PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses

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• dc.contributor.author Acera Mateos, Pablo
• dc.contributor.author Balboa, Renzo F.
• dc.contributor.author Easteal, Simon
• dc.contributor.author Eyras Jiménez, Eduardo
• dc.contributor.author Patel, Hardip R.
• dc.date.accessioned 2021-07-13T06:34:24Z
• dc.date.available 2021-07-13T06:34:24Z
• dc.date.issued 2021
• dc.description.abstract Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
• dc.format.mimetype application/pdf
• dc.identifier.citation Acera Mateos P, Balboa RF, Easteal S, Eyras E, Patel HR. PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. Sci Rep. 2021;11(1):3209. DOI: 10.1038/s41598-021-82043-4
• dc.identifier.doi http://dx.doi.org/10.1038/s41598-021-82043-4
• dc.identifier.issn 2045-2322
• dc.identifier.uri http://hdl.handle.net/10230/48162
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Sci Rep. 2021;11(1):3209
• dc.rights © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Clinical microbiology
• dc.subject.keyword Computational biology and bioinformatics
• dc.subject.keyword Genetics
• dc.subject.keyword Infectious-disease diagnostics
• dc.subject.keyword Microbiology
• dc.subject.keyword Molecular biology
• dc.subject.keyword Pathogens
• dc.subject.keyword Virology
• dc.title PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion