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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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1 Australian National University, John Curtin School of Medical Research, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477); EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477)
2 Australian National University, John Curtin School of Medical Research, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477); Australian National University, National Centre for Indigenous Genomics, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477)
3 Australian National University, John Curtin School of Medical Research, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477); EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia (GRID:grid.1001.0) (ISNI:0000 0001 2180 7477); IMIM - Hospital del Mar Medical Research Institute, Barcelona, Spain (GRID:grid.20522.37) (ISNI:0000 0004 1767 9005); Catalan Institution for Research and Advanced Studies, Barcelona, Spain (GRID:grid.425902.8) (ISNI:0000 0000 9601 989X)