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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest 2024; 134:e176640. [PMID: 38690733 PMCID: PMC11060740 DOI: 10.1172/jci176640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/12/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL REGISTRATIONClinicalTrials.gov NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).
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Affiliation(s)
| | - Cole Maguire
- The University of Texas at Austin, Austin, Texas, USA
| | | | - Pramod Shinde
- La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Casey P. Shannon
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Providence Research, Vancouver, British Columbia, Canada
| | - Leqi Xu
- Yale School of Public Health, New Haven, Connecticut, USA
| | - Annmarie Hoch
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Elias K. Haddad
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | - IMPACC Network
- The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) Network is detailed in Supplemental Acknowledgments
| | - Elaine F. Reed
- David Geffen School of Medicine at the UCLA, Los Angeles, California, USA
| | - Monica Kraft
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Grace A. McComsey
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Al Ozonoff
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Charles B. Cairns
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Lindsey B. Rosen
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | | | - Hanno Steen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Bali Pulendran
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Joann Diray-Arce
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Rafick P. Sekaly
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | | | - Slim Fourati
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, UCSD, La Jolla, California, USA
| | | | - Leying Guan
- Yale School of Public Health, New Haven, Connecticut, USA
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2
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Bell CF, Bobbili P, Desai R, Gibbons DC, Drysdale M, DerSarkissian M, Patel V, Birch HJ, Lloyd EJ, Zhang A, Duh MS. Real-World Effectiveness of Sotrovimab for the Early Treatment of COVID-19: Evidence from the US National COVID Cohort Collaborative (N3C). Clin Drug Investig 2024; 44:183-198. [PMID: 38379107 PMCID: PMC10912146 DOI: 10.1007/s40261-024-01344-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND AND OBJECTIVE The coronavirus disease 2019 (COVID-19) pandemic has been an unprecedented healthcare crisis, one that threatened to overwhelm health systems and prompted an urgent need for early treatment options for patients with mild-to-moderate COVID-19 at high risk for progression to severe disease. Randomised clinical trials established the safety and efficacy of monoclonal antibodies (mAbs) early in the pandemic; in vitro data subsequently led to use of the mAbs being discontinued, without clear evidence on how these data were linked to outcomes. In this study, we describe and compare real-world outcomes for patients with mild-to-moderate COVID-19 at high risk for progression to severe COVID-19 treated with sotrovimab versus untreated patients. METHODS Electronic health records from the National COVID Cohort Collaborative (N3C) were used to identify US patients (aged ≥ 12 years) diagnosed with COVID-19 (positive test or ICD-10: U07.1) in an ambulatory setting (27 September 2021-30 April 2022) who met Emergency Use Authorization (EUA) high-risk criteria. Patients receiving the mAb sotrovimab within 10 days of diagnosis were assigned to the sotrovimab cohort, with the day of infusion as the index date. Untreated patients (no evidence of early mAb treatment, prophylactic mAb or oral antiviral treatment) were assigned to the untreated cohort, with an imputed index date based on the time distribution between diagnosis and sotrovimab infusion in the sotrovimab cohort. The primary endpoint was hospitalisation or death (both all-cause) within 29 days of index, reported as descriptive rate and adjusted [via inverse probability of treatment weighting (IPTW)] odds ratio (OR) and 95% confidence interval (CI). RESULTS Of nearly 2.9 million patients diagnosed with COVID-19 during the analysis period, 4992 met the criteria for the sotrovimab cohort, and 541,325 were included in the untreated cohort. Before weighting, significant differences were noted between the cohorts; for example, patients in the sotrovimab cohort were older (60 years versus 54 years), were more likely to be white (85% versus 75%) and met more EUA criteria (mean 3.1 versus 2.2) versus the untreated cohort. The proportions of patients with 29-day hospitalisation or death were 3.5% (176/4992) and 4.5% (24,163/541,325) in the sotrovimab and untreated cohorts, respectively (unadjusted OR: 0.78; 95% CI: 0.67, 0.91; p = 0.001). In adjusted analysis, sotrovimab was associated with a 25% reduction in the odds of hospitalisation or death compared with the untreated cohort (IPTW-adjusted OR: 0.75; 95% CI: 0.61, 0.92; p = 0.005). CONCLUSIONS Sotrovimab demonstrated clinical effectiveness in preventing severe outcomes (hospitalisation, mortality) in the period 27 September 2021-30 April 2022, which included Delta and Omicron BA.1 variants and an early surge of Omicron BA.2 variant.
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Affiliation(s)
- Christopher F Bell
- GSK, Research Triangle Park, 410 Blackwell Street, Durham, NC, 27701, USA.
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Sun J, Zheng Q, Anzalone AJ, Abraham AG, Olex AL, Zhang Y, Mathew J, Safdar N, Haendel MA, Segev D, Islam JY, Singh JA, Mannon RB, Chute CG, Patel RC, Kirk GD. Effectiveness of mRNA Booster Vaccine Against Coronavirus Disease 2019 Infection and Severe Outcomes Among Persons With and Without Immune Dysfunction: A Retrospective Cohort Study of National Electronic Medical Record Data in the United States. Open Forum Infect Dis 2024; 11:ofae019. [PMID: 38379569 PMCID: PMC10878052 DOI: 10.1093/ofid/ofae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Background Real-world evidence of coronavirus disease 2019 (COVID-19) messenger RNA (mRNA) booster effectiveness among patients with immune dysfunction are limited. Methods We included data from patients in the United States National COVID Cohort Collaborative (N3C) who completed ≥2 doses of mRNA vaccination between 10 December 2020 and 27 May 2022. Immune dysfunction conditions included human immunodeficiency virus infection, solid organ or bone marrow transplant, autoimmune diseases, and cancer. We defined incident COVID-19 BTI as positive results from laboratory tests or diagnostic codes 14 days after at least 2 doses of mRNA vaccination; and severe COVID-19 BTI as hospitalization, invasive cardiopulmonary support, and/or death. We used propensity scores to match boosted versus nonboosted patients and evaluated hazards of incident and severe COVID-19 BTI using Cox regression after matching. Results Among patients without immune dysfunction, the relative effectiveness of booster (3 doses) after 6 months from the primary (2 doses) vaccination against BTI ranged from 69% to 81% during the Delta-predominant period and from 33% to 39% during the Omicron-predominant period. Relative effectiveness against BTI was lower among patients with immune dysfunction but remained statistically significant in both periods. Boosted patients had lower risk of COVID-19-related hospitalization (hazard ratios [HR] ranged from 0.5 [95% confidence interval {CI}, .48-.53] to 0.63 [95% CI, .56-.70]), invasive cardiopulmonary support, or death (HRs ranged from 0.46 [95% CI, .41-.52] to 0.63 [95% CI, .50-.79]) during both periods. Conclusions Booster vaccines remain effective against severe COVID-19 BTI throughout the Delta- and Omicron-predominant periods, regardless of patients' immune status.
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Affiliation(s)
- Jing Sun
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Qulu Zheng
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alfred J Anzalone
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Alison G Abraham
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Denver, Colorado, USA
| | - Amy L Olex
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yifan Zhang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jomol Mathew
- Department of Population Health Sciences, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Division of Infectious Diseases, William S. Middleton Veterans Affairs Hospital, Madison, Wisconsin, USA
| | - Melissa A Haendel
- Center for Health Artificial Intelligence, University of Colorado, Denver, Colorado, USA
| | - Dorry Segev
- Department of Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jessica Y Islam
- Center for Immunization and Infection in Cancer, Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncologic Sciences, University of South Florida, Tampa, Florida, USA
| | - Jasvinder A Singh
- Department of Medicine and Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Roslyn B Mannon
- Division of Nephrology, Department of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rena C Patel
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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4
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Sharathkumar A, Wendt L, Ortman C, Srinivasan R, Chute CG, Chrischilles E, Takemoto CM. COVID-19 outcomes in persons with hemophilia: results from a US-based national COVID-19 surveillance registry. J Thromb Haemost 2024; 22:61-75. [PMID: 37182697 PMCID: PMC10181864 DOI: 10.1016/j.jtha.2023.04.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND Hypercoagulable state contributing to thrombotic complications worsens COVID-19 severity and outcomes, whereas anticoagulation improves outcomes by alleviating hypercoagulability. OBJECTIVES To examine whether hemophilia, an inherent hypocoagulable condition, offers protection against COVID-19 severity and reduces venous thromboembolism (VTE) risk in persons with hemophilia (PwH). METHODS A 1:3 propensity score-matched retrospective cohort study used national COVID-19 registry data (January 2020 through January 2022) to compare outcomes between 300 male PwH and 900 matched controls without hemophilia. RESULTS Analyses of PwH demonstrated that known risk factors (older age, heart failure, hypertension, cancer/malignancy, dementia, and renal and liver disease) contributed to severe COVID-19 and/or 30-day all-cause mortality. Non-central nervous system bleeding was an additional risk factor for poor outcomes in PwH. Odds of developing VTE with COVID-19 in PwH were associated with pre-COVID VTE diagnosis (odds ratio [OR], 51.9; 95% CI, 12.8-266; p < .001), anticoagulation therapy (OR, 12.7; 95% CI, 3.01-48.6; p < .001), and pulmonary disease (OR, 16.1; 95% CI, 10.4-25.4; p < .001). Thirty-day all-cause mortality (OR, 1.27; 95% CI, 0.75-2.11; p = .3) and VTE events (OR, 1.32; 95% CI, 0.64-2.73; p = .4) were not significantly different between the matched cohorts; however, hospitalizations (OR, 1.58; 95% CI, 1.20-2.10; p = .001) and non-central nervous system bleeding events (OR, 4.78; 95% CI, 2.98-7.48; p < .001) were increased in PwH. In multivariate analyses, hemophilia did not reduce adverse outcomes (OR, 1.32; 95% CI, 0.74-2.31; p = .2) or VTE (OR, 1.14; 95% CI, 0.44-2.67; p = .8) but increased bleeding risk (OR, 4.70; 95% CI, 2.98-7.48; p < .001). CONCLUSION After adjusting for patient characteristics/comorbidities, hemophilia increased bleeding risk with COVID-19 but did not protect against severe disease and VTE.
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Affiliation(s)
- Anjali Sharathkumar
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
| | - Linder Wendt
- Institute for Clinical and Translational Science, University of Iowa, Iowa City, Iowa, USA
| | - Chris Ortman
- Department of Bioinformatics, University of Iowa, Iowa City, Iowa, USA; Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ragha Srinivasan
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Elizabeth Chrischilles
- Department of Bioinformatics, University of Iowa, Iowa City, Iowa, USA; Department of Epidemiology, School of Public Health, University of Iowa, Iowa, USA
| | - Clifford M Takemoto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics 2023; 39:btad418. [PMID: 37389415 PMCID: PMC10336030 DOI: 10.1093/bioinformatics/btad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/09/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. RESULTS Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification. AVAILABILITY AND IMPLEMENTATION https://kghub.org.
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Affiliation(s)
- J Harry Caufield
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Tim Putman
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Kevin Schaper
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Deepak R Unni
- SIB Swiss Institute of Bioinformatics, Basel 1015, Switzerland
| | - Harshad Hegde
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Luca Cappelletti
- Department of Computer Science, University of Milano, Milan 20126, Italy
| | - Sierra A T Moxon
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Vida Ravanmehr
- Department of Lymphoma-Myeloma, MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Seth Carbon
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, United States
| | - Katherina Cortes
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Kent A Shefchek
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Glass Elsarboukh
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Jim Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27517, United States
| | - Tommaso Fontana
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan 20133, Italy
| | | | | | - Anne E Thessen
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | | | - Melissa A Haendel
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Marcin P Joachimiak
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Justin T Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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Guo S, Zhang J, Yang X, Weissman S, Olatosi B, Patel RC, Li X. Impact of HIV on COVID-19 Outcomes: A Propensity Score Matching Analysis with Varying Age Differences. AIDS Behav 2023:10.1007/s10461-023-04088-y. [PMID: 37289345 PMCID: PMC10249542 DOI: 10.1007/s10461-023-04088-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
To exploratorily test (1) the impact of HIV and aging process among PLWH on COVID-19 outcomes; and (2) whether the effects of HIV on COVID-19 outcomes differed by immunity level. The data used in this study was retrieved from the COVID-19 positive cohort in National COVID Cohort Collaborative (N3C). Multivariable logistic regression models were conducted on populations that were matched using either exact matching or propensity score matching (PSM) with varying age difference between PLWH and non-PLWH to examine the impact of HIV and aging process on all-cause mortality and hospitalization among COVID-19 patients. Subgroup analyses by CD4 counts and viral load (VL) levels were conducted using similar approaches. Among the 2,422,864 adults with a COVID-19 diagnosis, 15,188 were PLWH. PLWH had a significantly higher odds of death compared to non-PLWH until age difference reached 6 years or more, while PLWH were still at an elevated risk of hospitalization across all matched cohorts. The odds of both severe outcomes were persistently higher among PLWH with CD4 < 200 cells/mm3. VL ≥ 200 copies/ml was only associated with higher hospitalization, regardless of the predefined age differences. Age advancement in HIV might significantly contribute to the higher risk of COVID-19 mortality and HIV infection may still impact COVID-19 hospitalization independent of the age advancement in HIV.
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Affiliation(s)
- Siyuan Guo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Xueying Yang
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
| | - Sharon Weissman
- Department of Internal Medicine, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Bankole Olatosi
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Rena C Patel
- Departments of Medicine and Global Health, University of Washington, Seattle, WA, USA
| | - Xiaoming Li
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
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Rahman MM, Mahi AM, Melamed R, Alam MAU. Effects of Antidepressants on COVID-19 Outcomes: Retrospective Study on Large-Scale Electronic Health Record Data. Interact J Med Res 2023; 12:e39455. [PMID: 36881541 PMCID: PMC10103094 DOI: 10.2196/39455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/15/2022] [Accepted: 03/05/2023] [Indexed: 03/07/2023] Open
Abstract
BACKGROUND Antidepressants exert an anticholinergic effect in varying degrees, and various classes of antidepressants can produce a different effect on immune function. While the early use of antidepressants has a notional effect on COVID-19 outcomes, the relationship between the risk of COVID-19 severity and the use of antidepressants has not been properly investigated previously owing to the high costs involved with clinical trials. Large-scale observational data and recent advancements in statistical analysis provide ample opportunity to virtualize a clinical trial to discover the detrimental effects of the early use of antidepressants. OBJECTIVE We primarily aimed to investigate electronic health records for causal effect estimation and use the data for discovering the causal effects of early antidepressant use on COVID-19 outcomes. As a secondary aim, we developed methods for validating our causal effect estimation pipeline. METHODS We used the National COVID Cohort Collaborative (N3C), a database aggregating health history for over 12 million people in the United States, including over 5 million with a positive COVID-19 test. We selected 241,952 COVID-19-positive patients (age >13 years) with at least 1 year of medical history. The study included a 18,584-dimensional covariate vector for each person and 16 different antidepressants. We used propensity score weighting based on the logistic regression method to estimate causal effects on the entire data. Then, we used the Node2Vec embedding method to encode SNOMED-CT (Systematized Nomenclature of Medicine-Clinical Terms) medical codes and applied random forest regression to estimate causal effects. We used both methods to estimate causal effects of antidepressants on COVID-19 outcomes. We also selected few negatively effective conditions for COVID-19 outcomes and estimated their effects using our proposed methods to validate their efficacy. RESULTS The average treatment effect (ATE) of using any one of the antidepressants was -0.076 (95% CI -0.082 to -0.069; P<.001) with the propensity score weighting method. For the method using SNOMED-CT medical embedding, the ATE of using any one of the antidepressants was -0.423 (95% CI -0.382 to -0.463; P<.001). CONCLUSIONS We applied multiple causal inference methods with novel application of health embeddings to investigate the effects of antidepressants on COVID-19 outcomes. Additionally, we proposed a novel drug effect analysis-based evaluation technique to justify the efficacy of the proposed method. This study offers causal inference methods on large-scale electronic health record data to discover the effects of common antidepressants on COVID-19 hospitalization or a worse outcome. We found that common antidepressants may increase the risk of COVID-19 complications and uncovered a pattern where certain antidepressants were associated with a lower risk of hospitalization. While discovering the detrimental effects of these drugs on outcomes could guide preventive care, identification of beneficial effects would allow us to propose drug repurposing for COVID-19 treatment.
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Affiliation(s)
- Md Mahmudur Rahman
- The Richard A Miner School of Computer & Information Sciences, University of Massachusetts, Lowell, MA, United States
| | - Atqiya Munawara Mahi
- The Richard A Miner School of Computer & Information Sciences, University of Massachusetts, Lowell, MA, United States
| | - Rachel Melamed
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Mohammad Arif Ul Alam
- The Richard A Miner School of Computer & Information Sciences, University of Massachusetts, Lowell, MA, United States
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
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8
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Lovis C, Zhang W, Visweswaran S, Raji M, Kuo YF. A Framework for Modeling and Interpreting Patient Subgroups Applied to Hospital Readmission: Visual Analytical Approach. JMIR Med Inform 2022; 10:e37239. [PMID: 35537203 PMCID: PMC9773032 DOI: 10.2196/37239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND A primary goal of precision medicine is to identify patient subgroups and infer their underlying disease processes with the aim of designing targeted interventions. Although several studies have identified patient subgroups, there is a considerable gap between the identification of patient subgroups and their modeling and interpretation for clinical applications. OBJECTIVE This study aimed to develop and evaluate a novel analytical framework for modeling and interpreting patient subgroups (MIPS) using a 3-step modeling approach: visual analytical modeling to automatically identify patient subgroups and their co-occurring comorbidities and determine their statistical significance and clinical interpretability; classification modeling to classify patients into subgroups and measure its accuracy; and prediction modeling to predict a patient's risk of an adverse outcome and compare its accuracy with and without patient subgroup information. METHODS The MIPS framework was developed using bipartite networks to identify patient subgroups based on frequently co-occurring high-risk comorbidities, multinomial logistic regression to classify patients into subgroups, and hierarchical logistic regression to predict the risk of an adverse outcome using subgroup membership compared with standard logistic regression without subgroup membership. The MIPS framework was evaluated for 3 hospital readmission conditions: chronic obstructive pulmonary disease (COPD), congestive heart failure (CHF), and total hip arthroplasty/total knee arthroplasty (THA/TKA) (COPD: n=29,016; CHF: n=51,550; THA/TKA: n=16,498). For each condition, we extracted cases defined as patients readmitted within 30 days of hospital discharge. Controls were defined as patients not readmitted within 90 days of discharge, matched by age, sex, race, and Medicaid eligibility. RESULTS In each condition, the visual analytical model identified patient subgroups that were statistically significant (Q=0.17, 0.17, 0.31; P<.001, <.001, <.05), significantly replicated (Rand Index=0.92, 0.94, 0.89; P<.001, <.001, <.01), and clinically meaningful to clinicians. In each condition, the classification model had high accuracy in classifying patients into subgroups (mean accuracy=99.6%, 99.34%, 99.86%). In 2 conditions (COPD and THA/TKA), the hierarchical prediction model had a small but statistically significant improvement in discriminating between readmitted and not readmitted patients as measured by net reclassification improvement (0.059, 0.11) but not as measured by the C-statistic or integrated discrimination improvement. CONCLUSIONS Although the visual analytical models identified statistically and clinically significant patient subgroups, the results pinpoint the need to analyze subgroups at different levels of granularity for improving the interpretability of intra- and intercluster associations. The high accuracy of the classification models reflects the strong separation of patient subgroups, despite the size and density of the data sets. Finally, the small improvement in predictive accuracy suggests that comorbidities alone were not strong predictors of hospital readmission, and the need for more sophisticated subgroup modeling methods. Such advances could improve the interpretability and predictive accuracy of patient subgroup models for reducing the risk of hospital readmission, and beyond.
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Affiliation(s)
| | - Weibin Zhang
- School of Public and Population Health, University of Texas Medical Branch, Galveston, TX, United States
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mukaila Raji
- Division of Geriatric Medicine, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Yong-Fang Kuo
- School of Public and Population Health, University of Texas Medical Branch, Galveston, TX, United States
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9
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Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris NL, Wilkins K, Antony B, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J. Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res Clin Pract 2022; 194:110157. [PMID: 36400170 PMCID: PMC9663381 DOI: 10.1016/j.diabres.2022.110157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022]
Abstract
AIMS Studies suggest that metformin is associated with reduced COVID-19 severity in individuals with diabetes compared to other antihyperglycemics. We assessed if metformin is associated with reduced incidence of severe COVID-19 for patients with prediabetes or polycystic ovary syndrome (PCOS), common diseases that increase the risk of severe COVID-19. METHODS This observational, retrospective study utilized EHR data from 52 hospitals for COVID-19 patients with PCOS or prediabetes treated with metformin or levothyroxine/ondansetron (controls). After balancing via inverse probability score weighting, associations with COVID-19 severity were assessed by logistic regression. RESULTS In the prediabetes cohort, when compared to levothyroxine, metformin was associated with a significantly lower incidence of COVID-19 with "mild-ED" or worse (OR [95% CI]: 0.636, [0.455-0.888]) and "moderate" or worse severity (0.493 [0.339-0.718]). Compared to ondansetron, metformin was associated with lower incidence of "mild-ED" or worse severity (0.039 [0.026-0.057]), "moderate" or worse (0.045 [0.03-0.069]), "severe" or worse (0.183 [0.077-0.431]), and "mortality/hospice" (0.223 [0.071-0.694]). For PCOS, metformin showed no significant differences in severity compared to levothyroxine, but was associated with a significantly lower incidence of "mild-ED" or worse (0.101 [0.061-0.166]), and "moderate" or worse (0.094 [0.049-0.18]) COVID-19 outcome compared to ondansetron. CONCLUSIONS Metformin use is associated with less severe COVID-19 in patients with prediabetes or PCOS.
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Affiliation(s)
- Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bryan Laraway
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Adnin Zaman
- Department of Medicine, Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kenneth Wilkins
- Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Blessy Antony
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Michael Gargano
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | | | - Melissa Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Carolyn Bramante
- Division of General Internal Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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10
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Martínez JA, Alonso-Bernáldez M, Martínez-Urbistondo D, Vargas-Nuñez JA, Ramírez de Molina A, Dávalos A, Ramos-Lopez O. Machine learning insights concerning inflammatory and liver-related risk comorbidities in non-communicable and viral diseases. World J Gastroenterol 2022; 28:6230-6248. [PMID: 36504554 PMCID: PMC9730439 DOI: 10.3748/wjg.v28.i44.6230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/07/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
The liver is a key organ involved in a wide range of functions, whose damage can lead to chronic liver disease (CLD). CLD accounts for more than two million deaths worldwide, becoming a social and economic burden for most countries. Among the different factors that can cause CLD, alcohol abuse, viruses, drug treatments, and unhealthy dietary patterns top the list. These conditions prompt and perpetuate an inflammatory environment and oxidative stress imbalance that favor the development of hepatic fibrogenesis. High stages of fibrosis can eventually lead to cirrhosis or hepatocellular carcinoma (HCC). Despite the advances achieved in this field, new approaches are needed for the prevention, diagnosis, treatment, and prognosis of CLD. In this context, the scientific com-munity is using machine learning (ML) algorithms to integrate and process vast amounts of data with unprecedented performance. ML techniques allow the integration of anthropometric, genetic, clinical, biochemical, dietary, lifestyle and omics data, giving new insights to tackle CLD and bringing personalized medicine a step closer. This review summarizes the investigations where ML techniques have been applied to study new approaches that could be used in inflammatory-related, hepatitis viruses-induced, and coronavirus disease 2019-induced liver damage and enlighten the factors involved in CLD development.
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Affiliation(s)
- J Alfredo Martínez
- Precision Nutrition and Cardiometabolic Health, Madrid Institute of Advanced Studies-Food Institute, Madrid 28049, Spain
| | - Marta Alonso-Bernáldez
- Precision Nutrition and Cardiometabolic Health, Madrid Institute of Advanced Studies-Food Institute, Madrid 28049, Spain
| | | | - Juan A Vargas-Nuñez
- Servicio de Medicina Interna, Hospital Universitario Puerta de Hierro Majadahonda, Madrid 28222, Majadahonda, Spain
| | - Ana Ramírez de Molina
- Molecular Oncology and Nutritional Genomics of Cancer, Madrid Institute of Advanced Studies-Food Institute, Madrid 28049, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute of Advanced Studies-Food Institute, Madrid 28049, Spain
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Baja California, Mexico
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11
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Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris N, Wilkins K, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J. Metformin is Associated with Reduced COVID-19 Severity in Patients with Prediabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.08.29.22279355. [PMID: 36093353 PMCID: PMC9460973 DOI: 10.1101/2022.08.29.22279355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Background With the continuing COVID-19 pandemic, identifying medications that improve COVID-19 outcomes is crucial. Studies suggest that use of metformin, an oral antihyperglycemic, is associated with reduced COVID-19 severity in individuals with diabetes compared to other antihyperglycemic medications. Some patients without diabetes, including those with polycystic ovary syndrome (PCOS) and prediabetes, are prescribed metformin for off-label use, which provides an opportunity to further investigate the effect of metformin on COVID-19. Participants In this observational, retrospective analysis, we leveraged the harmonized electronic health record data from 53 hospitals to construct cohorts of COVID-19 positive, metformin users without diabetes and propensity-weighted control users of levothyroxine (a medication for hypothyroidism that is not known to affect COVID-19 outcome) who had either PCOS (n = 282) or prediabetes (n = 3136). The primary outcome of interest was COVID-19 severity, which was classified as: mild, mild ED (emergency department), moderate, severe, or mortality/hospice. Results In the prediabetes cohort, metformin use was associated with a lower rate of COVID-19 with severity of mild ED or worse (OR: 0.630, 95% CI 0.450 - 0.882, p < 0.05) and a lower rate of COVID-19 with severity of moderate or worse (OR: 0.490, 95% CI 0.336 - 0.715, p < 0.001). In patients with PCOS, we found no significant association between metformin use and COVID-19 severity, although the number of patients was relatively small. Conclusions Metformin was associated with less severe COVID-19 in patients with prediabetes, as seen in previous studies of patients with diabetes. This is an important finding, since prediabetes affects between 19 and 38% of the US population, and COVID-19 is an ongoing public health emergency. Further observational and prospective studies will clarify the relationship between metformin and COVID-19 severity in patients with prediabetes, and whether metformin usage may reduce COVID-19 severity.
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Affiliation(s)
- Lauren E. Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | - Bryan Laraway
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Adnin Zaman
- Department of Medicine, Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nomi Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kenneth Wilkins
- Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Gargano
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | | | - Melissa Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Carolyn Bramante
- Division of General Internal Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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12
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Schons M, Pilgram L, Reese JP, Stecher M, Anton G, Appel KS, Bahmer T, Bartschke A, Bellinghausen C, Bernemann I, Brechtel M, Brinkmann F, Brünn C, Dhillon C, Fiessler C, Geisler R, Hamelmann E, Hansch S, Hanses F, Hanß S, Herold S, Heyder R, Hofmann AL, Hopff SM, Horn A, Jakob C, Jiru-Hillmann S, Keil T, Khodamoradi Y, Kohls M, Kraus M, Krefting D, Kunze S, Kurth F, Lieb W, Lippert LJ, Lorbeer R, Lorenz-Depiereux B, Maetzler C, Miljukov O, Nauck M, Pape D, Püntmann V, Reinke L, Römmele C, Rudolph S, Sass J, Schäfer C, Schaller J, Schattschneider M, Scheer C, Scherer M, Schmidt S, Schmidt J, Seibel K, Stahl D, Steinbeis F, Störk S, Tauchert M, Tebbe JJ, Thibeault C, Toepfner N, Ungethüm K, Vadasz I, Valentin H, Wiedmann S, Zoller T, Nagel E, Krawczak M, von Kalle C, Illig T, Schreiber S, Witzenrath M, Heuschmann P, Vehreschild JJ. The German National Pandemic Cohort Network (NAPKON): rationale, study design and baseline characteristics. Eur J Epidemiol 2022; 37:849-870. [PMID: 35904671 PMCID: PMC9336157 DOI: 10.1007/s10654-022-00896-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/22/2022] [Indexed: 11/25/2022]
Abstract
The German government initiated the Network University Medicine (NUM) in early 2020 to improve national research activities on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. To this end, 36 German Academic Medical Centers started to collaborate on 13 projects, with the largest being the National Pandemic Cohort Network (NAPKON). The NAPKON’s goal is creating the most comprehensive Coronavirus Disease 2019 (COVID-19) cohort in Germany. Within NAPKON, adult and pediatric patients are observed in three complementary cohort platforms (Cross-Sectoral, High-Resolution and Population-Based) from the initial infection until up to three years of follow-up. Study procedures comprise comprehensive clinical and imaging diagnostics, quality-of-life assessment, patient-reported outcomes and biosampling. The three cohort platforms build on four infrastructure core units (Interaction, Biosampling, Epidemiology, and Integration) and collaborations with NUM projects. Key components of the data capture, regulatory, and data privacy are based on the German Centre for Cardiovascular Research. By April 01, 2022, 34 university and 40 non-university hospitals have enrolled 5298 patients with local data quality reviews performed on 4727 (89%). 47% were female, the median age was 52 (IQR 36–62-) and 50 pediatric cases were included. 44% of patients were hospitalized, 15% admitted to an intensive care unit, and 12% of patients deceased while enrolled. 8845 visits with biosampling in 4349 patients were conducted by April 03, 2022. In this overview article, we summarize NAPKON’s design, relevant milestones including first study population characteristics, and outline the potential of NAPKON for German and international research activities. Trial registrationhttps://clinicaltrials.gov/ct2/show/NCT04768998.https://clinicaltrials.gov/ct2/show/NCT04747366.https://clinicaltrials.gov/ct2/show/NCT04679584
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Affiliation(s)
- Maximilian Schons
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lisa Pilgram
- Department II of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Jens-Peter Reese
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Melanie Stecher
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner-Site Cologne-Bonn, Cologne, Germany
| | - Gabriele Anton
- Institute of Epidemiology, Helmholtz Center Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Katharina S. Appel
- Department II of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Thomas Bahmer
- Internal Medicine Department I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Alexander Bartschke
- Core Facility Digital Medicine and Interoperability, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Carla Bellinghausen
- Department of Respiratory Medicine and Allergology, Medical Clinic 1, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Inga Bernemann
- Hannover Medical School, Hannover Unified Biobank, Hannover, Germany
| | - Markus Brechtel
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Folke Brinkmann
- Department of Paediatric Pneumology, Allergy and CF- Centre, University Children’s Hospital, Ruhr- University Bochum, Bochum, Germany
| | - Clara Brünn
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christine Dhillon
- COVID-19 Task Force, University Hospital Augsburg, Augsburg, Germany
| | - Cornelia Fiessler
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Ramsia Geisler
- Department II of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Eckard Hamelmann
- Department of Pediatrics, Children’s Center Bethel, University Hospital East Westphalia, University Bielefeld, Bielefeld, Germany
| | - Stefan Hansch
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Regensburg, Germany
| | - Frank Hanses
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Regensburg, Germany
- Emergency Department, University Hospital Regensburg, Regensburg, Germany
| | - Sabine Hanß
- University Medical Center Göttingen (UMG), Göttingen, Germany
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
| | - Susanne Herold
- Department of Internal Medicine V, University Hospital Giessen and Marburg, Justus-Liebig-University Giessen, Giessen, Germany
- Department of Internal Medicine, German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Giessen, Germany
| | - Ralf Heyder
- NUM Coordination Office, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anna-Lena Hofmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Sina Marie Hopff
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anna Horn
- Insitute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Carolin Jakob
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Steffi Jiru-Hillmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Thomas Keil
- Insitute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- State Institute of Health, Bavarian Health and Food Safety Authority, Bad Kissingen, Germany
| | - Yascha Khodamoradi
- Department of Infectious Diseases, Medical Clinic 2, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Mirjam Kohls
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Monika Kraus
- Institute of Epidemiology, Helmholtz Center Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich, Munich, Germany
| | - Dagmar Krefting
- University Medical Center Göttingen (UMG), Göttingen, Germany
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
| | - Sonja Kunze
- Institute of Epidemiology, Helmholtz Center Munich, Munich, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine I, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Lena Johanna Lippert
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Roberto Lorbeer
- Department of Radiology, University Hospital, LMU, Munich, Germany
- Medical Heart Center of Charité and German Heart Institute Berlin, Institute of Computer-Assisted Cardiovascular Medicine, Berlin, Germany
| | - Bettina Lorenz-Depiereux
- Institute of Epidemiology, Helmholtz Center Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich, Munich, Germany
| | - Corina Maetzler
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel University, Kiel, Germany
| | - Olga Miljukov
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Daniel Pape
- Department I of Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Valentina Püntmann
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
- Institute for Experimental and Translational Cardiovascular Imaging, University Hospital Frankfurt am Main, Frankfurt, Germany
| | - Lennart Reinke
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Christoph Römmele
- COVID-19 Task Force, University Hospital Augsburg, Augsburg, Germany
| | - Stefanie Rudolph
- Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Joint Charité and BIH Clinical Study Center, Charitéplatz 1, 10117 Berlin, Germany
| | - Julian Sass
- Core Facility Digital Medicine and Interoperability, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Schäfer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK e.V. (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Jens Schaller
- Medical Heart Center of Charité and German Heart Institute Berlin, Institute of Computer-Assisted Cardiovascular Medicine, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt – Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Mario Schattschneider
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christian Scheer
- Department of Anesthesiology and Intensive Care Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Margarete Scherer
- Department II of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Sein Schmidt
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Clinical Study Center, Charitéplatz 1, 10117 Berlin, Germany
| | - Julia Schmidt
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Kristina Seibel
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dana Stahl
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
- University Medicine Greifswald, Greifswald, Germany
| | - Fridolin Steinbeis
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Stefan Störk
- Comprehensive Heart Failure Center, University and University Hospital Würzburg, Würzburg, Germany
- Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Maike Tauchert
- Institute of Epidemiology, Helmholtz Center Munich, Munich, Germany
| | - Johannes Josef Tebbe
- Department of Gastroenterology and Infectious Disease, University Medical Center East Westphalia-Lippe, Klinikum Lippe, Detmold, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Nicole Toepfner
- Department of Pediatrics, Carl Gustav Carus University Hospital, TU Dresden, Dresden, Germany
| | - Kathrin Ungethüm
- Insitute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - Istvan Vadasz
- Institute for Lung Health (ILH), Giessen, Germany
- Department of Internal Medicine, University Hospital Giessen and Marburg, Justus Liebig University Giessen, Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Frankfurt, Germany
| | - Heike Valentin
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
- University Medicine Greifswald, Greifswald, Germany
| | - Silke Wiedmann
- NUM Coordination Office, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thomas Zoller
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Eike Nagel
- German Center for Cardiovascular Diseases (DZHK), Berlin, Germany
- Institute for Experimental and Translational Cardiovascular Imaging, University Hospital Frankfurt am Main, Frankfurt, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christof von Kalle
- Charité – Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Joint Charité and BIH Clinical Study Center, Charitéplatz 1, 10117 Berlin, Germany
| | - Thomas Illig
- Hannover Medical School, Hannover Unified Biobank, Hannover, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Hospital Schleswig Holstein, Kiel University, Kiel, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), Frankfurt, Germany
| | - Peter Heuschmann
- Insitute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
- Clinical Trial Center Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Jörg Janne Vehreschild
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt,, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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13
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Reese JT, Coleman B, Chan L, Blau H, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh JA, Mungall CJ, Williams AE, Robinson PN. NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study. Virol J 2022; 19:84. [PMID: 35570298 PMCID: PMC9107579 DOI: 10.1186/s12985-022-01813-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/04/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to reduce pain, fever, and inflammation but have been associated with complications in community-acquired pneumonia. Observations shortly after the start of the COVID-19 pandemic in 2020 suggested that ibuprofen was associated with an increased risk of adverse events in COVID-19 patients, but subsequent observational studies failed to demonstrate increased risk and in one case showed reduced risk associated with NSAID use. METHODS A 38-center retrospective cohort study was performed that leveraged the harmonized, high-granularity electronic health record data of the National COVID Cohort Collaborative. A propensity-matched cohort of 19,746 COVID-19 inpatients was constructed by matching cases (treated with NSAIDs at the time of admission) and 19,746 controls (not treated) from 857,061 patients with COVID-19 available for analysis. The primary outcome of interest was COVID-19 severity in hospitalized patients, which was classified as: moderate, severe, or mortality/hospice. Secondary outcomes were acute kidney injury (AKI), extracorporeal membrane oxygenation (ECMO), invasive ventilation, and all-cause mortality at any time following COVID-19 diagnosis. RESULTS Logistic regression showed that NSAID use was not associated with increased COVID-19 severity (OR: 0.57 95% CI: 0.53-0.61). Analysis of secondary outcomes using logistic regression showed that NSAID use was not associated with increased risk of all-cause mortality (OR 0.51 95% CI: 0.47-0.56), invasive ventilation (OR: 0.59 95% CI: 0.55-0.64), AKI (OR: 0.67 95% CI: 0.63-0.72), or ECMO (OR: 0.51 95% CI: 0.36-0.7). In contrast, the odds ratios indicate reduced risk of these outcomes, but our quantitative bias analysis showed E-values of between 1.9 and 3.3 for these associations, indicating that comparatively weak or moderate confounder associations could explain away the observed associations. CONCLUSIONS Study interpretation is limited by the observational design. Recording of NSAID use may have been incomplete. Our study demonstrates that NSAID use is not associated with increased COVID-19 severity, all-cause mortality, invasive ventilation, AKI, or ECMO in COVID-19 inpatients. A conservative interpretation in light of the quantitative bias analysis is that there is no evidence that NSAID use is associated with risk of increased severity or the other measured outcomes. Our results confirm and extend analogous findings in previous observational studies using a large cohort of patients drawn from 38 centers in a nationally representative multicenter database.
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Affiliation(s)
- Justin T Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Lauren Chan
- Translational and Integrative Sciences Center, Oregon State University, Corvallis, OR, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Tiffany J Callahan
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Boulder, CO, USA
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Luca Cappelletti
- AnacletoLab, Dipartimento Di Informatica, Università Degli Studi Di Milano, Milan, Italy
| | - Tommaso Fontana
- AnacletoLab, Dipartimento Di Informatica, Università Degli Studi Di Milano, Milan, Italy
| | | | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento Di Informatica, Università Degli Studi Di Milano, Milan, Italy
- CINI, National Laboratory in Artificial Intelligence and Intelligent Systems-AIIS, Rome, Italy
| | - Giorgio Valentini
- AnacletoLab, Dipartimento Di Informatica, Università Degli Studi Di Milano, Milan, Italy
- CINI, National Laboratory in Artificial Intelligence and Intelligent Systems-AIIS, Rome, Italy
| | - Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rachel Deer
- University of Texas Medical Branch, Galveston, TX, USA
| | - Julie A McMurry
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Melissa A Haendel
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA
| | - Emily Pfaff
- North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Heidi Spratt
- University of Texas Medical Branch, Galveston, TX, USA
| | - Jasvinder A Singh
- University of Alabama at Birmingham, Birmingham, AL, USA
- Medicine Service, VA Medical Center, Birmingham, AL, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew E Williams
- Tufts Medical Center Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA
- Institute for Clinical Research and Health Policy Studies, Tufts University School of Medicine, Boston, USA
- OHDSI Center at the Roux Institute, Northeastern University, Boston, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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14
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Chen UI, Xu H, Krause TM, Greenberg R, Dong X, Jiang X. Factors Associated With COVID-19 Death in the United States: Cohort Study. JMIR Public Health Surveill 2022; 8:e29343. [PMID: 35377319 PMCID: PMC9132142 DOI: 10.2196/29343] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/21/2021] [Accepted: 04/01/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Since the initial COVID-19 cases were identified in the United States in February 2020, the United States has experienced a high incidence of the disease. Understanding the risk factors for severe outcomes identifies the most vulnerable populations and helps in decision-making. OBJECTIVE This study aims to assess the factors associated with COVID-19-related deaths from a large, national, individual-level data set. METHODS A cohort study was conducted using data from the Optum de-identified COVID-19 electronic health record (EHR) data set; 1,271,033 adult participants were observed from February 1, 2020, to August 31, 2020, until their deaths due to COVID-19, deaths due to other reasons, or the end of the study. Cox proportional hazards models were constructed to evaluate the risks for each patient characteristic. RESULTS A total of 1,271,033 participants (age: mean 52.6, SD 17.9 years; male: 507,574/1,271,033, 39.93%) were included in the study, and 3315 (0.26%) deaths were attributed to COVID-19. Factors associated with COVID-19-related death included older age (80 vs 50-59 years old: hazard ratio [HR] 13.28, 95% CI 11.46-15.39), male sex (HR 1.68, 95% CI 1.57-1.80), obesity (BMI 40 vs <30 kg/m2: HR 1.71, 95% CI 1.50-1.96), race (Hispanic White, African American, Asian vs non-Hispanic White: HR 2.46, 95% CI 2.01-3.02; HR 2.27, 95% CI 2.06-2.50; HR 2.06, 95% CI 1.65-2.57), region (South, Northeast, Midwest vs West: HR 1.62, 95% CI 1.33-1.98; HR 2.50, 95% CI 2.06-3.03; HR 1.35, 95% CI 1.11-1.64), chronic respiratory disease (HR 1.21, 95% CI 1.12-1.32), cardiac disease (HR 1.10, 95% CI 1.01-1.19), diabetes (HR 1.92, 95% CI 1.75-2.10), recent diagnosis of lung cancer (HR 1.70, 95% CI 1.14-2.55), severely reduced kidney function (HR 1.92, 95% CI 1.69-2.19), stroke or dementia (HR 1.25, 95% CI 1.15-1.36), other neurological diseases (HR 1.77, 95% CI 1.59-1.98), organ transplant (HR 1.35, 95% CI 1.09-1.67), and other immunosuppressive conditions (HR 1.21, 95% CI 1.01-1.46). CONCLUSIONS This is one of the largest national cohort studies in the United States; we identified several patient characteristics associated with COVID-19-related deaths, and the results can serve as the basis for policy making. The study also offered directions for future studies, including the effect of other socioeconomic factors on the increased risk for minority groups.
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Affiliation(s)
- Uan-I Chen
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Trudy Millard Krause
- Department of Management, Policy, and Community Heath, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Raymond Greenberg
- Department of Population and Data Sciences, Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Epidemiology, Human Genetics, and Environmental Health, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiao Dong
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiaoqian Jiang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
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15
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Reese JT, Coleman B, Chan L, Blau H, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh J, Mungall CJ, Williams AE, Robinson PN. NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.13.21255438. [PMID: 33907758 PMCID: PMC8077581 DOI: 10.1101/2021.04.13.21255438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to reduce pain, fever, and inflammation but have been associated with complications in community-acquired pneumonia. Observations shortly after the start of the COVID-19 pandemic in 2020 suggested that ibuprofen was associated with an increased risk of adverse events in COVID-19 patients, but subsequent observational studies failed to demonstrate increased risk and in one case showed reduced risk associated with NSAID use. METHODS A 38-center retrospective cohort study was performed that leveraged the harmonized, high-granularity electronic health record data of the National COVID Cohort Collaborative. A propensity-matched cohort of COVID-19 inpatients was constructed by matching cases (treated with NSAIDs) and controls (not treated) from 857,061 patients with COVID-19. The primary outcome of interest was COVID-19 severity in hospitalized patients, which was classified as: moderate, severe, or mortality/hospice. Secondary outcomes were acute kidney injury (AKI), extracorporeal membrane oxygenation (ECMO), invasive ventilation, and all-cause mortality at any time following COVID-19 diagnosis. RESULTS Logistic regression showed that NSAID use was not associated with increased COVID-19 severity (OR: 0.57 95% CI: 0.53-0.61). Analysis of secondary outcomes using logistic regression showed that NSAID use was not associated with increased risk of all-cause mortality (OR 0.51 95% CI: 0.47-0.56), invasive ventilation (OR: 0.59 95% CI: 0.55-0.64), AKI (OR: 0.67 95% CI: 0.63-0.72), or ECMO (OR: 0.51 95% CI: 0.36-0.7). In contrast, the odds ratios indicate reduced risk of these outcomes, but our quantitative bias analysis showed E-values of between 1.9 and 3.3 for these associations, indicating that comparatively weak or moderate confounder associations could explain away the observed associations. CONCLUSIONS Study interpretation is limited by the observational design. Recording of NSAID use may have been incomplete. Our study demonstrates that NSAID use is not associated with increased COVID-19 severity, all-cause mortality, invasive ventilation, AKI, or ECMO in COVID-19 inpatients. A conservative interpretation in light of the quantitative bias analysis is that there is no evidence that NSAID use is associated with risk of increased severity or the other measured outcomes. Our findings are the largest EHR-based analysis of the effect of NSAIDs on outcome in COVID-19 patients to date. Our results confirm and extend analogous findings in previous observational studies using a large cohort of patients drawn from 38 centers in a nationally representative multicenter database.
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Affiliation(s)
- Justin T Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Lauren Chan
- Translational and Integrative Sciences Center, Oregon State University, Corvallis, OR, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Tiffany J Callahan
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Boulder, CO, USA
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Luca Cappelletti
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | - Tommaso Fontana
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
| | | | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elena Casiraghi
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
- CINI, National Laboratory in Artificial Intelligence and Intelligent Systems-AIIS, Roma, Italy
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Italy
- CINI, National Laboratory in Artificial Intelligence and Intelligent Systems-AIIS, Roma, Italy
| | - Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rachel Deer
- University of Texas Medical Branch, Galveston, TX, USA
| | - Julie A McMurry
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Melissa A Haendel
- Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA
| | - Emily Pfaff
- North Carolina Translational and Clinical Sciences Institute (NC TraCS), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Heidi Spratt
- University of Texas Medical Branch, Galveston, TX, USA
| | - Jasvinder Singh
- University of Alabama at Birmingham, Birmingham, AL, USA
- Medicine Service, VA Medical Center, Birmingham, AL, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew E Williams
- Tufts Medical Center Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA
- Tufts University School of Medicine, Institute for Clinical Research and Health Policy Studies
- Northeastern University, OHDSI Center at the Roux Institute
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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16
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Schmidt M, Guidet B, Demoule A, Ponnaiah M, Fartoukh M, Puybasset L, Combes A, Hajage D. Predicting 90-day survival of patients with COVID-19: Survival of Severely Ill COVID (SOSIC) scores. Ann Intensive Care 2021; 11:170. [PMID: 34897559 PMCID: PMC8665857 DOI: 10.1186/s13613-021-00956-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Predicting outcomes of critically ill intensive care unit (ICU) patients with coronavirus-19 disease (COVID-19) is a major challenge to avoid futile, and prolonged ICU stays. METHODS The objective was to develop predictive survival models for patients with COVID-19 after 1-to-2 weeks in ICU. Based on the COVID-ICU cohort, which prospectively collected characteristics, management, and outcomes of critically ill patients with COVID-19. Machine learning was used to develop dynamic, clinically useful models able to predict 90-day mortality using ICU data collected on day (D) 1, D7 or D14. RESULTS Survival of Severely Ill COVID (SOSIC)-1, SOSIC-7, and SOSIC-14 scores were constructed with 4244, 2877, and 1349 patients, respectively, randomly assigned to development or test datasets. The three models selected 15 ICU-entry variables recorded on D1, D7, or D14. Cardiovascular, renal, and pulmonary functions on prediction D7 or D14 were among the most heavily weighted inputs for both models. For the test dataset, SOSIC-7's area under the ROC curve was slightly higher (0.80 [0.74-0.86]) than those for SOSIC-1 (0.76 [0.71-0.81]) and SOSIC-14 (0.76 [0.68-0.83]). Similarly, SOSIC-1 and SOSIC-7 had excellent calibration curves, with similar Brier scores for the three models. CONCLUSION The SOSIC scores showed that entering 15 to 27 baseline and dynamic clinical parameters into an automatable XGBoost algorithm can potentially accurately predict the likely 90-day mortality post-ICU admission (sosic.shinyapps.io/shiny). Although external SOSIC-score validation is still needed, it is an additional tool to strengthen decisions about life-sustaining treatments and informing family members of likely prognosis.
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Affiliation(s)
- Matthieu Schmidt
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMRS) 1166, Institute of Cardiometabolism and Nutrition, Paris, France. .,Service de Médecine Intensive-Réanimation, Institut de Cardiologie, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), 47, bd de l'Hôpital, 75651, Paris Cedex 13, France. .,Sorbonne Université, GRC 30, RESPIRE, APHP, Hôpital Pitié-Salpêtrière, Paris, France.
| | - Bertrand Guidet
- Sorbonne Université, GRC 30, RESPIRE, APHP, Hôpital Pitié-Salpêtrière, Paris, France.,Institut Pierre-Louis d'Epidémiologie et de Santé Publique, APHP, Hôpital Saint-Antoine, INSERM, Service de Réanimation, Sorbonne Université, Paris, France
| | - Alexandre Demoule
- Sorbonne Université, GRC 30, RESPIRE, APHP, Hôpital Pitié-Salpêtrière, Paris, France.,Service de Pneumologie, Médecine Intensive-Réanimation (Département R3S), Groupe Hospitalier Universitaire APHP-Sorbonne Université, site Pitié-Salpêtrière, Paris, France.,Sorbonne Université, INSERM UMRS_1158, Neurophysiologie Respiratoire Expérimentale et Clinique, Paris, France
| | - Maharajah Ponnaiah
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMRS) 1166, Institute of Cardiometabolism and Nutrition, Paris, France
| | - Muriel Fartoukh
- Sorbonne Université, GRC 30, RESPIRE, APHP, Hôpital Pitié-Salpêtrière, Paris, France.,Service de Médecine Intensive-Réanimation, Hôpital Tenon, Département Médico-Universitaire APPROCHES, APHP, Paris, France.,Groupe de Recherche Clinique CARMAS, Université Paris-Est Créteil, Créteil, France
| | - Louis Puybasset
- CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, Sorbonne Université, Paris, France.,Department of Anesthesiology & Critical Care, APHP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Alain Combes
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMRS) 1166, Institute of Cardiometabolism and Nutrition, Paris, France.,Service de Médecine Intensive-Réanimation, Institut de Cardiologie, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), 47, bd de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, GRC 30, RESPIRE, APHP, Hôpital Pitié-Salpêtrière, Paris, France
| | - David Hajage
- Département de Santé Publique, Centre de Pharmacoépidémiologie (Cephepi), INSER, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, APHP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
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17
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Ge J, Pletcher MJ, Lai JC. Outcomes of SARS-CoV-2 Infection in Patients With Chronic Liver Disease and Cirrhosis: A National COVID Cohort Collaborative Study. Gastroenterology 2021; 161:1487-1501.e5. [PMID: 34284037 PMCID: PMC8286237 DOI: 10.1053/j.gastro.2021.07.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS In patients with chronic liver disease (CLD) with or without cirrhosis, existing studies on the outcomes with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have limited generalizability. We used the National COVID Cohort Collaborative (N3C), a harmonized electronic health record dataset of 6.4 million, to describe SARS-CoV-2 outcomes in patients with CLD and cirrhosis. METHODS We identified all patients with CLD with or without cirrhosis who had SARS-CoV-2 testing in the N3C Data Enclave as of July 1, 2021. We used survival analyses to associate SARS-CoV-2 infection, presence of cirrhosis, and clinical factors with the primary outcome of 30-day mortality. RESULTS We isolated 220,727 patients with CLD and SARS-CoV-2 test status: 128,864 (58%) were noncirrhosis/negative, 29,446 (13%) were noncirrhosis/positive, 53,476 (24%) were cirrhosis/negative, and 8941 (4%) were cirrhosis/positive patients. Thirty-day all-cause mortality rates were 3.9% in cirrhosis/negative and 8.9% in cirrhosis/positive patients. Compared to cirrhosis/negative patients, cirrhosis/positive patients had 2.38 times adjusted hazard of death at 30 days. Compared to noncirrhosis/positive patients, cirrhosis/positive patients had 3.31 times adjusted hazard of death at 30 days. In stratified analyses among patients with cirrhosis with increased age, obesity, and comorbid conditions (ie, diabetes, heart failure, and pulmonary disease), SARS-CoV-2 infection was associated with increased adjusted hazard of death. CONCLUSIONS In this study of approximately 221,000 nationally representative, diverse, and sex-balanced patients with CLD; we found SARS-CoV-2 infection in patients with cirrhosis was associated with 2.38 times mortality hazard, and the presence of cirrhosis among patients with CLD infected with SARS-CoV-2 was associated with 3.31 times mortality hazard. These results provide an additional impetus for increasing vaccination uptake and further research regarding immune responses to vaccines in patients with severe liver disease.
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Affiliation(s)
- Jin Ge
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, California.
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, California; Division of General Internal Medicine, Department of Medicine, University of California-San Francisco, San Francisco, California
| | - Jennifer C Lai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, California
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18
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Murri R, Lenkowicz J, Masciocchi C, Iacomini C, Fantoni M, Damiani A, Marchetti A, Sergi PDA, Arcuri G, Cesario A, Patarnello S, Antonelli M, Bellantone R, Bernabei R, Boccia S, Calabresi P, Cambieri A, Cauda R, Colosimo C, Crea F, De Maria R, De Stefano V, Franceschi F, Gasbarrini A, Parolini O, Richeldi L, Sanguinetti M, Urbani A, Zega M, Scambia G, Valentini V. A machine-learning parsimonious multivariable predictive model of mortality risk in patients with Covid-19. Sci Rep 2021; 11:21136. [PMID: 34707184 PMCID: PMC8551240 DOI: 10.1038/s41598-021-99905-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic is impressively challenging the healthcare system. Several prognostic models have been validated but few of them are implemented in daily practice. The objective of the study was to validate a machine-learning risk prediction model using easy-to-obtain parameters to help to identify patients with COVID-19 who are at higher risk of death. The training cohort included all patients admitted to Fondazione Policlinico Gemelli with COVID-19 from March 5, 2020, to November 5, 2020. Afterward, the model was tested on all patients admitted to the same hospital with COVID-19 from November 6, 2020, to February 5, 2021. The primary outcome was in-hospital case-fatality risk. The out-of-sample performance of the model was estimated from the training set in terms of Area under the Receiving Operator Curve (AUROC) and classification matrix statistics by averaging the results of fivefold cross validation repeated 3-times and comparing the results with those obtained on the test set. An explanation analysis of the model, based on the SHapley Additive exPlanations (SHAP), is also presented. To assess the subsequent time evolution, the change in paO2/FiO2 (P/F) at 48 h after the baseline measurement was plotted against its baseline value. Among the 921 patients included in the training cohort, 120 died (13%). Variables selected for the model were age, platelet count, SpO2, blood urea nitrogen (BUN), hemoglobin, C-reactive protein, neutrophil count, and sodium. The results of the fivefold cross-validation repeated 3-times gave AUROC of 0.87, and statistics of the classification matrix to the Youden index as follows: sensitivity 0.840, specificity 0.774, negative predictive value 0.971. Then, the model was tested on a new population (n = 1463) in which the case-fatality rate was 22.6%. The test model showed AUROC 0.818, sensitivity 0.813, specificity 0.650, negative predictive value 0.922. Considering the first quartile of the predicted risk score (low-risk score group), the case-fatality rate was 1.6%, 17.8% in the second and third quartile (high-risk score group) and 53.5% in the fourth quartile (very high-risk score group). The three risk score groups showed good discrimination for the P/F value at admission, and a positive correlation was found for the low-risk class to P/F at 48 h after admission (adjusted R-squared = 0.48). We developed a predictive model of death for people with SARS-CoV-2 infection by including only easy-to-obtain variables (abnormal blood count, BUN, C-reactive protein, sodium and lower SpO2). It demonstrated good accuracy and high power of discrimination. The simplicity of the model makes the risk prediction applicable for patients in the Emergency Department, or during hospitalization. Although it is reasonable to assume that the model is also applicable in not-hospitalized persons, only appropriate studies can assess the accuracy of the model also for persons at home.
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Affiliation(s)
- Rita Murri
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Jacopo Lenkowicz
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Chiara Iacomini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Massimo Fantoni
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | | | | | - Giovanni Arcuri
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alfredo Cesario
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Massimo Antonelli
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rocco Bellantone
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberto Bernabei
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefania Boccia
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paolo Calabresi
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Cambieri
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Roberto Cauda
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cesare Colosimo
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Filippo Crea
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Valerio De Stefano
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Franceschi
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Luca Richeldi
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Urbani
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Zega
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Vincenzo Valentini
- Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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19
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Gupta AK, Grannis SJ, Kasthurirathne SN. Evaluation of a Parsimonious COVID-19 Outbreak Prediction Model: Heuristic Modeling Approach Using Publicly Available Data Sets. J Med Internet Res 2021; 23:e28812. [PMID: 34156964 PMCID: PMC8315156 DOI: 10.2196/28812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/02/2021] [Accepted: 06/12/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic has changed public health policies and human and community behaviors through lockdowns and mandates. Governments are rapidly evolving policies to increase hospital capacity and supply personal protective equipment and other equipment to mitigate disease spread in affected regions. Current models that predict COVID-19 case counts and spread are complex by nature and offer limited explainability and generalizability. This has highlighted the need for accurate and robust outbreak prediction models that balance model parsimony and performance. OBJECTIVE We sought to leverage readily accessible data sets extracted from multiple states to train and evaluate a parsimonious predictive model capable of identifying county-level risk of COVID-19 outbreaks on a day-to-day basis. METHODS Our modeling approach leveraged the following data inputs: COVID-19 case counts per county per day and county populations. We developed an outbreak gold standard across California, Indiana, and Iowa. The model utilized a per capita running 7-day sum of the case counts per county per day and the mean cumulative case count to develop baseline values. The model was trained with data recorded between March 1 and August 31, 2020, and tested on data recorded between September 1 and October 31, 2020. RESULTS The model reported sensitivities of 81%, 92%, and 90% for California, Indiana, and Iowa, respectively. The precision in each state was above 85% while specificity and accuracy scores were generally >95%. CONCLUSIONS Our parsimonious model provides a generalizable and simple alternative approach to outbreak prediction. This methodology can be applied to diverse regions to help state officials and hospitals with resource allocation and to guide risk management, community education, and mitigation strategies.
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Affiliation(s)
- Agrayan K Gupta
- Indiana University, Bloomington, IN, United States.,Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, IN, United States
| | - Shaun J Grannis
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, IN, United States.,School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Suranga N Kasthurirathne
- Center for Biomedical Informatics, Regenstrief Institute, Indianapolis, IN, United States.,School of Medicine, Indiana University, Indianapolis, IN, United States
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20
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Völlmy F, van den Toorn H, Zenezini Chiozzi R, Zucchetti O, Papi A, Volta CA, Marracino L, Vieceli Dalla Sega F, Fortini F, Demichev V, Tober-Lau P, Campo G, Contoli M, Ralser M, Kurth F, Spadaro S, Rizzo P, Heck AJ. A serum proteome signature to predict mortality in severe COVID-19 patients. Life Sci Alliance 2021; 4:4/9/e202101099. [PMID: 34226277 PMCID: PMC8321673 DOI: 10.26508/lsa.202101099] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we recorded serum proteome profiles of 33 severe COVID-19 patients admitted to respiratory and intensive care units because of respiratory failure. We received, for most patients, blood samples just after admission and at two more later time points. With the aim to predict treatment outcome, we focused on serum proteins different in abundance between the group of survivors and non-survivors. We observed that a small panel of about a dozen proteins were significantly different in abundance between these two groups. The four structurally and functionally related type-3 cystatins AHSG, FETUB, histidine-rich glycoprotein, and KNG1 were all more abundant in the survivors. The family of inter-α-trypsin inhibitors, ITIH1, ITIH2, ITIH3, and ITIH4, were all found to be differentially abundant in between survivors and non-survivors, whereby ITIH1 and ITIH2 were more abundant in the survivor group and ITIH3 and ITIH4 more abundant in the non-survivors. ITIH1/ITIH2 and ITIH3/ITIH4 also showed opposite trends in protein abundance during disease progression. We defined an optimal panel of nine proteins for mortality risk assessment. The prediction power of this mortality risk panel was evaluated against two recent COVID-19 serum proteomics studies on independent cohorts measured in other laboratories in different countries and observed to perform very well in predicting mortality also in these cohorts. This panel may not be unique for COVID-19 as some of the proteins in the panel have previously been annotated as mortality markers in aging and in other diseases caused by different pathogens, including bacteria.
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Affiliation(s)
- Franziska Völlmy
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Ottavio Zucchetti
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, University of Ferrara, Ferrara, Italy
| | - Alberto Papi
- Respiratory Section, Department of Translational Medicine, University of Ferrara, Ferrara, Italy and Respiratory Disease Unit, Azienda Ospedaliero-Universitaria di Ferrara, Ferrara, Italy
| | - Carlo Alberto Volta
- Department of Translational Medicine University of Ferrara, Ferrara, Italy and Intensive Care Unit, Azienda Ospedaliero-Universitaria di Ferrara, Italy
| | - Luisa Marracino
- Department of Translational Medicine and Laboratory for Technology of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | | | | | - Vadim Demichev
- Charité-Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.,The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, UK.,The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, UK
| | - Pinkus Tober-Lau
- Charité-Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Gianluca Campo
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, University of Ferrara, Ferrara, Italy.,Maria Cecilia Hospital, GVM Care & Research, Cotignola, Italy
| | - Marco Contoli
- Respiratory Section, Department of Translational Medicine, University of Ferrara, Ferrara, Italy and Respiratory Disease Unit, Azienda Ospedaliero-Universitaria di Ferrara, Ferrara, Italy
| | - Markus Ralser
- Charité-Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.,The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, UK
| | - Florian Kurth
- Charité-Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Savino Spadaro
- Department of Translational Medicine University of Ferrara, Ferrara, Italy and Intensive Care Unit, Azienda Ospedaliero-Universitaria di Ferrara, Italy
| | - Paola Rizzo
- Department of Translational Medicine and Laboratory for Technology of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy.,Maria Cecilia Hospital, GVM Care & Research, Cotignola, Italy
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands .,Netherlands Proteomics Center, Utrecht, The Netherlands
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21
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Ge J, Pletcher MJ, Lai JC. Outcomes of SARS-CoV-2 Infection in Patients with Chronic Liver Disease and Cirrhosis: a N3C Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.03.21258312. [PMID: 34127981 PMCID: PMC8202438 DOI: 10.1101/2021.06.03.21258312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background and Aims In patients with chronic liver diseases (CLD) with or without cirrhosis, existing data on the risk of adverse outcomes with SARS-CoV-2 infection have been mixed or have limited generalizability. We used the National COVID Cohort Collaborative (N3C) Data Enclave, a harmonized electronic health record (EHR) dataset of 5.9 million nationally-representative, diverse, and gender-balanced patients, to describe outcomes in patients with CLD and cirrhosis with SARS-CoV-2. Methods We identified all chronic liver diseases patients with and without cirrhosis who had SARS-CoV-2 testing documented in the N3C Data Enclave as of data release date 5/15/2021. The primary outcome was 30-day all-cause mortality. Survival analysis methods were used to estimate cumulative incidences of death, hospitalization, and mechanical ventilation, and to calculate the associations of SARS-CoV-2 infection, presence of cirrhosis, and demographic and clinical factors to 30-day mortality. Results We isolated 217,143 patients with CLD: 129,097 (59%) without cirrhosis and SARS-CoV-2 negative, 25,844 (12%) without cirrhosis and SARS-CoV-2 positive, 54,065 (25%) with cirrhosis and SARS-CoV-2 negative, and 8,137 (4%) with cirrhosis and SARS-CoV-2 positive. Among CLD patients without cirrhosis, 30-day all-cause mortality rates were 0.4% in SARS-CoV-2 negative patients and 1.8% in positive patients. Among CLD patients with cirrhosis, 30-day all-cause mortality rates were 4.0% in SARS-CoV-2 negative patients and 9.7% in positive patients.Compared to those who tested SARS-CoV-2 negative, SARS-CoV-2 positivity was associated with more than two-fold (aHR 2.43, 95% CI 2.23-2.64) hazard of death at 30 days among patients with cirrhosis. Compared to patients without cirrhosis, the presence of cirrhosis was associated with a three-fold (aHR 3.39, 95% CI 2.96-3.89) hazard of death at 30 days among patients who tested SARS-CoV-2 positive. Age (aHR 1.03 per year, 95% CI 1.03-1.04) was associated with death at 30 days among patients with cirrhosis who were SARS-CoV-2 positive. Conclusions In this study of nearly 220,000 CLD patients, we found SARS-CoV-2 infection in patients with cirrhosis was associated with 2.43-times mortality hazard, and the presence of cirrhosis among CLD patients infected with SARS-CoV-2 were associated with 3.39-times mortality hazard. Compared to previous studies, our use of a nationally-representative, diverse, and gender-balanced dataset enables wide generalizability of these findings.
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Affiliation(s)
- Jin Ge
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California – San Francisco, San Francisco, CA
| | - Mark J. Pletcher
- Department of Epidemiology and Biostatistics, University of California – San Francisco, San Francisco, CA
- Division of General Internal Medicine, Department of Medicine, University of California – San Francisco, San Francisco, CA
| | - Jennifer C. Lai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California – San Francisco, San Francisco, CA
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22
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Galbraith MD, Kinning KT, Sullivan KD, Baxter R, Araya P, Jordan KR, Russell S, Smith KP, Granrath RE, Shaw JR, Dzieciatkowska M, Ghosh T, Monte AA, D'Alessandro A, Hansen KC, Benett TD, Hsieh EWY, Espinosa JM. Seroconversion stages COVID19 into distinct pathophysiological states. eLife 2021; 10:e65508. [PMID: 33724185 PMCID: PMC7963480 DOI: 10.7554/elife.65508] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
COVID19 is a heterogeneous medical condition involving diverse underlying pathophysiological processes including hyperinflammation, endothelial damage, thrombotic microangiopathy, and end-organ damage. Limited knowledge about the molecular mechanisms driving these processes and lack of staging biomarkers hamper the ability to stratify patients for targeted therapeutics. We report here the results of a cross-sectional multi-omics analysis of hospitalized COVID19 patients revealing that seroconversion status associates with distinct underlying pathophysiological states. Low antibody titers associate with hyperactive T cells and NK cells, high levels of IFN alpha, gamma and lambda ligands, markers of systemic complement activation, and depletion of lymphocytes, neutrophils, and platelets. Upon seroconversion, all of these processes are attenuated, observing instead increases in B cell subsets, emergency hematopoiesis, increased D-dimer, and hypoalbuminemia. We propose that seroconversion status could potentially be used as a biosignature to stratify patients for therapeutic intervention and to inform analysis of clinical trial results in heterogenous patient populations.
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Affiliation(s)
- Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pharmacology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kohl T Kinning
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, Division of Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ryan Baxter
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Paula Araya
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kimberly R Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Seth Russell
- Data Science to Patient Value, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Keith P Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ross E Granrath
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Jessica R Shaw
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public HealthAuroraUnited States
| | - Andrew A Monte
- Department of Emergency Medicine, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Tellen D Benett
- Department of Pediatrics, Sections of Informatics and Data Science and Critical Care Medicine, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Elena WY Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, Division of Allergy/Immunology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pharmacology, University of Colorado Anschutz Medical CampusAuroraUnited States
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23
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Antar AAR, Yu T, Pisanic N, Azamfirei R, Tornheim JA, Brown DM, Kruczynski K, Hardick JP, Sewell T, Jang M, Church T, Walch SN, Reuland C, Bachu VS, Littlefield K, Park HS, Ursin RL, Ganesan A, Kusemiju O, Barnaba B, Charles C, Prizzi M, Johnstone JR, Payton C, Dai W, Fuchs J, Massaccesi G, Armstrong DT, Townsend JL, Keller SC, Demko ZO, Hu C, Wang MC, Sauer LM, Mostafa HH, Keruly JC, Mehta SH, Klein SL, Cox AL, Pekosz A, Heaney CD, Thomas DL, Blair PW, Manabe YC. Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in an longitudinally sampled cohort of COVID-19 outpatients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33688688 DOI: 10.1101/2021.03.02.21252420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background Sustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection. Methods Ninety-five outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models. Results Viral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI ≥ 25kg/m 2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044). Conclusions We demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.
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