Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study.
COVID-19
Electronic health records
PASC
Post-acute sequelae of SARS-CoV-2
SARS-CoV-2
Journal
EClinicalMedicine
ISSN: 2589-5370
Titre abrégé: EClinicalMedicine
Pays: England
ID NLM: 101733727
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
received:
07
06
2023
revised:
29
08
2023
accepted:
29
08
2023
medline:
25
9
2023
pubmed:
25
9
2023
entrez:
25
9
2023
Statut:
epublish
Résumé
Characterizing Post-Acute Sequelae of COVID (SARS-CoV-2 Infection), or We conducted a retrospective multi-centre observational cohort study, leveraging longitudinal electronic health record (EHR) data of 30,422 patients from three healthcare systems in the Consortium for the Clinical Characterization of COVID-19 by EHR (4CE). From the total cohort, we applied a deductive approach on 12,424 individuals with follow-up data and developed a distributed representation learning process for providing augmented definitions for PASC sub-phenotypes. Our framework characterized seven PASC sub-phenotypes. We estimated that on average 15.7% of the hospitalized COVID-19 patients were likely to suffer from at least one PASC symptom and almost 5.98%, on average, had multiple symptoms. Joint pain and dyspnea had the highest prevalence, with an average prevalence of 5.45% and 4.53%, respectively. We provided a scalable framework to every participating healthcare system for estimating PASC sub-phenotypes prevalence and temporal attributes, thus developing a unified model that characterizes augmented sub-phenotypes across the different systems. Authors are supported by National Institute of Allergy and Infectious Diseases, National Institute on Aging, National Center for Advancing Translational Sciences, National Medical Research Council, National Institute of Neurological Disorders and Stroke, European Union, National Institutes of Health, National Center for Advancing Translational Sciences.
Sections du résumé
Background
UNASSIGNED
Characterizing Post-Acute Sequelae of COVID (SARS-CoV-2 Infection), or
Methods
UNASSIGNED
We conducted a retrospective multi-centre observational cohort study, leveraging longitudinal electronic health record (EHR) data of 30,422 patients from three healthcare systems in the Consortium for the Clinical Characterization of COVID-19 by EHR (4CE). From the total cohort, we applied a deductive approach on 12,424 individuals with follow-up data and developed a distributed representation learning process for providing augmented definitions for PASC sub-phenotypes.
Findings
UNASSIGNED
Our framework characterized seven PASC sub-phenotypes. We estimated that on average 15.7% of the hospitalized COVID-19 patients were likely to suffer from at least one PASC symptom and almost 5.98%, on average, had multiple symptoms. Joint pain and dyspnea had the highest prevalence, with an average prevalence of 5.45% and 4.53%, respectively.
Interpretation
UNASSIGNED
We provided a scalable framework to every participating healthcare system for estimating PASC sub-phenotypes prevalence and temporal attributes, thus developing a unified model that characterizes augmented sub-phenotypes across the different systems.
Funding
UNASSIGNED
Authors are supported by National Institute of Allergy and Infectious Diseases, National Institute on Aging, National Center for Advancing Translational Sciences, National Medical Research Council, National Institute of Neurological Disorders and Stroke, European Union, National Institutes of Health, National Center for Advancing Translational Sciences.
Identifiants
pubmed: 37745021
doi: 10.1016/j.eclinm.2023.102210
pii: S2589-5370(23)00387-5
pmc: PMC10511779
doi:
Types de publication
Journal Article
Langues
eng
Pagination
102210Subventions
Organisme : British Heart Foundation
ID : FS/19/52/34563
Pays : United Kingdom
Organisme : NIEHS NIH HHS
ID : P30 ES017885
Pays : United States
Investigateurs
James R Aaron
(JR)
Giuseppe Agapito
(G)
Adem Albayrak
(A)
Giuseppe Albi
(G)
Mario Alessiani
(M)
Anna Alloni
(A)
Danilo F Amendola
(DF)
None François Angoulvant
Li Llj Anthony
(LL)
Bruce J Aronow
(BJ)
Fatima Ashraf
(F)
Andrew Atz
(A)
Paul Avillach
(P)
Paula S Azevedo
(PS)
James Balshi
(J)
Brett K Beaulieu-Jones
(BK)
Douglas S Bell
(DS)
Antonio Bellasi
(A)
Riccardo Bellazzi
(R)
Vincent Benoit
(V)
Michele Beraghi
(M)
José Luis Bernal-Sobrino
(JL)
Mélodie Bernaux
(M)
Romain Bey
(R)
Surbhi Bhatnagar
(S)
Alvar Blanco-Martínez
(A)
Clara-Lea Bonzel
(CL)
John Booth
(J)
Silvano Bosari
(S)
Florence T Bourgeois
(FT)
Robert L Bradford
(RL)
Gabriel A Brat
(GA)
Stéphane Bréant
(S)
Nicholas W Brown
(NW)
Raffaele Bruno
(R)
William A Bryant
(WA)
Mauro Bucalo
(M)
Emily Bucholz
(E)
Anita Burgun
(A)
Tianxi Cai
(T)
Mario Cannataro
(M)
Aldo Carmona
(A)
Charlotte Caucheteux
(C)
Julien Champ
(J)
Jin Chen
(J)
Krista Y Chen
(KY)
Luca Chiovato
(L)
Lorenzo Chiudinelli
(L)
Kelly Cho
(K)
James J Cimino
(JJ)
Tiago K Colicchio
(TK)
Sylvie Cormont
(S)
Sébastien Cossin
(S)
Jean B Craig
(JB)
Juan Luis Cruz-Bermúdez
(JL)
Jaime Cruz-Rojo
(J)
Arianna Dagliati
(A)
Mohamad Daniar
(M)
Christel Daniel
(C)
Priyam Das
(P)
Batsal Devkota
(B)
Audrey Dionne
(A)
Rui Duan
(R)
Julien Dubiel
(J)
Scott L DuVall
(SL)
Loic Esteve
(L)
Hossein Estiri
(H)
Shirley Fan
(S)
Robert W Follett
(RW)
Thomas Ganslandt
(T)
Noelia García- Barrio
(NG)
Lana X Garmire
(LX)
Nils Gehlenborg
(N)
Emily J Getzen
(EJ)
Alon Geva
(A)
Tobias Gradinger
(T)
Alexandre Gramfort
(A)
Romain Griffier
(R)
Nicolas Griffon
(N)
Olivier Grisel
(O)
Alba Gutiérrez-Sacristán
(A)
Larry Han
(L)
David A Hanauer
(DA)
Christian Haverkamp
(C)
Derek Y Hazard
(DY)
Bing He
(B)
Darren W Henderson
(DW)
Martin Hilka
(M)
Yuk-Lam Ho
(YL)
John H Holmes
(JH)
Chuan Hong
(C)
Kenneth M Huling
(KM)
Meghan R Hutch
(MR)
Richard W Issitt
(RW)
Anne Sophie Jannot
(AS)
Vianney Jouhet
(V)
Ramakanth Kavuluru
(R)
Mark S Keller
(MS)
Chris J Kennedy
(CJ)
Daniel A Key
(DA)
Katie Kirchoff
(K)
Jeffrey G Klann
(JG)
Isaac S Kohane
(IS)
Ian D Krantz
(ID)
Detlef Kraska
(D)
Ashok K Krishnamurthy
(AK)
Sehi L'Yi
(S)
Trang T Le
(TT)
Judith Leblanc
(J)
Guillaume Lemaitre
(G)
Leslie Lenert
(L)
Damien Leprovost
(D)
Molei Liu
(M)
Ne Hooi Will Loh
(NH)
Qi Long
(Q)
Sara Lozano-Zahonero
(S)
Yuan Luo
(Y)
Kristine E Lynch
(KE)
Sadiqa Mahmood
(S)
Sarah E Maidlow
(SE)
Adeline Makoudjou
(A)
Alberto Malovini
(A)
Kenneth D Mandl
(KD)
Chengsheng Mao
(C)
Anupama Maram
(A)
Patricia Martel
(P)
Marcelo R Martins
(MR)
Jayson S Marwaha
(JS)
Aaron J Masino
(AJ)
Maria Mazzitelli
(M)
Arthur Mensch
(A)
Marianna Milano
(M)
Marcos F Minicucci
(MF)
Bertrand Moal
(B)
Taha Mohseni Ahooyi
(TM)
Jason H Moore
(JH)
Cinta Moraleda
(C)
Jeffrey S Morris
(JS)
Michele Morris
(M)
Karyn L Moshal
(KL)
Sajad Mousavi
(S)
Danielle L Mowery
(DL)
Douglas A Murad
(DA)
Shawn N Murphy
(SN)
Thomas P Naughton
(TP)
Carlos Tadeu Breda Neto
(CT)
Antoine Neuraz
(A)
Jane Newburger
(J)
Kee Yuan Ngiam
(KY)
Wanjiku Fm Njoroge
(WF)
James B Norman
(JB)
Jihad Obeid
(J)
Marina P Okoshi
(MP)
Karen L Olson
(KL)
Gilbert S Omenn
(GS)
Nina Orlova
(N)
Brian D Ostasiewski
(BD)
Nathan P Palmer
(NP)
Nicolas Paris
(N)
Lav P Patel
(LP)
Miguel Pedrera-Jiménez
(M)
Emily R Pfaff
(ER)
Ashley C Pfaff
(AC)
Danielle Pillion
(D)
Sara Pizzimenti
(S)
Hans U Prokosch
(HU)
Robson A Prudente
(RA)
Andrea Prunotto
(A)
Víctor Quirós-González
(V)
Rachel B Ramoni
(RB)
Maryna Raskin
(M)
Siegbert Rieg
(S)
Gustavo Roig-Domínguez
(G)
Pablo Rojo
(P)
Paula Rubio-Mayo
(P)
Paolo Sacchi
(P)
Carlos Sáez
(C)
Elisa Salamanca
(E)
Malarkodi Jebathilagam Samayamuthu
(MJ)
L Nelson Sanchez-Pinto
(LN)
Arnaud Sandrin
(A)
Nandhini Santhanam
(N)
Janaina Cc Santos
(JC)
Fernando J Sanz Vidorreta
(FJ)
Maria Savino
(M)
Emily R Schriver
(ER)
Petra Schubert
(P)
Juergen Schuettler
(J)
Luigia Scudeller
(L)
Neil J Sebire
(NJ)
Pablo Serrano-Balazote
(P)
Patricia Serre
(P)
Arnaud Serret-Larmande
(A)
Mohsin Shah
(M)
Zahra Shakeri Hossein Abad
(ZS)
Domenick Silvio
(D)
Piotr Sliz
(P)
Jiyeon Son
(J)
Charles Sonday
(C)
Andrew M South
(AM)
Anastasia Spiridou
(A)
Zachary H Strasser
(ZH)
Amelia Lm Tan
(AL)
Bryce Wq Tan
(BW)
Byorn Wl Tan
(BW)
Suzana E Tanni
(SE)
Deanne M Taylor
(DM)
Ana I Terriza-Torres
(AI)
Valentina Tibollo
(V)
Patric Tippmann
(P)
Emma Ms Toh
(EM)
Carlo Torti
(C)
Enrico M Trecarichi
(EM)
Yi-Ju Tseng
(YJ)
Andrew K Vallejos
(AK)
Gael Varoquaux
(G)
Margaret E Vella
(ME)
Guillaume Verdy
(G)
Jill-Jênn Vie
(JJ)
Shyam Visweswaran
(S)
Michele Vitacca
(M)
Kavishwar B Wagholikar
(KB)
Lemuel R Waitman
(LR)
Xuan Wang
(X)
Demian Wassermann
(D)
Griffin M Weber
(GM)
Martin Wolkewitz
(M)
Scott Wong
(S)
Zongqi Xia
(Z)
Xin Xiong
(X)
Ye Ye
(Y)
Nadir Yehya
(N)
William Yuan
(W)
Alberto Zambelli
(A)
Harrison G Zhang
(HG)
Daniela Zo Ller
(D)
Valentina Zuccaro
(V)
Chiara Zucco
(C)
Informations de copyright
© 2023 The Author(s).
Déclaration de conflit d'intérêts
Riccardo Bellazzi is shareholder of Biomeris s. r.l. Gilbert Omenn holds patents for U.S. Application No. 16/169,048 Filed: 24-October- 2018 and License 2023–0632 with Radial Therapeutics, Inc.; Invention Disclosure No. 2022-382.
Références
JAMA Cardiol. 2020 Jul 1;5(7):819-824
pubmed: 32219357
Nat Med. 2023 Jan;29(1):226-235
pubmed: 36456834
JAMA Cardiol. 2020 Jul 1;5(7):811-818
pubmed: 32219356
NPJ Digit Med. 2022 Jun 29;5(1):81
pubmed: 35768548
J Am Med Inform Assoc. 2021 Mar 1;28(3):559-568
pubmed: 33043366
Brief Bioinform. 2021 Mar 22;22(2):812-822
pubmed: 33454728
EBioMedicine. 2023 Jan;87:104413
pubmed: 36563487
Lancet Digit Health. 2022 Jul;4(7):e542-e557
pubmed: 35690576
Sci Rep. 2021 Mar 5;11(1):5322
pubmed: 33674708
J Am Med Inform Assoc. 2022 Jul 12;29(8):1334-1341
pubmed: 35511151
Lancet. 2021 Aug 28;398(10302):747-758
pubmed: 34454673
NPJ Digit Med. 2022 Jun 13;5(1):74
pubmed: 35697747
BMJ Open. 2022 Jul 1;12(7):e062439
pubmed: 35777877
Cell Death Differ. 2022 Oct;29(10):1891-1900
pubmed: 36071155
BMC Med. 2021 Sep 27;19(1):249
pubmed: 34565368
JAMA Netw Open. 2022 Oct 3;5(10):e2235089
pubmed: 36201207
Nat Med. 2021 Apr;27(4):626-631
pubmed: 33692530
PLOS Digit Health. 2023 Jul 25;2(7):e0000301
pubmed: 37490472
Lancet Infect Dis. 2022 Apr;22(4):e102-e107
pubmed: 34951953
Nature. 2021 Jun;594(7862):259-264
pubmed: 33887749
NPJ Digit Med. 2020 Aug 19;3:109
pubmed: 32864472
EClinicalMedicine. 2023 Jun;60:102000
pubmed: 37197226
JAMA Netw Open. 2022 Oct 3;5(10):e2238804
pubmed: 36301542
J Am Med Inform Assoc. 2021 Mar 18;28(4):772-781
pubmed: 33313899
EClinicalMedicine. 2022 Dec 01;55:101762
pubmed: 36474804
JMIR Public Health Surveill. 2022 Aug 11;8(8):e36989
pubmed: 35861678
Nat Commun. 2022 Apr 5;13(1):1812
pubmed: 35383197