Browsing by Author "Butte, Atul J."

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    Real-world performance of SARS-Cov-2 serology tests in the United States, 2020
    (Public Library of Science, 2023-02-03) Rodriguez-Watson, Carla V.; Louder, Anthony M.; Kabelac, Carly; Frederick, Christopher M.; Sheils, Natalie E.; Eldridge, Elizabeth H.; Lin, Nancy D.; Pollock, Benjamin D.; Gatz, Jennifer L.; Grannis, Shaun J.; Vashisht, Rohit; Ghauri, Kanwal; Knepper, Camille; Leonard, Sandy; Embi, Peter J.; Jenkinson, Garrett; Klesh, Reyna; Garner, Omai B.; Patel, Ayan; Dahm, Lisa; Barin, Aiden; Cooper, Dan M.; Andriola, Tom; Byington, Carrie L.; Crews, Bridgit O.; Butte, Atul J.; Allen, Jeff; Medicine, School of Medicine
    Background: Real-world performance of COVID-19 diagnostic tests under Emergency Use Authorization (EUA) must be assessed. We describe overall trends in the performance of serology tests in the context of real-world implementation. Methods: Six health systems estimated the odds of seropositivity and positive percent agreement (PPA) of serology test among people with confirmed SARS-CoV-2 infection by molecular test. In each dataset, we present the odds ratio and PPA, overall and by key clinical, demographic, and practice parameters. Results: A total of 15,615 people were observed to have at least one serology test 14-90 days after a positive molecular test for SARS-CoV-2. We observed higher PPA in Hispanic (PPA range: 79-96%) compared to non-Hispanic (60-89%) patients; in those presenting with at least one COVID-19 related symptom (69-93%) as compared to no such symptoms (63-91%); and in inpatient (70-97%) and emergency department (93-99%) compared to outpatient (63-92%) settings across datasets. PPA was highest in those with diabetes (75-94%) and kidney disease (83-95%); and lowest in those with auto-immune conditions or who are immunocompromised (56-93%). The odds ratios (OR) for seropositivity were higher in Hispanics compared to non-Hispanics (OR range: 2.59-3.86), patients with diabetes (1.49-1.56), and obesity (1.63-2.23); and lower in those with immunocompromised or autoimmune conditions (0.25-0.70), as compared to those without those comorbidities. In a subset of three datasets with robust information on serology test name, seven tests were used, two of which were used in multiple settings and met the EUA requirement of PPA ≥87%. Tests performed similarly across datasets. Conclusion: Although the EUA requirement was not consistently met, more investigation is needed to understand how serology and molecular tests are used, including indication and protocol fidelity. Improved data interoperability of test and clinical/demographic data are needed to enable rapid assessment of the real-world performance of in vitro diagnostic tests.
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    Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States
    (Public Library of Science, 2023-02-10) Rodriguez-Watson, Carla V.; Sheils, Natalie E.; Louder, Anthony M.; Eldridge, Elizabeth H.; Lin, Nancy D.; Pollock, Benjamin D.; Gatz, Jennifer L.; Grannis, Shaun J.; Vashisht, Rohit; Ghauri, Kanwal; Valo, Gina; Chakravarty, Aloka G.; Lasky, Tamar; Jung, Mary; Lovell, Stephen L.; Major, Jacqueline M.; Kabelac, Carly; Knepper, Camille; Leonard, Sandy; Embi, Peter J.; Jenkinson, William G.; Klesh, Reyna; Garner, Omai B.; Patel, Ayan; Dahm, Lisa; Barin, Aiden; Cooper, Dan M.; Andriola, Tom; Byington, Carrie L.; Crews, Bridgit O.; Butte, Atul J.; Allen, Jeff; Medicine, School of Medicine
    Background: As diagnostic tests for COVID-19 were broadly deployed under Emergency Use Authorization, there emerged a need to understand the real-world utilization and performance of serological testing across the United States. Methods: Six health systems contributed electronic health records and/or claims data, jointly developed a master protocol, and used it to execute the analysis in parallel. We used descriptive statistics to examine demographic, clinical, and geographic characteristics of serology testing among patients with RNA positive for SARS-CoV-2. Results: Across datasets, we observed 930,669 individuals with positive RNA for SARS-CoV-2. Of these, 35,806 (4%) were serotested within 90 days; 15% of which occurred <14 days from the RNA positive test. The proportion of people with a history of cardiovascular disease, obesity, chronic lung, or kidney disease; or presenting with shortness of breath or pneumonia appeared higher among those serotested compared to those who were not. Even in a population of people with active infection, race/ethnicity data were largely missing (>30%) in some datasets-limiting our ability to examine differences in serological testing by race. In datasets where race/ethnicity information was available, we observed a greater distribution of White individuals among those serotested; however, the time between RNA and serology tests appeared shorter in Black compared to White individuals. Test manufacturer data was available in half of the datasets contributing to the analysis. Conclusion: Our results inform the underlying context of serotesting during the first year of the COVID-19 pandemic and differences observed between claims and EHR data sources-a critical first step to understanding the real-world accuracy of serological tests. Incomplete reporting of race/ethnicity data and a limited ability to link test manufacturer data, lab results, and clinical data challenge the ability to assess the real-world performance of SARS-CoV-2 tests in different contexts and the overall U.S. response to current and future disease pandemics.
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    Use of Electronic Health Records to Support a Public Health Response to the COVID-19 Pandemic in the United States: A Perspective from Fifteen Academic Medical Centers
    (Oxford University Press, 2020-11-03) Madhavan, Subha; Bastarache, Lisa; Brown, Jeffrey S.; Dorr, David A.; Embi, Peter J.; Friedman, Charles P.; Johnson, Kevin B.; Moore, Jason H.; Kohane, Isaac S.; Payne, Philip R.O.; Tenenbaum, Jessica D.; Weiner, Mark G.; Wilcox, Adam B.; Ohno-Machado, Lucila; Butte, Atul J.; Medicine, School of Medicine
    Our goal is to summarize the collective experience of 15 organizations in dealing with uncoordinated efforts that result in unnecessary delays in understanding, predicting, preparing for, containing, and mitigating the COVID-19 pandemic in the US. Response efforts involve the collection and analysis of data corresponding to healthcare organizations, public health departments, socioeconomic indicators, as well as additional signals collected directly from individuals and communities. We focused on electronic health record (EHR) data, since EHRs can be leveraged and scaled to improve clinical care, research, and to inform public health decision-making. We outline the current challenges in the data ecosystem and the technology infrastructure that are relevant to COVID-19, as witnessed in our 15 institutions. The infrastructure includes registries and clinical data networks to support population-level analyses. We propose a specific set of strategic next steps to increase interoperability, overall organization, and efficiencies