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Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N, Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, McEnaney K, Barton B, Lentucci C, Saluvan M, Chang AC, Hoch A, Albert M, Shaheen T, Kho AT, Thomas S, Chen J, Murphy MD, Cooney M, Presnell S, Fragiadakis GK, Patel R, Guan L, Gygi J, Pawar S, Brito A, Khalil Z, Maguire C, Fourati S, Overton JA, Vita R, Westendorf K, Salehi-Rad R, Leligdowicz A, Matthay MA, Singer JP, Kangelaris KN, Hendrickson CM, Krummel MF, Langelier CR, Woodruff PG, Powell DL, Kim JN, Simmons B, Goonewardene IM, Smith CM, Martens M, Mosier J, Kimura H, Sherman AC, Walsh SR, Issa NC, Dela Cruz C, Farhadian S, Iwasaki A, Ko AI, Chinthrajah S, Ahuja N, Rogers AJ, Artandi M, Siegel SA, Lu Z, Drevets DA, Brown BR, Anderson ML, Guirgis FW, Thyagarajan RV, Rousseau JF, Wylie D, Busch J, Gandhi S, Triplett TA, Yendewa G, Giddings O, Anderson EJ, Mehta AK, Sevransky JE, Khor B, Rahman A, Stadlbauer D, Dutta J, Xie H, Kim-Schulze S, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khan Z, Maecker HT, Elashoff D, Brook J, Ramires-Sanchez E, Llamas M, Rivera A, Perdomo C, Ward DC, Magyar CE, Fulcher JA, Abe-Jones Y, Asthana S, Beagle A, Bhide S, Carrillo SA, Chak S, Fragiadakis GK, Ghale R, Gonzalez A, Jauregui A, Jones N, Lea T, Lee D, Lota R, Milush J, Nguyen V, Pierce L, Prasad PA, Rao A, Samad B, Shaw C, Sigman A, Sinha P, Ward A, Willmore A, Zhan J, Rashid S, Rodriguez N, Tang K, Altamirano LT, Betancourt L, Curiel C, Sutter N, Paz MT, Tietje-Ulrich G, Leroux C, Connors J, Bernui M, Kutzler MA, Edwards C, Lee E, Lin E, Croen B, Semenza NC, Rogowski B, Melnyk N, Woloszczuk K, Cusimano G, Bell MR, Furukawa S, McLin R, Marrero P, Sheidy J, Tegos GP, Nagle C, Mege N, Ulring K, Seyfert-Margolis V, Conway M, Francisco D, Molzahn A, Erickson H, Wilson CC, Schunk R, Sierra B, Hughes T, Smolen K, Desjardins M, van Haren S, Mitre X, Cauley J, Li X, Tong A, Evans B, Montesano C, Licona JH, Krauss J, Chang JBP, Izaguirre N, Chaudhary O, Coppi A, Fournier J, Mohanty S, Muenker MC, Nelson A, Raddassi K, Rainone M, Ruff WE, Salahuddin S, Schulz WL, Vijayakumar P, Wang H, Wunder Jr. E, Young HP, Zhao Y, Saksena M, Altman D, Kojic E, Srivastava K, Eaker LQ, Bermúdez-González MC, Beach KF, Sominsky LA, Azad AR, Carreño JM, Singh G, Raskin A, Tcheou J, Bielak D, Kawabata H, Mulder LCF, Kleiner G, Lee AS, Do ED, Fernandes A, Manohar M, Hagan T, Blish CA, Din HN, Roque J, Yang S, Brunton A, Sullivan PE, Strnad M, Lyski ZL, Coulter FJ, Booth JL, Sinko LA, Moldawer LL, Borresen B, Roth-Manning B, Song LZ, Nelson E, Lewis-Smith M, Smith J, Tipan PG, Siles N, Bazzi S, Geltman J, Hurley K, Gabriele G, Sieg S, Vaysman T, Bristow L, Hussaini L, Hellmeister K, Samaha H, Cheng A, Spainhour C, Scherer EM, Johnson B, Bechnak A, Ciric CR, Hewitt L, Carter E, Mcnair N, Panganiban B, Huerta C, Usher J, Ribeiro SP, Altman MC, Becker PM, Rouphael N. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 2022; 83:104208. [PMID: 35952496 PMCID: PMC9359694 DOI: 10.1016/j.ebiom.2022.104208] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management. METHODS Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed. FINDINGS The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC. INTERPRETATION Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19. FUNDING NIH.
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Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Carly E. Milliren
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Carolyn S. Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Charles B. Cairns
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - Monica Kraft
- University of Arizona, Tucson, AZ, United States
| | - Lindsey R. Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | - Albert C. Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Denise A. Esserman
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ruth R. Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Steven H. Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | | | - Elias K. Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - David J. Erle
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | | | | | | | | | | | | | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma, OK, United States
| | - Mark A. Atkinson
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - Scott C. Brakenridge
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - David Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | | | - Esther Melamed
- The University of Texas at Austin, Austin, TX, United States
| | | | - Rafick Sekaly
- Case Western Reserve University, Cleveland, OH, United States
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison D. Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
| | - Elaine F. Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 PMCID: PMC8983481 DOI: 10.1016/j.medj.2022.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Background The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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3
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 DOI: 10.1101/2022.01.22.22269660] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. METHODS We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. FINDINGS For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). CONCLUSION The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. FUNDING This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Jiang G, Dhruva SS, Chen J, Schulz WL, Doshi AA, Noseworthy PA, Zhang S, Yu Y, Patrick Young H, Brandt E, Ervin KR, Shah ND, Ross JS, Coplan P, Drozda JP. Feasibility of capturing real-world data from health information technology systems at multiple centers to assess cardiac ablation device outcomes: A fit-for-purpose informatics analysis report. J Am Med Inform Assoc 2021; 28:2241-2250. [PMID: 34313748 PMCID: PMC8449615 DOI: 10.1093/jamia/ocab117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE The study sought to conduct an informatics analysis on the National Evaluation System for Health Technology Coordinating Center test case of cardiac ablation catheters and to demonstrate the role of informatics approaches in the feasibility assessment of capturing real-world data using unique device identifiers (UDIs) that are fit for purpose for label extensions for 2 cardiac ablation catheters from the electronic health records and other health information technology systems in a multicenter evaluation. MATERIALS AND METHODS We focused on data capture and transformation and data quality maturity model specified in the National Evaluation System for Health Technology Coordinating Center data quality framework. The informatics analysis included 4 elements: the use of UDIs for identifying device exposure data, the use of standardized codes for defining computable phenotypes, the use of natural language processing for capturing unstructured data elements from clinical data systems, and the use of common data models for standardizing data collection and analyses. RESULTS We found that, with the UDI implementation at 3 health systems, the target device exposure data could be effectively identified, particularly for brand-specific devices. Computable phenotypes for study outcomes could be defined using codes; however, ablation registries, natural language processing tools, and chart reviews were required for validating data quality of the phenotypes. The common data model implementation status varied across sites. The maturity level of the key informatics technologies was highly aligned with the data quality maturity model. CONCLUSIONS We demonstrated that the informatics approaches can be feasibly used to capture safety and effectiveness outcomes in real-world data for use in medical device studies supporting label extensions.
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Affiliation(s)
- Guoqian Jiang
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sanket S Dhruva
- School of Medicine, University of California, San Francisco, and San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Jiajing Chen
- Mercy Research, Mercy, Chesterfield, Missouri, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, Connecticut, USA
| | | | - Peter A Noseworthy
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Shumin Zhang
- Medical Device Epidemiology and Real-World Data Science, Office of the Chief Medical Officer, Johnson & Johnson, New Brunswick, New Jersey, USA
| | - Yue Yu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - H Patrick Young
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eric Brandt
- Mercy Research, Mercy, Chesterfield, Missouri, USA
| | - Keondae R Ervin
- National Evaluation System for Health Technology Coordinating Center, Medical Device Innovation Consortium, Arlington, Virginia, USA
| | - Nilay D Shah
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph S Ross
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, Connecticut, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Paul Coplan
- Medical Device Epidemiology and RWD Science, Office of the Chief Medical Officer, Johnson & Johnson, New Brunswick, New Jersey, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Khera R, Mortazavi BJ, Sangha V, Warner F, Young HP, Ross JS, Shah ND, Theel ES, Jenkinson WG, Knepper C, Wang K, Peaper D, Martinello RA, Brandt CA, Lin Z, Ko AI, Krumholz HM, Pollock BD, Schulz WL. Accuracy of Computable Phenotyping Approaches for SARS-CoV-2 Infection and COVID-19 Hospitalizations from the Electronic Health Record. medRxiv 2021. [PMID: 34013299 PMCID: PMC8132274 DOI: 10.1101/2021.03.16.21253770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Objective: Real-world data have been critical for rapid-knowledge generation throughout the COVID-19 pandemic. To ensure high-quality results are delivered to guide clinical decision making and the public health response, as well as characterize the response to interventions, it is essential to establish the accuracy of COVID-19 case definitions derived from administrative data to identify infections and hospitalizations. Methods: Electronic Health Record (EHR) data were obtained from the clinical data warehouse of the Yale New Haven Health System (Yale, primary site) and 3 hospital systems of the Mayo Clinic (validation site). Detailed characteristics on demographics, diagnoses, and laboratory results were obtained for all patients with either a positive SARS-CoV-2 PCR or antigen test or ICD-10 diagnosis of COVID-19 (U07.1) between April 1, 2020 and March 1, 2021. Various computable phenotype definitions were evaluated for their accuracy to identify SARS-CoV-2 infection and COVID-19 hospitalizations. Results: Of the 69,423 individuals with either a diagnosis code or a laboratory diagnosis of a SARS-CoV-2 infection at Yale, 61,023 had a principal or a secondary diagnosis code for COVID-19 and 50,355 had a positive SARS-CoV-2 test. Among those with a positive laboratory test, 38,506 (76.5%) and 3449 (6.8%) had a principal and secondary diagnosis code of COVID-19, respectively, while 8400 (16.7%) had no COVID-19 diagnosis. Moreover, of the 61,023 patients with a COVID-19 diagnosis code, 19,068 (31.2%) did not have a positive laboratory test for SARS-CoV-2 in the EHR. Of the 20 cases randomly sampled from this latter group for manual review, all had a COVID-19 diagnosis code related to asymptomatic testing with negative subsequent test results. The positive predictive value (precision) and sensitivity (recall) of a COVID-19 diagnosis in the medical record for a documented positive SARS-CoV-2 test were 68.8% and 83.3%, respectively. Among 5,109 patients who were hospitalized with a principal diagnosis of COVID-19, 4843 (94.8%) had a positive SARS-CoV-2 test within the 2 weeks preceding hospital admission or during hospitalization. In addition, 789 hospitalizations had a secondary diagnosis of COVID-19, of which 446 (56.5%) had a principal diagnosis consistent with severe clinical manifestation of COVID-19 (e.g., sepsis or respiratory failure). Compared with the cohort that had a principal diagnosis of COVID-19, those with a secondary diagnosis had a more than 2-fold higher in-hospital mortality rate (13.2% vs 28.0%, P<0.001). In the validation sample at Mayo Clinic, diagnosis codes more consistently identified SARS-CoV-2 infection (precision of 95%) but had lower recall (63.5%) with substantial variation across the 3 Mayo Clinic sites. Similar to Yale, diagnosis codes consistently identified COVID-19 hospitalizations at Mayo, with hospitalizations defined by secondary diagnosis code with 2-fold higher in-hospital mortality compared to those with a primary diagnosis of COVID-19. Conclusions: COVID-19 diagnosis codes misclassified the SARS-CoV-2 infection status of many people, with implications for clinical research and epidemiological surveillance. Moreover, the codes had different performance across two academic health systems and identified groups with different risks of mortality. Real-world data from the EHR can be used to in conjunction with diagnosis codes to improve the identification of people infected with SARS-CoV-2.
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McPadden J, Warner F, Young HP, Hurley NC, Pulk RA, Singh A, Durant TJS, Gong G, Desai N, Haimovich A, Taylor RA, Gunel M, Dela Cruz CS, Farhadian SF, Siner J, Villanueva M, Churchwell K, Hsiao A, Torre CJ, Velazquez EJ, Herbst RS, Iwasaki A, Ko AI, Mortazavi BJ, Krumholz HM, Schulz WL. Clinical characteristics and outcomes for 7,995 patients with SARS-CoV-2 infection. PLoS One 2021; 16:e0243291. [PMID: 33788846 PMCID: PMC8011821 DOI: 10.1371/journal.pone.0243291] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVE Severe acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2. DESIGN This was an observational, retrospective study based on real-world data for 7,995 patients with SARS-CoV-2 from a clinical data repository. SETTING Yale New Haven Health (YNHH) is a five-hospital academic health system serving a diverse patient population with community and teaching facilities in both urban and suburban areas. POPULATIONS The study included adult patients who had SARS-CoV-2 testing at YNHH between March 1 and April 30, 2020. MAIN OUTCOME AND PERFORMANCE MEASURES Primary outcomes were admission and in-hospital mortality for patients with SARS-CoV-2 infection as determined by RT-PCR testing. We also assessed features associated with the need for respiratory support. RESULTS Of the 28605 patients tested for SARS-CoV-2, 7995 patients (27.9%) had an infection (median age 52.3 years) and 2154 (26.9%) of these had an associated admission (median age 66.2 years). Of admitted patients, 2152 (99.9%) had a discharge disposition at the end of the study period. Of these, 329 (15.3%) required invasive mechanical ventilation and 305 (14.2%) expired. Increased age and male sex were positively associated with admission and in-hospital mortality (median age 80.7 years), while comorbidities had a much weaker association with the risk of admission or mortality. Black race (OR 1.43, 95%CI 1.14-1.78) and Hispanic ethnicity (OR 1.81, 95%CI 1.50-2.18) were identified as risk factors for admission, but, among discharged patients, age-adjusted in-hospital mortality was not significantly different among racial and ethnic groups. CONCLUSIONS This observational study identified, among people testing positive for SARS-CoV-2 infection, older age and male sex as the most strongly associated risks for admission and in-hospital mortality in patients with SARS-CoV-2 infection. While minority racial and ethnic groups had increased burden of disease and risk of admission, age-adjusted in-hospital mortality for discharged patients was not significantly different among racial and ethnic groups. Ongoing studies will be needed to continue to evaluate these risks, particularly in the setting of evolving treatment guidelines.
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Affiliation(s)
- Jacob McPadden
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - H. Patrick Young
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Nathan C. Hurley
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Rebecca A. Pulk
- Corporate Pharmacy Services, Yale New Haven Health, New Haven, Connecticut, United States of America
| | - Avinainder Singh
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Thomas J. S. Durant
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Guannan Gong
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Nihar Desai
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
| | - Adrian Haimovich
- Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Richard Andrew Taylor
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Murat Gunel
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Charles S. Dela Cruz
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shelli F. Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jonathan Siner
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Merceditas Villanueva
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Center for Interdisciplinary Research on AIDS, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Keith Churchwell
- Yale New Haven Hospital, New Haven, Connecticut, United States of America
| | - Allen Hsiao
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Information Technology Services, Yale New Haven Health, New Haven, Connecticut, United States of America
| | - Charles J. Torre
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Information Technology Services, Yale New Haven Health, New Haven, Connecticut, United States of America
| | - Eric J. Velazquez
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Roy S. Herbst
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Bobak J. Mortazavi
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, Texas, United States of America
| | - Harlan M. Krumholz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Wade L. Schulz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
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Schulz WL, Young HP, Coppi A, Mortazavi BJ, Lin Z, Jean RA, Krumholz HM. Temporal relationship of computed and structured diagnoses in electronic health record data. BMC Med Inform Decis Mak 2021; 21:61. [PMID: 33596898 PMCID: PMC7890604 DOI: 10.1186/s12911-021-01416-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/31/2021] [Indexed: 12/13/2022] Open
Abstract
Background The electronic health record (EHR) holds the prospect of providing more complete and timely access to clinical information for biomedical research, quality assessments, and quality improvement compared to other data sources, such as administrative claims. In this study, we sought to assess the completeness and timeliness of structured diagnoses in the EHR compared to computed diagnoses for hypertension (HTN), hyperlipidemia (HLD), and diabetes mellitus (DM). Methods We determined the amount of time for a structured diagnosis to be recorded in the EHR from when an equivalent diagnosis could be computed from other structured data elements, such as vital signs and laboratory results. We used EHR data for encounters from January 1, 2012 through February 10, 2019 from an academic health system. Diagnoses for HTN, HLD, and DM were computed for patients with at least two observations above threshold separated by at least 30 days, where the thresholds were outpatient blood pressure of ≥ 140/90 mmHg, any low-density lipoprotein ≥ 130 mg/dl, or any hemoglobin A1c ≥ 6.5%, respectively. The primary measure was the length of time between the computed diagnosis and the time at which a structured diagnosis could be identified within the EHR history or problem list. Results We found that 39.8% of those with HTN, 21.6% with HLD, and 5.2% with DM did not receive a corresponding structured diagnosis recorded in the EHR. For those who received a structured diagnosis, a mean of 389, 198, and 166 days elapsed before the patient had the corresponding diagnosis of HTN, HLD, or DM, respectively, recorded in the EHR. Conclusions We found a marked temporal delay between when a diagnosis can be computed or inferred and when an equivalent structured diagnosis is recorded within the EHR. These findings demonstrate the continued need for additional study of the EHR to avoid bias when using observational data and reinforce the need for computational approaches to identify clinical phenotypes.
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Affiliation(s)
- Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.,Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Andreas Coppi
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Bobak J Mortazavi
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.,Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA.,Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX, USA
| | - Zhenqiu Lin
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Raymond A Jean
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA.,Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Harlan M Krumholz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA. .,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA. .,Department of Health Policy and Management, Yale School of Public Health, New Haven, CT, USA.
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McPadden J, Warner F, Young HP, Hurley NC, Pulk RA, Singh A, Durant TJS, Gong G, Desai N, Haimovich A, Taylor RA, Gunel M, Cruz CSD, Farhadian SF, Siner J, Villanueva M, Churchwell K, Hsiao A, Torre CJ, Velazquez EJ, Herbst RS, Iwasaki A, Ko AI, Mortazavi BJ, Krumholz HM, Schulz WL. Clinical Characteristics and Outcomes for 7,995 Patients with SARS-CoV-2 Infection. medRxiv 2020:2020.07.19.20157305. [PMID: 32743602 PMCID: PMC7386526 DOI: 10.1101/2020.07.19.20157305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Severe acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2. DESIGN This was an observational, retrospective study based on real-world data for 7,995 patients with SARS-CoV-2 from a clinical data repository. SETTING Yale New Haven Health (YNHH) is a five-hospital academic health system serving a diverse patient population with community and teaching facilities in both urban and suburban areas. POPULATIONS The study included adult patients who had SARS-CoV-2 testing at YNHH between March 1 and April 30, 2020. MAIN OUTCOME AND PERFORMANCE MEASURES Primary outcomes were admission and in-hospital mortality for patients with SARS-CoV-2 infection as determined by RT-PCR testing. We also assessed features associated with the need for respiratory support. RESULTS Of the 28605 patients tested for SARS-CoV-2, 7995 patients (27.9%) had an infection (median age 52.3 years) and 2154 (26.9%) of these had an associated admission (median age 66.2 years). Of admitted patients, 2152 (99.9%) had a discharge disposition at the end of the study period. Of these, 329 (15.3%) required invasive mechanical ventilation and 305 (14.2%) expired. Increased age and male sex were positively associated with admission and in-hospital mortality (median age 80.7 years), while comorbidities had a much weaker association with the risk of admission or mortality. Black race (OR 1.43, 95%CI 1.14-1.78) and Hispanic ethnicity (OR 1.81, 95%CI 1.50-2.18) were identified as risk factors for admission, but, among discharged patients, age-adjusted in-hospital mortality was not significantly different among racial and ethnic groups. CONCLUSIONS This observational study identified, among people testing positive for SARSCoV-2 infection, older age and male sex as the most strongly associated risks for admission and in-hospital mortality in patients with SARS-CoV-2 infection. While minority racial and ethnic groups had increased burden of disease and risk of admission, age-adjusted in-hospital mortality for discharged patients was not significantly different among racial and ethnic groups. Ongoing studies will be needed to continue to evaluate these risks, particularly in the setting of evolving treatment guidelines.
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Affiliation(s)
- Jacob McPadden
- Department of Pediatrics, Yale School of Medicine, New Haven, CT
| | - Frederick Warner
- Department of Pediatrics, Yale School of Medicine, New Haven, CT
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - H. Patrick Young
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Nathan C. Hurley
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX
| | - Rebecca A. Pulk
- Corporate Pharmacy Services, Yale New Haven Health, New Haven, CT
| | - Avinainder Singh
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Thomas JS Durant
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Guannan Gong
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, CT
| | - Nihar Desai
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
| | | | | | - Murat Gunel
- Department of Genetics, Yale University School of Medicine, New Haven, CT
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT
| | - Charles S. Dela Cruz
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT
| | - Shelli F. Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
| | - Jonathan Siner
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT
| | - Merceditas Villanueva
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
- Center for Interdisciplinary Research on AIDS, Yale School of Public Health, New Haven, CT
| | | | - Allen Hsiao
- Department of Pediatrics, Yale School of Medicine, New Haven, CT
- Information Technology Services, Yale New Haven Health, New Haven, CT
| | - Charles J. Torre
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
- Information Technology Services, Yale New Haven Health, New Haven, CT
| | - Eric J. Velazquez
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Roy S. Herbst
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | - Bobak J. Mortazavi
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX
| | - Harlan M. Krumholz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- Department of Health Policy and Management, Yale School of Public Health, New Haven, CT
| | - Wade L. Schulz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
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Haimovich AD, Ravindra NG, Stoytchev S, Young HP, Wilson FP, van Dijk D, Schulz WL, Taylor RA. Development and Validation of the Quick COVID-19 Severity Index: A Prognostic Tool for Early Clinical Decompensation. Ann Emerg Med 2020; 76:442-453. [PMID: 33012378 PMCID: PMC7373004 DOI: 10.1016/j.annemergmed.2020.07.022] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
STUDY OBJECTIVE The goal of this study is to create a predictive, interpretable model of early hospital respiratory failure among emergency department (ED) patients admitted with coronavirus disease 2019 (COVID-19). METHODS This was an observational, retrospective, cohort study from a 9-ED health system of admitted adult patients with severe acute respiratory syndrome coronavirus 2 (COVID-19) and an oxygen requirement less than or equal to 6 L/min. We sought to predict respiratory failure within 24 hours of admission as defined by oxygen requirement of greater than 10 L/min by low-flow device, high-flow device, noninvasive or invasive ventilation, or death. Predictive models were compared with the Elixhauser Comorbidity Index, quick Sequential [Sepsis-related] Organ Failure Assessment, and the CURB-65 pneumonia severity score. RESULTS During the study period, from March 1 to April 27, 2020, 1,792 patients were admitted with COVID-19, 620 (35%) of whom had respiratory failure in the ED. Of the remaining 1,172 admitted patients, 144 (12.3%) met the composite endpoint within the first 24 hours of hospitalization. On the independent test cohort, both a novel bedside scoring system, the quick COVID-19 Severity Index (area under receiver operating characteristic curve mean 0.81 [95% confidence interval {CI} 0.73 to 0.89]), and a machine-learning model, the COVID-19 Severity Index (mean 0.76 [95% CI 0.65 to 0.86]), outperformed the Elixhauser mortality index (mean 0.61 [95% CI 0.51 to 0.70]), CURB-65 (0.50 [95% CI 0.40 to 0.60]), and quick Sequential [Sepsis-related] Organ Failure Assessment (0.59 [95% CI 0.50 to 0.68]). A low quick COVID-19 Severity Index score was associated with a less than 5% risk of respiratory decompensation in the validation cohort. CONCLUSION A significant proportion of admitted COVID-19 patients progress to respiratory failure within 24 hours of admission. These events are accurately predicted with bedside respiratory examination findings within a simple scoring system.
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Affiliation(s)
- Adrian D Haimovich
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT
| | - Neal G Ravindra
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT; Department of Computer Science, Yale University, New Haven, CT
| | - Stoytcho Stoytchev
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT
| | - H Patrick Young
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT
| | - Francis P Wilson
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT; Clinical and Translational Research Accelerator, Department of Medicine, Yale University School of Medicine, New Haven, CT
| | - David van Dijk
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT; Department of Computer Science, Yale University, New Haven, CT
| | - Wade L Schulz
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT
| | - R Andrew Taylor
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT; Center for Medical Informatics, Yale University School of Medicine, New Haven, CT.
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10
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Haimovich AD, Warner F, Young HP, Ravindra NG, Sehanobish A, Gong G, Wilson FP, van Dijk D, Schulz W, Taylor RA. Patient factors associated with SARS-CoV-2 in an admitted emergency department population. J Am Coll Emerg Physicians Open 2020; 1:569-577. [PMID: 32838371 PMCID: PMC7280703 DOI: 10.1002/emp2.12145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/08/2023] Open
Abstract
Background The SARS-CoV-2 (COVID-19) virus has wide community spread. The aim of this study was to describe patient characteristics and to identify factors associated with COVID-19 among emergency department (ED) patients under investigation for COVID-19 who were admitted to the hospital. Methods This was a retrospective observational study from 8 EDs within a 9-hospital health system. Patients with COVID-19 testing around the time of hospital admission were included. The primary outcome measure was COVID-19 test result. Patient characteristics were described and a multivariable logistic regression model was used to identify factors associated with a positive COVID-19 test. Results During the study period from March 1, 2020 to April 8, 2020, 2182 admitted patients had a test resulted for COVID-19. Of these patients, 786 (36%) had a positive test result. For COVID-19-positive patients, 63 (8.1%) died during hospitalization. COVID-19-positive patients had lower pulse oximetry (0.91 [95% confidence interval, CI], [0.88-0.94]), higher temperatures (1.36 [1.26-1.47]), and lower leukocyte counts than negative patients (0.78 [0.75-0.82]). Chronic lung disease (odds ratio [OR] 0.68, [0.52-0.90]) and histories of alcohol (0.64 [0.42-0.99]) or substance abuse (0.39 [0.25-0.62]) were less likely to be associated with a positive COVID-19 result. Conclusion We observed a high percentage of positive results among an admitted ED cohort under investigation for COVID-19. Patient factors may be useful in early differentiation of patients with COVID-19 from similarly presenting respiratory illnesses although no single factor will serve this purpose.
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Affiliation(s)
- Adrian D. Haimovich
- Department of Emergency MedicineYale University School of MedicineNew HavenConnecticutUSA
| | - Frederick Warner
- Center for Outcomes Research and EvaluationYale New Haven HospitalNew HavenConnecticutUSA
| | - H. Patrick Young
- Center for Outcomes Research and EvaluationYale New Haven HospitalNew HavenConnecticutUSA
- Department of Internal MedicineYale University School of MedicineNew HavenConnecticutUSA
| | - Neal G. Ravindra
- Department of Internal MedicineSection of Cardiovascular MedicineYale University School of MedicineNew HavenConnecticutUSA
- Department of Computer ScienceYale UniversityNew HavenConnecticutUSA
| | - Arijit Sehanobish
- Department of Internal MedicineSection of Cardiovascular MedicineYale University School of MedicineNew HavenConnecticutUSA
- Department of Computer ScienceYale UniversityNew HavenConnecticutUSA
| | - Guannan Gong
- Interdepartmental Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
| | - Francis Perry Wilson
- Clinical and Translational Research AcceleratorDepartment of MedicineYale University School of MedicineNew HavenConnecticutUSA
| | - David van Dijk
- Department of Internal MedicineSection of Cardiovascular MedicineYale University School of MedicineNew HavenConnecticutUSA
- Department of Computer ScienceYale UniversityNew HavenConnecticutUSA
| | - Wade Schulz
- Center for Outcomes Research and EvaluationYale New Haven HospitalNew HavenConnecticutUSA
- Center for Medical InformaticsYale University School of MedicineNew HavenConnecticutUSA
- Department of Laboratory MedicineYale University School of MedicineNew HavenConnecticutUSA
| | - Richard Andrew Taylor
- Department of Emergency MedicineYale University School of MedicineNew HavenConnecticutUSA
- Center for Medical InformaticsYale University School of MedicineNew HavenConnecticutUSA
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11
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Abstract
Several results concerning the problem of U.S. Congressional apportionment are given which, together, indicate that a method first proposed by Daniel Webster (also known as the "Major Fractions" method) seems fairest when judged on the basis of criteria suggested by common sense and precedent.
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Affiliation(s)
- M L Balinski
- School of Organization and Management, Yale University, Box 1A, New Haven, Connecticut 06520
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12
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Abstract
The problem of Congressional apportionment is explained together with a brief history of the methods used or considered for its solution. Reasons are given for rejecting the presently used method of equal proportions and for accepting a new method, the quota method, which is the unique method satisfying three essential axioms.
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Affiliation(s)
- M L Balinski
- Ph.D. Program in Mathematics, Graduate School and University Center, The City University of New York, 33 West 42 Street, New York, N.Y. 10036
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13
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Abstract
A foundational assumption in economics is that people are rational: they choose optimal plans of action given their predictions about future states of the world. In games of strategy this means that each player's strategy should be optimal given his or her prediction of the opponents' strategies. We demonstrate that there is an inherent tension between rationality and prediction when players are uncertain about their opponents' payoff functions. Specifically, there are games in which it is impossible for perfectly rational players to learn to predict the future behavior of their opponents (even approximately) no matter what learning rule they use. The reason is that in trying to predict the next-period behavior of an opponent, a rational player must take an action this period that the opponent can observe. This observation may cause the opponent to alter his next-period behavior, thus invalidating the first player's prediction. The resulting feedback loop has the property that, a positive fraction of the time, the predicted probability of some action next period differs substantially from the actual probability with which the action is going to occur. We conclude that there are strategic situations in which it is impossible in principle for perfectly rational agents to learn to predict the future behavior of other perfectly rational agents based solely on their observed actions.
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Affiliation(s)
- D P Foster
- Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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Young HP, Bachmann JA, Schal C. Food intake in blattella germanica (L.) nymphs affects hydrocarbon synthesis and its allocation in adults between epicuticle and reproduction. Arch Insect Biochem Physiol 1999; 41:214-224. [PMID: 10421895 DOI: 10.1002/(sici)1520-6327(1999)41:4<214::aid-arch5>3.0.co;2-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The causal relationship between food intake and hydrocarbon synthesis was examined in vivo and in vitro. Fed Blattella germanica (L.) nymphs synthesized hydrocarbons in a stage-specific manner, with high rates occurring in the first 6 days of a 13-day last stadium, in relation to feeding. A similar pattern was exhibited in vitro by sternites and tergites from fed nymphs. In contrast, starved nymphs synthesized hydrocarbons at normal rates for the first 2 days, but then synthesis declined and ceased by day 6. Their abdominal sternites and tergites displayed a similar biosynthetic pattern in vitro, showing that starved tissues lost the capacity to synthesize hydrocarbons, even when provided appropriate nutrients. Synthesis resumed within 2 days of being fed on day 6, reaching a maximum rate 6 days later. Some hydrocarbon appeared on the nymphal cuticle, but almost 4-fold more hydrocarbon was internal in hemolymph lipophorin, fat body, and the developing imaginal cuticle. Because most hydrocarbon synthesized in nymphs provisions the adult, and synthesis is related to food intake, we examined trade-offs in allocations in food-limited insects. Nymphs provided with insufficient quantities of food allocated normal amounts of hydrocarbons to the nymphal epicuticle, but molted into smaller adults with significantly less internal hydrocarbons. These cockroaches directed nearly normal amounts of hydrocarbons to their epicuticle, oocytes, and oothecae, at the cost of internal hydrocarbon reserves for repair and subsequent gonotrophic cycles. Hydrocarbons, thus, appear to serve an important cross-stadial resource and the object of competition among several nymphal and adult tissues. Arch. Copyright 1999 Wiley-Liss, Inc.
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Affiliation(s)
- HP Young
- Department of Entomology, North Carolina State University, Raleigh
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15
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Abstract
Synaptosomes incorporated mixed brain gangliosides at a rapid initial rate followed by a slower phase of net movement from the protein-associated fraction into the membrane core. The pattern of incorporated gangliosides reflected the pattern available for incorporation. Intact synaptosomes incorporated approximately 100 pmol GM1/mg protein. Synaptosomes preincubated with proteolytic enzymes (trypsin, chymotrypsin, and papain) at different pH values (6.2, 7.4, 7.8) incorporated more exogenous gangliosides than synaptosomes preincubated in buffer alone. This effect was maximal at pH 7.8, though analysis of variance revealed that the proteolytic treatment and pH effects were probably independent processes. Overall uptake of exogenous gangliosides correlated significantly with amount of membrane protein loss, indicating that initial access of exogenous gangliosides to synaptosomal membranes is retarded by cell-surface proteins. These results suggest synaptosomes as a useful alternative to cultured cells for investigating the interaction of gangliosides with other cell surface constituents.
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Affiliation(s)
- H P Young
- Department of Biological Sciences, University of Texas at El Paso 79968, USA
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16
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Lucius R, Young HP, Tidow S, Sievers J. Growth stimulation and chemotropic attraction of rat retinal ganglion cell axons in vitro by co-cultured optic nerves, astrocytes and astrocyte conditioned medium. Int J Dev Neurosci 1996; 14:387-98. [PMID: 8884372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The effects of explants of optic nerves of different ontogenetic ages (P0 P14, adult), and of cultured astrocytes of various ages on the neurite regeneration of rat retinal ganglion cells (RGC) were assessed in vitro, using a three-dimensional culture system which allows the co-cultivation of various explants. Both co-cultured P0-P12 optic nerves and astrocyte cultures from P2 cerebral cortex stimulated the regeneration of neurites from the retinal explants after 3 days in culture. By contrast, P14 and older explants of the optic nerve, astrocytes from P17 optic nerve and astrocytes that had previously been grown in culture for more than 6 weeks had no effect on RGC neurite outgrowth. Moreover, both the P0-P12 optic nerve explants and the astrocytes from P2 cerebral cortex also seemed to have a chemotropic effect on the regenerating neurites, because the latter were longer on the side facing the co-explantat. The absence of a cellular bridge between retinal and optic nerve explants suggests that the effects are mediated by astroglia-derived diffusible neurite growth promoting factors. Accordingly, astrocyte-conditioned medium from P2 astrocytes also stimulated the outgrowth of neurites from the retinal explants. These findings show that immature astrocytes of a limited ontogenetic period release as yet unknown diffusible neurite growth-promoting factors which stimulate the regeneration of neurites from retinal explants.
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Affiliation(s)
- R Lucius
- Anatomisches Institut, Universität Kiel, Germany
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Young HP. Equitable selection of kidney recipients. JAMA 1989; 261:2957-8. [PMID: 2654425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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