of pathogen genomics is that different infectious particles (virions, bacterial cells, etc.) within an infected individual may be genetically distinct, with patterns of relatedness amongst infectious particles being the result of both within-host evolution and transmission from one host to the next. Here we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbour subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner
U2 - https://doi.org/10.1093/molbev/msx304
DO - https://doi.org/10.1093/molbev/msx304
M3 - Article
C2 - 29186559
SN - 0737-4038
VL - 35
SP - 719
EP - 733
JO - Molecular Biology and evolution
JF - Molecular Biology and evolution
IS - 1
ER -