Automated detection and classification of polioviruses from nanopore sequencing reads using piranha.

Autor:	O'Toole Á; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK., Colquhoun R; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK., Ansley C; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK., Troman C; Department of Infectious Disease Epidemiology, Imperial College London, London W120BZ, UK., Maloney D; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK., Vance Z; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK., Akello J; Department of Infectious Disease Epidemiology, Imperial College London, London W120BZ, UK., Bujaki E; Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN63QG, UK., Majumdar M; Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN63QG, UK., Khurshid A; Department of Virology, National Institute for Health, Islamabad 44000, Pakistan., Arshad Y; Department of Virology, National Institute for Health, Islamabad 44000, Pakistan., Alam MM; Department of Virology, National Institute for Health, Islamabad 44000, Pakistan., Martin J; Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN63QG, UK., Shaw AG; Department of Infectious Disease Epidemiology, Imperial College London, London W120BZ, UK., Grassly NC; Department of Infectious Disease Epidemiology, Imperial College London, London W120BZ, UK., Rambaut A; Institute of Ecology & Evolution, University of Edinburgh, Edinburgh EH93FL, UK.
Jazyk:	angličtina
Zdroj:	Virus evolution [Virus Evol] 2024 Feb 29; Vol. 10 (1), pp. veae023. Date of Electronic Publication: 2024 Feb 29 (Print Publication: 2024).
DOI:	10.1093/ve/veae023
Abstrakt:	Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource automating nanopore haplotype analysis), a 'sequencing reads-to-report' solution to aid routine poliovirus testing of both stool and environmental samples and alleviate the bioinformatic bottleneck that often exists for laboratories adopting novel NGS approaches. Piranha can be used for efficient intratypic differentiation of poliovirus serotypes, for classification of Sabin-like polioviruses, and for detection of wild-type and vaccine-derived polioviruses. It produces interactive, distributable reports, as well as summary comma-separated values files and consensus poliovirus FASTA sequences. Piranha optionally provides phylogenetic analysis, with the ability to incorporate a local database, processing from raw sequencing reads to an interactive, annotated phylogeny in a single step. The reports describe each nanopore sequencing run with interpretable plots, enabling researchers to easily detect the presence of poliovirus in samples and quickly disseminate their results. Poliovirus eradication efforts are hindered by the lack of real-time detection and reporting, and piranha can be used to complement direct detection sequencing approaches. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu