PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity.
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...
| Main Authors: | , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Oxford University Press
2017
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| _version_ | 1797090597371117568 |
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| author | Wymant, C Hall, M Ratmann, O Bonsall, D Golubchik, T de Cesare, M Gall, A Cornelissen, M Fraser, C |
| author_facet | Wymant, C Hall, M Ratmann, O Bonsall, D Golubchik, T de Cesare, M Gall, A Cornelissen, M Fraser, C |
| author_sort | Wymant, C |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T03:20:56Z |
| format | Journal article |
| id | oxford-uuid:b7652459-cbc0-4acf-8906-97f69449bca3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:20:56Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:b7652459-cbc0-4acf-8906-97f69449bca32022-03-27T04:48:16ZPHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:b7652459-cbc0-4acf-8906-97f69449bca3EnglishSymplectic Elements at OxfordOxford University Press2017Wymant, CHall, MRatmann, OBonsall, DGolubchik, Tde Cesare, MGall, ACornelissen, MFraser, CA 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. |
| spellingShingle | Wymant, C Hall, M Ratmann, O Bonsall, D Golubchik, T de Cesare, M Gall, A Cornelissen, M Fraser, C PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title | PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title_full | PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title_fullStr | PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title_full_unstemmed | PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title_short | PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. |
| title_sort | phyloscanner inferring transmission from within and petween host pathogen genetic diversity |
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