Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis

• Main Authors: Tyler Wagner, FNU Shweta, Karthik Murugadoss, Samir Awasthi, AJ Venkatakrishnan, Sairam Bade, Arjun Puranik, Martin Kang, Brian W Pickering, John C O'Horo, Philippe R Bauer, Raymund R Razonable, Paschalis Vergidis, Zelalem Temesgen, Stacey Rizza, Maryam Mahmood, Walter R Wilson, Douglas Challener, Praveen Anand, Matt Liebers, Zainab Doctor, Eli Silvert, Hugo Solomon, Akash Anand, Rakesh Barve, Gregory Gores, Amy W Williams, William G Morice II, John Halamka, Andrew Badley, Venky Soundararajan
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2020-07-01
• Series: eLife
• Subjects: electronic health record; neural networks; machine learning; artificial intelligence; COVID-19; SARS-CoV-2
• Online Access: https://elifesciences.org/articles/58227

Understanding temporal dynamics of COVID-19 symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation of clinical notes from 77,167 patients subjected to COVID-19 PCR testing. By contrasting Electronic Health Record (EHR)-derived symptoms of COVID-19-positive (COVIDpos; n = 2,317) versus COVID-19-negative (COVIDneg; n = 74,850) patients for the week preceding the PCR testing date, we identify anosmia/dysgeusia (27.1-fold), fever/chills (2.6-fold), respiratory difficulty (2.2-fold), cough (2.2-fold), myalgia/arthralgia (2-fold), and diarrhea (1.4-fold) as significantly amplified in COVIDpos over COVIDneg patients. The combination of cough and fever/chills has 4.2-fold amplification in COVIDpos patients during the week prior to PCR testing, in addition to anosmia/dysgeusia, constitutes the earliest EHR-derived signature of COVID-19. This study introduces an Augmented Intelligence platform for the real-time synthesis of institutional biomedical knowledge. The platform holds tremendous potential for scaling up curation throughput, thus enabling EHR-powered early disease diagnosis.