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bioRxiv · 10.1101/2020.07.24.219097

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

Acera Mateos, P.·Balboa, R. F.·Easteal, S.·Eyras, E.·Patel, H. R.
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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.

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Acera Mateos, P., Balboa, R. F., Easteal, S., Eyras, E., Patel, H. R.. 2020-07-24. PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. https://doi.org/10.1101/2020.07.24.219097

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