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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Email addresses: pablo.aceramateos{at}anu.edu.au (PAM), renzo.balboa{at}anu.edu.au (RFB), simon.easteal{at}anu.edu.au (SE), eduardo.eyras{at}anu.edu.au (EE), hardip.patel{at}anu.edu.au (HRP).