PHYLOSCANNER: inferring transmission from within- and between-host pathogen genetic diversity

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Title: PHYLOSCANNER: inferring transmission from within- and between-host pathogen genetic diversity
Authors: 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, and The BEEHIVE Collaboration
Item Type: Journal Article
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
Issue Date: 23-Nov-2017
Date of Acceptance: 13-Nov-2017
ISSN: 1537-1719
Publisher: Oxford University Press (OUP)
Start Page: 719
End Page: 733
Journal / Book Title: Molecular Biology and Evolution
Volume: 35
Issue: 3
Copyright Statement: © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: Medical Research Council (MRC)
Commission of the European Communities
Bill & Melinda Gates Foundation
Funder's Grant Number: MR/K010174/1B
GCAEN 511473
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Evolutionary Biology
Genetics & Heredity
molecular epidemiology
pathogen transmission
multiple infection
pathogen genomics
pathogen diversity
STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration
0604 Genetics
0603 Evolutionary Biology
0601 Biochemistry And Cell Biology
Publication Status: Published
Open Access location:
Appears in Collections:Mathematics
Faculty of Medicine
Faculty of Natural Sciences
Epidemiology, Public Health and Primary Care

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