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

Pablo Acera Mateos0, Renzo Balboa0, Simon Easteal0, Eduardo Eyras0, Hardip Patel0
(0) Australian National University

Find me on Tues Nov 24th, 1:40-3pm AEDT in Remo, table 91

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.

Biorxiv: https://doi.org/10.1101/2020.07.24.219097