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

Tyler Wagner,Zelalem Temesgen,Praveen Anand,Karthik Murugadoss,Paschalis Vergidis,Fnu Shweta,Martin Kang,Sairam Bade,Matt Liebers,Venky Soundararajan,Maryam Mahmood,Akash Anand,Arjun Puranik,Samir Awasthi,Aj Venkatakrishnan,Eli Silvert,Rakesh Barve,Hugo Solomon,John Halamka,Gregory J Gores ,Amy W Williams ,Douglas W Challener ,Zainab M Doctor ,Stacey A Rizza ,Walter R Wilson ,Brian Pickering ,William G Morice ,Raymund R Razonable ,John C O’horo ,Philippe R Bauer ,Andrew D Badley

doi:10.7554/elife.58227

Tyler Wagner, Zelalem Temesgen + Show 29 more

Open Access

https://doi.org/10.7554/elife.58227

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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.

Highlights

Coronavirus disease 2019 (COVID-19) is a respiratory infection caused by the novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2)
The clinical determination of the COVID-19 status for each patient was conducted using the SARSCoV-2 PCR (RNA) test approved for human nasopharyngeal and oropharyngeal swab specimens under the U.S FDA emergency use authorization (EUA)[8]
The COVIDpos cohort had a mean age of 41.9 years and was 51% male and 49% female while the COVIDneg cohort had a mean age of 50.7 years and was 43% male and 57% female

Summary

Introduction

Coronavirus disease 2019 (COVID-19) is a respiratory infection caused by the novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2). Following exposure and initial infection with SARS-CoV-2, likely through the upper respiratory tract, patients can remain asymptomatic with active viral replication for days before symptoms manifest[1,2,3]. The asymptomatic nature of initial SARSCoV-2 infection patients may be exacerbating the rampant community transmission observed[4]. It remains unknown why certain patients become symptomatic, and in those that do, the timeline of symptoms remains poorly characterized and non-specific. A small proportion of COVID-19 patients progress to severe illness, requiring hospitalization or intensive care management; among these individuals, mortality due to Acute Respiratory Distress Syndrome (ARDS) is higher[6].

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