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

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...

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Autores principales:	Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b82366e3d40b4510b6e44d39f34ef2d9
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spelling	oai:doaj.org-article:b82366e3d40b4510b6e44d39f34ef2d92021-12-02T14:06:32ZPACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses10.1038/s41598-021-82043-42045-2322https://doaj.org/article/b82366e3d40b4510b6e44d39f34ef2d92021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82043-4https://doaj.org/toc/2045-2322Abstract 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.Pablo Acera MateosRenzo F. BalboaSimon EastealEduardo EyrasHardip R. PatelNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pablo Acera Mateos Renzo F. Balboa Simon Easteal Eduardo Eyras Hardip R. Patel PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
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.
format	article
author	Pablo Acera Mateos Renzo F. Balboa Simon Easteal Eduardo Eyras Hardip R. Patel
author_facet	Pablo Acera Mateos Renzo F. Balboa Simon Easteal Eduardo Eyras Hardip R. Patel
author_sort	Pablo Acera Mateos
title	PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
title_short	PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
title_full	PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
title_fullStr	PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
title_full_unstemmed	PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
title_sort	pacific: a lightweight deep-learning classifier of sars-cov-2 and co-infecting rna viruses
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b82366e3d40b4510b6e44d39f34ef2d9
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PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses

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