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

Acera Mateos, PabloBalboa, Renzo F.Easteal, SimonEyras Jiménez, EduardoPatel, Hardip R.2021-07-132021-07-132021Acera 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/s41598-021-82043-42045-2322http://hdl.handle.net/10230/48162Viral 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.application/pdfeng© 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/.PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA virusesinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41598-021-82043-4Clinical microbiologyComputational biology and bioinformaticsGeneticsInfectious-disease diagnosticsMicrobiologyMolecular biologyPathogensVirologyinfo:eu-repo/semantics/openAccess