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[Preprint]. 2021 Mar 1:rs.3.rs-279400.
doi: 10.21203/rs.3.rs-279400/v1.

Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS

Daniel Prieto-Alhambra  1 Kristin Kostka  2 Talita Duarte-Salles  3 Albert Prats-Uribe  4 Anthony Sena  5 Andrea Pistillo  3 Sara Khalid  6 Lana Lai  7 Asieh Golozar  8 Thamir M Alshammari  9 Dalia Dawoud  10 Fredrik Nyberg  11 Adam Wilcox  12 Alan Andryc  13 Andrew Williams  14 Anna Ostropolets  15 Carlos Areia  16 Chi Young Jung  17 Christopher Harle  18 Christian Reich  2 Clair Blacketer  5 Daniel Morales  19 David A Dorr  20 Edward Burn  3 Elena RoelEng Hooi Tan  6 Evan Minty  21 Frank DeFalco  13 Gabriel de Maeztu  22 Gigi Lipori  23 Heba Alghoul  24 Hong Zhu  25 Jason Thomas  26 Jiang Bian  27 Jimyung Park  28 Jordi Martínez Roldán  29 Jose Posada  30 Juan M Banda  31 Juan P Horcajada  32 Julianna Kohler  33 Karishma Shah  34 Karthik Natarajan  35 Kristine Lynch  36 Li Liu  37 Lisa Schilling  38 Martina Recalde  3 Matthew Spotnitz  15 Mengchun Gong  39 Michael Matheny  40 Neus Valveny  41 Nicole Weiskopf  20 Nigam Shah  42 Osaid Alser  43 Paula Casajust  44 Rae Woong Park  28 Robert Schuff  45 Sarah Seager  2 Scott DuVall  46 Seng Chan You  47 Seokyoung Song  48 Sergio Fernández-Bertolín  3 Stephen Fortin  49 Tanja Magoc  23 Thomas Falconer  15 Vignesh Subbian  50 Vojtech Huser  51 Waheed-Ul-Rahman Ahmed  52 William Carter  53 Yin Guan  39 Yankuic Galvan  23 Xing He  23 Peter Rijnbeek  54 George Hripcsak  35 Patrick Ryan  55 Marc Suchard  56
Affiliations

Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS

Daniel Prieto-Alhambra et al. Res Sq. .

Update in

  • Unraveling COVID-19: A Large-Scale Characterization of 4.5 Million COVID-19 Cases Using CHARYBDIS.
    Kostka K, Duarte-Salles T, Prats-Uribe A, Sena AG, Pistillo A, Khalid S, Lai LYH, Golozar A, Alshammari TM, Dawoud DM, Nyberg F, Wilcox AB, Andryc A, Williams A, Ostropolets A, Areia C, Jung CY, Harle CA, Reich CG, Blacketer C, Morales DR, Dorr DA, Burn E, Roel E, Tan EH, Minty E, DeFalco F, de Maeztu G, Lipori G, Alghoul H, Zhu H, Thomas JA, Bian J, Park J, Martínez Roldán J, Posada JD, Banda JM, Horcajada JP, Kohler J, Shah K, Natarajan K, Lynch KE, Liu L, Schilling LM, Recalde M, Spotnitz M, Gong M, Matheny ME, Valveny N, Weiskopf NG, Shah N, Alser O, Casajust P, Park RW, Schuff R, Seager S, DuVall SL, You SC, Song S, Fernández-Bertolín S, Fortin S, Magoc T, Falconer T, Subbian V, Huser V, Ahmed WU, Carter W, Guan Y, Galvan Y, He X, Rijnbeek PR, Hripcsak G, Ryan PB, Suchard MA, Prieto-Alhambra D. Kostka K, et al. Clin Epidemiol. 2022 Mar 22;14:369-384. doi: 10.2147/CLEP.S323292. eCollection 2022. Clin Epidemiol. 2022. PMID: 35345821 Free PMC article.

Abstract

Background: Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response [1,2]. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) [3] Characterizing Health Associated Risks, and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD. Methods: We conducted a descriptive cohort study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11 th June 2020 and are iteratively updated via GitHub [4]. Findings: We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19 , and 113,627 hospitalized with COVID-19 requiring intensive services . All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts, and are available in an interactive website: https://data.ohdsi.org/Covid19CharacterizationCharybdis/. Interpretation: CHARYBDIS findings provide benchmarks that contribute to our understanding of COVID-19 progression, management and evolution over time. This can enable timely assessment of real-world outcomes of preventative and therapeutic options as they are introduced in clinical practice.

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Conflict of interest statement

Competing interest statement

All authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare:

Ms. Kostka is an employee of IQVIA. Mr. Sena is an employee and holds stock at Janssen Research & Development, a Johnson and Johnson family of companies. Dr. Golozar reports personal fees from Regeneron Pharmaceuticals, outside the submitted work. She is a full-time employee at Regeneron Pharmaceuticals. This work was not conducted at Regeneron Pharmaceuticals. Dr. Nyberg reports other funding from AstraZeneca, outside the submitted work. Dr. Wilcox reports grants from Bill and Melinda Gates Foundation, grants from National Institute of Health, during the conduct of the study Mr. Andryc is an employee of Janssen Research & Development, a subsidiary of Johnson & Johnson. Dr. Reich is an employee of IQVIA. Dr. Blacketer reports she is an employee and holds stock at Janssen Research & Development, a Johnson and Johnson family of companies. Dr. Morales is supported by a Wellcome Trust Clinical Research Development Fellowship (Grant 214588/Z/18/Z) and reports grants from Chief Scientist Office (CSO), grants from Health Data Research UK (HDR-UK), grants from National Institute of Health Research (NIHR), outside the submitted work. Mr. DeFalco reports he is an employee and holds stock at Janssen Research & Development, a Johnson and Johnson family of companies. Jason Thomas reports grants from Bill and Melinda Gates Foundation, grants from National Institute of Health, during the conduct of the study. Dr. Posada reports grants from National Library of Medicine, during the conduct of the study. Dr. Natarajan reports grants from US NIH, during the conduct of the study. Dr. Matheny reports grants from US NIH, grants from US VA HSR&D, during the conduct of the study. Dr. Weiskopf reports personal fees from Merck, outside the submitted work. Dr. Shah reports grants from National Library of Medicine, during the conduct of the study. Dr. Park reports grants from Ministry of Trade, Industry & Energy, Republic of Korea, grants from Ministry of Health & Welfare, Republic of Korea, grants from Bill & Melinda Gates Foundation, during the conduct of the study. Ms. Seager is an employee of IQVIA. Dr. DuVall reports grants from Anolinx, LLC, grants from Astellas Pharma, Inc, grants from AstraZeneca Pharmaceuticals LP, grants from Boehringer Ingelheim International GmbH, grants from Celgene Corporation, grants from Eli Lilly and Company, grants from Genentech Inc., grants from Genomic Health, Inc., grants from Gilead Sciences Inc., grants from GlaxoSmithKline PLC, grants from Innocrin Pharmaceuticals Inc., grants from Janssen Pharmaceuticals, Inc., grants from Kantar Health, grants from Myriad Genetic Laboratories, Inc., grants from Novartis International AG, grants from Parexel International Corporation through the University of Utah or Western Institute for Veteran Research outside the submitted work. Dr. Fortin is an employee of Janssen R&D, a subsidiary of Johnson and Johnson. Dr. Vignesh reports grants from State of Arizona; Arizona Board of Regents, during the conduct of the study; grants from National Science Foundation, grants from Agency for Healthcare Research and Quality, grants from National Institutes of Health, outside the submitted work; .Dr. Subbian reports grants from State of Arizona; Arizona Board of Regents, during the conduct of the study; grants from National Science Foundation, grants from Agency for Healthcare Research and Quality, grants from National Institutes of Health, outside the submitted work. Dr. Rijnbeek reports grants from Innovative Medicines Initiative, from Janssen Research and Development, during the conduct of the study. Dr. Hripcsak reports grants from US NIH, during the conduct of the study. Dr. Ryan reports and is employee of Janssen Research and Development and shareholder of Johnson & Johnson. Dr. Suchard reports grants from US National Institutes of Health, grants from Department of Veterans Affairs, during the conduct of the study; grants from IQVIA, personal fees from Janssen Research and Development, grants from US Food and Drug Administration, personal fees from Private Health Management, outside the submitted work. Dr. Prieto-Alhambra reports grants and other from AMGEN, grants, non-financial support and other from UCB Biopharma, grants from Les Laboratoires Servier, outside the submitted work; and Janssen, on behalf of IMI-funded EHDEN and EMIF consortiums, and Synapse Management Partners have supported training programmes organised by DPA’s department and open for external participants.

The views expressed are those of the authors and do not necessarily represent the views or policy of the Department of Veterans Affairs or the United States Government. No other relationships or activities that could appear to have influenced the submitted work.

Figures

Figure 1
Figure 1
COVID-19 cases across the OHDSI COVID-19 network. Note: The designations employed and the presentation of the material on this map do not imply the expression of any opinion whatsoever on the part of Research Square concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. This map has been provided by the authors.
Figure 2
Figure 2
Distribution of diagnosed, hospitalized and requiring intensive services COVID-19 cases by age and sex across the OHDSI COVID-19 network in the United States NB: In each subplot, the x-axis represents what proportion of all women (left) and all men (right) fall in each age category. No prior observation period required in the cohorts shown in this figure. Cohorts must be >=140 people to be reported in this analysis. Abbreviations: diag: diagnosed; hosp: hospitalized; i.s.: hospitalized and requiring intensive services. Abbreviations: CU-AMC-HDC: U of Colorado Anschuz Medical Campus Health Data Compass; CUIMC: Columbia University Irving Medical Center; IQVIAHospitalCDM: IQVIA Hospital Charge Data Master; OHSU: Oregon Health and Science University; OPTUM-EHR: Optum© de-identified Electronic Health Record Dataset; OPTUM-SES: Optum® De-Identified Clinformatics® Data Mart Database – Socio-Economic Status (SES); STARR-OMOP: Stanford Medicine Research Data Repository; TRDW: Tufts MC Research Data Warehouse; UWM-CRD: UW Medicine COVID Research Dataset; VA-OMOP: Department of Veterans Affairs

References

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