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

Author:

Wagner Tyler1,Shweta FNU2ORCID,Murugadoss Karthik1,Awasthi Samir1,Venkatakrishnan AJ1ORCID,Bade Sairam3,Puranik Arjun1,Kang Martin1,Pickering Brian W2,O'Horo John C2,Bauer Philippe R2,Razonable Raymund R2,Vergidis Paschalis2,Temesgen Zelalem2,Rizza Stacey2,Mahmood Maryam2,Wilson Walter R2,Challener Douglas2ORCID,Anand Praveen3ORCID,Liebers Matt1,Doctor Zainab1,Silvert Eli1,Solomon Hugo1,Anand Akash3,Barve Rakesh3,Gores Gregory2,Williams Amy W2,Morice William G24,Halamka John2,Badley Andrew2,Soundararajan Venky1ORCID

Affiliation:

1. nference, Cambridge, United States

2. Mayo Clinic, Rochester, United States

3. nference Labs, Bangalore, India

4. Mayo Clinic Laboratories, Rochester, United States

Abstract

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.

Funder

National Institute of Allergy and Infectious Diseases

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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