1. Medicine
  2. Microbiology and Infectious Disease

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

  1. Tyler Wagner
  2. FNU Shweta
  3. Karthik Murugadoss
  4. Samir Awasthi
  5. AJ Venkatakrishnan
  6. Sairam Bade
  7. Arjun Puranik
  8. Martin Kang
  9. Brian W Pickering
  10. John C O'Horo
  11. Philippe R Bauer
  12. Raymund R Razonable
  13. Paschalis Vergidis
  14. Zelalem Temesgen
  15. Stacey Rizza
  16. Maryam Mahmood
  17. Walter R Wilson
  18. Douglas Challener
  19. Praveen Anand
  20. Matt Liebers
  21. Zainab Doctor
  22. Eli Silvert
  23. Hugo Solomon
  24. Akash Anand
  25. Rakesh Barve
  26. Gregory Gores
  27. Amy W Williams  Is a corresponding author
  28. William G Morice
  29. John Halamka
  30. Andrew Badley, MD  Is a corresponding author
  31. Venky Soundararajan  Is a corresponding author
  1. nference, United States
  2. Mayo Clinic, United States
  3. nference Labs, India
  4. nference, India
  5. Mayo Clinic Laboratories, United States
https://doi.org/10.7554/eLife.58227
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Cite this article
  1. Tyler Wagner
  2. FNU Shweta
  3. Karthik Murugadoss
  4. Samir Awasthi
  5. AJ Venkatakrishnan
  6. Sairam Bade
  7. Arjun Puranik
  8. Martin Kang
  9. Brian W Pickering
  10. John C O'Horo
  11. Philippe R Bauer
  12. Raymund R Razonable
  13. Paschalis Vergidis
  14. Zelalem Temesgen
  15. Stacey Rizza
  16. Maryam Mahmood
  17. Walter R Wilson
  18. Douglas Challener
  19. Praveen Anand
  20. Matt Liebers
  21. Zainab Doctor
  22. Eli Silvert
  23. Hugo Solomon
  24. Akash Anand
  25. Rakesh Barve
  26. Gregory Gores
  27. Amy W Williams
  28. William G Morice
  29. John Halamka
  30. Andrew Badley, MD
  31. Venky Soundararajan
(2020)
Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis
eLife 9:e58227.
https://doi.org/10.7554/eLife.58227
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  3. Download .RIS

Abstract

Understanding temporal dynamics of COVID-19 patient 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, and along with 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.

Data availability

The EHR dataset where augmented curation was conducted from the Mayo Clinic records was accessed under IRB 20-003278, "Study of COVID-19 patient characteristics with augmented curation of Electronic Health Records (EHR) to inform strategic and operational decisions". The EHR data cannot be shared or released due to HIPAA regulations. Contact corresponding authors for additional details regarding the IRB, and please refer to the Mayo Clinic IRB website for further details on our commitment to patient privacy (https://www.mayo.edu/research/institutional-review-board/overview). The summary statistics derived from the EHRs are enclosed within the manuscript.

Article and author information

Author details

  1. Tyler Wagner

    R and D, nference, Cambridge, United States
    Competing interests
    Tyler Wagner, is an employee of nference and has financial interests in the company..

  2. FNU Shweta

    Department of Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    FNU Shweta, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6634-6272

  3. Karthik Murugadoss

    Data Sciences, nference, Cambridge, United States
    Competing interests
    Karthik Murugadoss, is an employee of nference and has financial interests in the company..

  4. Samir Awasthi

    R and D, nference, Cambridge, United States
    Competing interests
    Samir Awasthi, is an employee of nference and has financial interests in the company..

  5. AJ Venkatakrishnan

    R and D, nference, Cambridge, United States
    Competing interests
    AJ Venkatakrishnan, is an employee of nference and has financial interests in the company..

  6. Sairam Bade

    Data Sciences, nference Labs, Bangalore, India
    Competing interests
    Sairam Bade, is an employee of nference and has financial interests in the company..

  7. Arjun Puranik

    Data Science, nference, San Francisco, United States
    Competing interests
    Arjun Puranik, is an employee of nference and has financial interests in the company..

  8. Martin Kang

    R and D, nference, Cambridge, United States
    Competing interests
    Martin Kang, is an employee of nference and has financial interests in the company..

  9. Brian W Pickering

    Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Brian W Pickering, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  10. John C O'Horo

    Division of Infectious Diseases, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    John C O'Horo, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  11. Philippe R Bauer

    Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Philippe R Bauer, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  12. Raymund R Razonable

    Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Raymund R Razonable, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  13. Paschalis Vergidis

    Infectious Diseases, Mayo Clinic, Rochester, United States
    Competing interests
    Paschalis Vergidis, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  14. Zelalem Temesgen

    Infectious Diseases, Mayo Clinic, Rochester, United States
    Competing interests
    Zelalem Temesgen, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  15. Stacey Rizza

    Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Stacey Rizza, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  16. Maryam Mahmood

    Infectious Diseases, Mayo Clinic, Rochester, United States
    Competing interests
    Maryam Mahmood, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  17. Walter R Wilson

    Department of Orthopedic Surgery, Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Walter R Wilson, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  18. Douglas Challener

    Infectious Diseases, Mayo Clinic, Rochester, United States
    Competing interests
    Douglas Challener, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6964-9639

  19. Praveen Anand

    R and D, nference, Bangalore, India
    Competing interests
    Praveen Anand, is an employee of nference and has financial interests in the company..

  20. Matt Liebers

    R and D, nference, Cambridge, United States
    Competing interests
    Matt Liebers, is an employee of nference and has financial interests in the company..

  21. Zainab Doctor

    R and D, nference, Cambridge, United States
    Competing interests
    Zainab Doctor, is an employee of nference and has financial interests in the company..

  22. Eli Silvert

    Data Sciences, nference, Cambridge, United States
    Competing interests
    Eli Silvert, is an employee of nference and has financial interests in the company..

  23. Hugo Solomon

    R&D, nference, Cambridge, United States
    Competing interests
    Hugo Solomon, is an employee of nference and has financial interests in the company..

  24. Akash Anand

    Data Science, nference, Bangalore, India
    Competing interests
    Akash Anand, is an employee of nference and has financial interests in the company..

  25. Rakesh Barve

    Data Sciences, nference, Bangalore, India
    Competing interests
    Rakesh Barve, is an employee of nference and has financial interests in the company..

  26. Gregory Gores

    Department of Orthopedic Surgery, Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    Competing interests
    Gregory Gores, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  27. Amy W Williams

    Division of Nephrology & Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, United States
    For correspondence
    Williams.Amy@mayo.edu
    Competing interests
    Amy W Williams, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  28. William G Morice

    Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic Laboratories, Rochester, United States
    Competing interests
    William G Morice, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  29. John Halamka

    Mayo Clinic Platform, Mayo Clinic, Rochester, United States
    Competing interests
    John Halamka, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  30. Andrew Badley, MD

    Mayo Clinic Platform, Mayo Clinic, Rochester, United States
    For correspondence
    Badley.Andrew@mayo.edu
    Competing interests
    Andrew Badley, MD, has a Financial Conflict of Interest in technology used in the research and with Mayo Clinic may stand to gain financially from the successful outcome of the research. This research has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies..

  31. Venky Soundararajan

    R&D, nference, Cambridge, United States
    For correspondence
    venky@nference.net
    Competing interests
    Venky Soundararajan, is an employee of nference and has financial interests in the company..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7434-9211

Funding

National Institute of Allergy and Infectious Diseases (AI 110173)

  • Andrew Badley, MD

National Institute of Allergy and Infectious Diseases (AI120698)

  • Andrew Badley, MD

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Frank L van de Veerdonk, Radboud University Medical Center, Netherlands

Ethics

Human subjects: This research was conducted under IRB 20-003278, "Study of COVID-19 patient characteristics with augmented curation of Electronic Health Records (EHR) to inform strategic and operational decisions". All analysis of EHRs was performed in the privacy-preserving environment secured and controlled by the Mayo Clinic. nference and the Mayo Clinic subscribe to the basic ethical principles underlying the conduct of research involving human subjects as set forth in the Belmont Report and strictly ensures compliance with the Common Rule in the Code of Federal Regulations (45 CFR 46) on Protection of Human Subjects. Please refer to the Mayo Clinic IRB website for further information - https://www.mayo.edu/research/institutional-review-board/overview

Version history

  1. Received: April 24, 2020
  2. Accepted: July 6, 2020
  3. Accepted Manuscript published: July 7, 2020 (version 1)
  4. Accepted Manuscript updated: July 8, 2020 (version 2)
  5. Version of Record published: August 6, 2020 (version 3)

Copyright

© 2020, Wagner et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Tyler Wagner
  2. FNU Shweta
  3. Karthik Murugadoss
  4. Samir Awasthi
  5. AJ Venkatakrishnan
  6. Sairam Bade
  7. Arjun Puranik
  8. Martin Kang
  9. Brian W Pickering
  10. John C O'Horo
  11. Philippe R Bauer
  12. Raymund R Razonable
  13. Paschalis Vergidis
  14. Zelalem Temesgen
  15. Stacey Rizza
  16. Maryam Mahmood
  17. Walter R Wilson
  18. Douglas Challener
  19. Praveen Anand
  20. Matt Liebers
  21. Zainab Doctor
  22. Eli Silvert
  23. Hugo Solomon
  24. Akash Anand
  25. Rakesh Barve
  26. Gregory Gores
  27. Amy W Williams
  28. William G Morice
  29. John Halamka
  30. Andrew Badley, MD
  31. Venky Soundararajan
(2020)
Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis
eLife 9:e58227.
https://doi.org/10.7554/eLife.58227

Share this article

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

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