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?:abstract
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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.
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?:doi
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10.1038/s41598-021-82043-4
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document_parses/pmc_json/PMC7864945.xml.json
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?:title
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PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
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