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PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.
- Source :
-
Scientific reports [Sci Rep] 2021 Feb 05; Vol. 11 (1), pp. 3209. Date of Electronic Publication: 2021 Feb 05. - Publication Year :
- 2021
-
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.
- Subjects :
- COVID-19 Testing
Coinfection virology
Coronaviridae isolation & purification
Humans
Metapneumovirus classification
Metapneumovirus isolation & purification
Neural Networks, Computer
Orthomyxoviridae classification
Orthomyxoviridae isolation & purification
RNA Virus Infections virology
RNA Viruses classification
RNA-Seq
Rhinovirus classification
Rhinovirus isolation & purification
SARS-CoV-2 classification
Sensitivity and Specificity
COVID-19 diagnosis
Coinfection diagnosis
Deep Learning
RNA Virus Infections diagnosis
RNA Viruses isolation & purification
SARS-CoV-2 isolation & purification
Subjects
Details
- Language :
- English
- ISSN :
- 2045-2322
- Volume :
- 11
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Scientific reports
- Publication Type :
- Academic Journal
- Accession number :
- 33547380
- Full Text :
- https://doi.org/10.1038/s41598-021-82043-4