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

Acera Mateos, Pablo; Balboa, Renzo F.; Easteal, Simon; Eyras Jiménez, Eduardo; Patel, Hardip R.

doi:http://dx.doi.org/10.1038/s41598-021-82043-4

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

License

Citation

Acera 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/s41598-021-82043-4

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.