PHYLOSCANNER: Analysing Within- and Between-Host Pathogen Genetic Diversity to Identify Transmission, Multiple Infection, Recombination and Contamination

Wymant, C.; Hall, M.; Ratmann, O.; Bonsall, D.; Golubchik, T.; de Cesare, M.; Gall, A.; Cornelissen, M.; Fraser, C.; - STOP-HCV Consortium,; - The Maela Pneumococcal Collaboration,; - The BEEHIVE Collaboration,

doi:10.1101/157768

bioRxiv · 10.1101/157768

PHYLOSCANNER: Analysing Within- and Between-Host Pathogen Genetic Diversity to Identify Transmission, Multiple Infection, Recombination and Contamination

Wymant, C.·Hall, M.·Ratmann, O.·Bonsall, D.·Golubchik, T.·de Cesare, M.·Gall, A.·Cornelissen, M.·Fraser, C.·- STOP-HCV Consortium,·- The Maela Pneumococcal Collaboration,·- The BEEHIVE Collaboration,

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Abstract

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.

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Wymant, C., Hall, M., Ratmann, O., Bonsall, D., Golubchik, T., de Cesare, M., Gall, A., Cornelissen, M., Fraser, C., - STOP-HCV Consortium,, - The Maela Pneumococcal Collaboration,, - The BEEHIVE Collaboration,. 2017-06-30. PHYLOSCANNER: Analysing Within- and Between-Host Pathogen Genetic Diversity to Identify Transmission, Multiple Infection, Recombination and Contamination. https://doi.org/10.1101/157768

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