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Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline. bioRxiv 2024:2024.04.12.589250. [PMID: 38645206 PMCID: PMC11030322 DOI: 10.1101/2024.04.12.589250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
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Affiliation(s)
- Dan Lu
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Victoria T. Chu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Nina Bernick
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Kirsty Ewing
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | - Erin Hoops
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ann E. Jones
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ryan Lim
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | | | | | | | - Peter M. Mourani
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s, Little Rock, AR, USA
| | - Amy J. Pickering
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- University of California, Berkeley, Berkeley, CA, USA
| | - Amogelang R. Raphenya
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Brian P. Alcock
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Charles R. Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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2
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Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023; 620:128-136. [PMID: 37468623 PMCID: PMC10396966 DOI: 10.1038/s41586-023-06331-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [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: 10/10/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lawton D Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Noah D Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karoline Guthrie
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Victoria W Murray
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gurjot S Gill
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Colin T Maguire
- Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Cynthia A Vierra-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | - Michael J Dewar-Oldis
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sulggi Lee
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gregory M Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey E Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Division of General Internal Medicine, University of California, San Francisco, CA, USA
| | - Martin Maiers
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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3
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Augusto DG, Yusufali T, Sabatino JJ, Peyser ND, Murdolo LD, Butcher X, Murray V, Pae V, Sarvadhavabhatla S, Beltran F, Gill G, Lynch K, Yun C, Maguire C, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Viera-Green CA, Spellman SR, Langton DJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Gras S, Maiers M, Hollenbach JA. A common allele of HLA mediates asymptomatic SARS-CoV-2 infection. medRxiv 2022:2021.05.13.21257065. [PMID: 34031661 PMCID: PMC8142661 DOI: 10.1101/2021.05.13.21257065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/24/2022]
Abstract
Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph J. Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Noah D. Peyser
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lawton D. Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victoria Murray
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gurjot Gill
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kara Lynch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Colin Maguire
- University of Utah, Clinical and Translational Science Institute, Salt Lake City, UT
| | - Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A. Goldberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Cynthia A. Viera-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - David J. Langton
- ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK
| | - Sulggi Lee
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gregory M. Marcus
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey E. Olgin
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Pletcher
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
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4
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Eastman JA, Kaup AR, Bahorik AL, Butcher X, Attarha M, Marcus GM, Pletcher MJ, Olgin JE, Barnes DE, Yaffe K. Remote Assessment of Cardiovascular Risk Factors and Cognition in Middle-Aged and Older Adults: Proof-of-Concept Study. JMIR Form Res 2022; 6:e30410. [PMID: 35107430 PMCID: PMC8851369 DOI: 10.2196/30410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
Background Adults with cardiovascular disease risk factors (CVRFs) are also at increased risk of developing cognitive decline and dementia. However, it is often difficult to study the relationships between CVRFs and cognitive function because cognitive assessment typically requires time-consuming in-person neuropsychological evaluations that may not be feasible for real-world situations. Objective We conducted a proof-of-concept study to determine if the association between CVRFs and cognitive function could be detected using web-based, self-administered cognitive tasks and CVRF assessment. Methods We recruited 239 participants aged ≥50 years (mean age 62.7 years, SD 8.8; 42.7% [n=102] female, 88.7% [n=212] White) who were enrolled in the Health eHeart Study, a web-based platform focused on cardiac disease. The participants self-reported CVRFs (hypertension, high cholesterol, diabetes, and atrial fibrillation) using web-based health surveys between August 2016 and July 2018. After an average of 3 years of follow-up, we remotely evaluated episodic memory, working memory, and executive function via the web-based Posit Science platform, BrainHQ. Raw data were normalized and averaged into 3 domain scores. We used linear regression models to examine the association between CVRFs and cognitive function. Results CVRF prevalence was 62.8% (n=150) for high cholesterol, 45.2% (n=108) for hypertension, 10.9% (n=26) for atrial fibrillation, and 7.5% (n=18) for diabetes. In multivariable models, atrial fibrillation was associated with worse working memory (β=-.51, 95% CI -0.91 to -0.11) and worse episodic memory (β=-.31, 95% CI -0.59 to -0.04); hypertension was associated with worse episodic memory (β=-.27, 95% CI -0.44 to -0.11). Diabetes and high cholesterol were not associated with cognitive performance. Conclusions Self-administered web-based tools can be used to detect both CVRFs and cognitive health. We observed that atrial fibrillation and hypertension were associated with worse cognitive function even in those in their 60s and 70s. The potential of mobile assessments to detect risk factors for cognitive aging merits further investigation.
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Affiliation(s)
- Jennifer A Eastman
- San Francisco VA Medical Center, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, United States
| | - Allison R Kaup
- San Francisco VA Medical Center, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, United States.,The Neurology Center of Southern California, Carlsbad, CA, United States
| | - Amber L Bahorik
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, United States
| | - Xochitl Butcher
- Department of Medicine, University of California, San Francisco, CA, United States
| | - Mouna Attarha
- Posit Science Corporation, San Francisco, CA, United States
| | - Gregory M Marcus
- Department of Medicine, University of California, San Francisco, CA, United States
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States
| | - Jeffrey E Olgin
- Department of Medicine, University of California, San Francisco, CA, United States
| | - Deborah E Barnes
- San Francisco VA Medical Center, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States
| | - Kristine Yaffe
- San Francisco VA Medical Center, San Francisco, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, CA, United States
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5
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Dewland TA, Whitman IR, Win S, Sanchez JM, Olgin JE, Pletcher MJ, Santhosh L, Kumar U, Joyce S, Yang V, Hwang J, Ogomori K, Peyser N, Horner C, Wen D, Butcher X, Marcus GM. Prospective arrhythmia surveillance after a COVID-19 diagnosis. Open Heart 2022; 9:openhrt-2021-001758. [PMID: 35058344 PMCID: PMC8783964 DOI: 10.1136/openhrt-2021-001758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/31/2021] [Indexed: 01/19/2023] Open
Abstract
Background Cardiac arrhythmias have been observed among patients hospitalised with acute COVID-19 infection, and palpitations remain a common symptom among the much larger outpatient population of COVID-19 survivors in the convalescent stage of the disease. Objective To determine arrhythmia prevalence among outpatients after a COVID-19 diagnosis. Methods Adults with a positive COVID-19 test and without a history of arrhythmia were prospectively evaluated with 14-day ambulatory electrocardiographic monitoring. Participants were instructed to trigger the monitor for palpitations. Results A total of 51 individuals (mean age 42±11 years, 65% women) underwent monitoring at a median 75 (IQR 34–126) days after a positive COVID-19 test. Median monitoring duration was 13.2 (IQR 10.5–13.8) days. No participant demonstrated atrial fibrillation, atrial flutter, sustained supraventricular tachycardia (SVT), sustained ventricular tachycardia or infranodal atrioventricular block. Nearly all participants (96%) had an ectopic burden of <1%; one participant had a 2.8% supraventricular ectopic burden and one had a 15.4% ventricular ectopic burden. While 47 (92%) participants triggered their monitor for palpitation symptoms, 78% of these triggers were for either sinus rhythm or sinus tachycardia. Conclusions We did not find evidence of malignant or sustained arrhythmias in outpatients after a positive COVID-19 diagnosis. While palpitations were common, symptoms frequently corresponded to sinus rhythm/sinus tachycardia or non-malignant arrhythmias such as isolated ectopy or non-sustained SVT. While these findings cannot exclude the possibility of serious arrhythmias in select individuals, they do not support a strong or widespread proarrhythmic effect of COVID-19 infection after resolution of acute illness.
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Affiliation(s)
- Thomas A Dewland
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Isaac R Whitman
- Department of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Sithu Win
- Department of Medicine, ZSFGH, San Francisco, California, USA
| | - Jose M Sanchez
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - Jeffrey E Olgin
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | | | - Uday Kumar
- Element Science, Inc, San Francisco, California, USA
| | - Sean Joyce
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Vivian Yang
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Janet Hwang
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Kelsey Ogomori
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Noah Peyser
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Cathy Horner
- Department of Medicine, UCSF, San Francisco, California, USA
| | - David Wen
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Xochitl Butcher
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Gregory M Marcus
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
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6
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Marcus GM, Modrow MF, Schmid CH, Sigona K, Nah G, Yang J, Chu TC, Joyce S, Gettabecha S, Ogomori K, Yang V, Butcher X, Hills MT, McCall D, Sciarappa K, Sim I, Pletcher MJ, Olgin JE. Individualized Studies of Triggers of Paroxysmal Atrial Fibrillation: The I-STOP-AFib Randomized Clinical Trial. JAMA Cardiol 2021; 7:167-174. [PMID: 34775507 DOI: 10.1001/jamacardio.2021.5010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Importance Atrial fibrillation (AF) is the most common arrhythmia. Although patients have reported that various exposures determine when and if an AF event will occur, a prospective evaluation of patient-selected triggers has not been conducted, and the utility of characterizing presumed AF-related triggers for individual patients remains unknown. Objective To test the hypothesis that n-of-1 trials of self-selected AF triggers would enhance AF-related quality of life. Design, Setting, and Participants A randomized clinical trial lasting a minimum of 10 weeks tested a smartphone mobile application used by symptomatic patients with paroxysmal AF who owned a smartphone and were interested in testing a presumed AF trigger. Participants were screened between December 22, 2018, and March 29, 2020. Interventions n-of-1 Participants received instructions to expose or avoid self-selected triggers in random 1-week blocks for 6 weeks, and the probability their trigger influenced AF risk was then communicated. Controls monitored their AF over the same time period. Main Outcomes and Measures AF was assessed daily by self-report and using a smartphone-based electrocardiogram recording device. The primary outcome comparing n-of-1 and control groups was the Atrial Fibrillation Effect on Quality-of-Life (AFEQT) score at 10 weeks. All participants could subsequently opt for additional trigger testing. Results Of 446 participants who initiated (mean [SD] age, 58 [14] years; 289 men [58%]; 461 White [92%]), 320 (72%) completed all study activities. Self-selected triggers included caffeine (n = 53), alcohol (n = 43), reduced sleep (n = 31), exercise (n = 30), lying on left side (n = 17), dehydration (n = 10), large meals (n = 7), cold food or drink (n = 5), specific diets (n = 6), and other customized triggers (n = 4). No significant differences in AFEQT scores were observed between the n-of-1 vs AF monitoring-only groups. In the 4-week postintervention follow-up period, significantly fewer daily AF episodes were reported after trigger testing compared with controls over the same time period (adjusted relative risk, 0.60; 95% CI, 0.43- 0.83; P < .001). In a meta-analysis of the individualized trials, only exposure to alcohol was associated with significantly heightened risks of AF events. Conclusions and Relevance n-of-1 Testing of AF triggers did not improve AF-associated quality of life but was associated with a reduction in AF events. Acute exposure to alcohol increased AF risk, with no evidence that other exposures, including caffeine, more commonly triggered AF. Trial Registration ClinicalTrials.gov Identifier: NCT03323099.
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Affiliation(s)
- Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Madelaine Faulkner Modrow
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco
| | - Christopher H Schmid
- Department of Biostatistics, Center for Statistical Sciences and Center for Evidence Synthesis in Health, School of Public Health, Brown University, Providence, Rhode Island
| | - Kathi Sigona
- Health eHeart Alliance member and atrial fibrillation patient
| | - Gregory Nah
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Jiabei Yang
- Department of Biostatistics, Center for Statistical Sciences and Center for Evidence Synthesis in Health, School of Public Health, Brown University, Providence, Rhode Island
| | - Tzu-Chun Chu
- Department of Biostatistics, Center for Statistical Sciences and Center for Evidence Synthesis in Health, School of Public Health, Brown University, Providence, Rhode Island
| | - Sean Joyce
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Shiffen Gettabecha
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco
| | - Kelsey Ogomori
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Vivian Yang
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Xochitl Butcher
- Division of Cardiology, University of California, San Francisco, San Francisco
| | - Mellanie True Hills
- Health eHeart Alliance member and atrial fibrillation patient.,StopAfib.org, American Foundation for Women's Health, Greenwood, Texas
| | - Debbe McCall
- Health eHeart Alliance member and atrial fibrillation patient
| | | | - Ida Sim
- Division of General Internal Medicine, University of California, San Francisco, San Francisco
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco
| | - Jeffrey E Olgin
- Division of Cardiology, University of California, San Francisco, San Francisco
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Lin A, Vittinghoff E, Olgin J, Peyser N, Aung S, Joyce S, Yang V, Hwang J, Avram R, Nah G, Tison GH, Beatty A, Runge R, Wen D, Butcher X, Horner C, Eitel H, Pletcher M, Marcus GM. Predictors of incident SARS-CoV-2 infections in an international prospective cohort study. BMJ Open 2021; 11:e052025. [PMID: 34548363 PMCID: PMC8457993 DOI: 10.1136/bmjopen-2021-052025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Until effective treatments and vaccines are made readily and widely available, preventative behavioural health measures will be central to the SARS-CoV-2 public health response. While current recommendations are grounded in general infectious disease prevention practices, it is still not entirely understood which particular behaviours or exposures meaningfully affect one's own risk of incident SARS-CoV-2 infection. Our objective is to identify individual-level factors associated with one's personal risk of contracting SARS-CoV-2. DESIGN Prospective cohort study of adult participants from 26 March 2020 to 8 October 2020. SETTING The COVID-19 Citizen Science Study, an international, community and mobile-based study collecting daily, weekly and monthly surveys in a prospective and time-updated manner. PARTICIPANTS All adult participants over the age of 18 years were eligible for enrolment. PRIMARY OUTCOME MEASURE The primary outcome was incident SARS-CoV-2 infection confirmed via PCR or antigen testing. RESULTS 28 575 unique participants contributed 2 479 149 participant-days of data across 99 different countries. Of these participants without a history of SARS-CoV-2 infection at the time of enrolment, 112 developed an incident infection. Pooled logistic regression models showed that increased age was associated with lower risk (OR 0.98 per year, 95% CI 0.97 to 1.00, p=0.019), whereas increased number of non-household contacts (OR 1.10 per 10 contacts, 95% CI 1.01 to 1.20, p=0.024), attending events of at least 10 people (OR 1.26 per 10 events, 95% CI 1.07 to 1.50, p=0.007) and restaurant visits (OR 1.95 per 10 visits, 95% CI 1.42 to 2.68, p<0.001) were associated with significantly higher risk of incident SARS-CoV-2 infection. CONCLUSIONS Our study identified three modifiable health behaviours, namely the number of non-household contacts, attending large gatherings and restaurant visits, which may meaningfully influence individual-level risk of contracting SARS-CoV-2.
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Affiliation(s)
- Anthony Lin
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Eric Vittinghoff
- Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey Olgin
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Noah Peyser
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sidney Aung
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sean Joyce
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Vivian Yang
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Janet Hwang
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Robert Avram
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Gregory Nah
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Geoffrey H Tison
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Alexis Beatty
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Ryan Runge
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - David Wen
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Xochitl Butcher
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Cathy Horner
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Helena Eitel
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Mark Pletcher
- Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Gregory M Marcus
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
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Marcus GM, Olgin JE, Peyser ND, Vittinghoff E, Yang V, Joyce S, Avram R, Tison GH, Wen D, Butcher X, Eitel H, Pletcher MJ. Predictors of incident viral symptoms ascertained in the era of COVID-19. PLoS One 2021; 16:e0253120. [PMID: 34138915 PMCID: PMC8211176 DOI: 10.1371/journal.pone.0253120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/04/2020] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
Background In the absence of universal testing, effective therapies, or vaccines, identifying risk factors for viral infection, particularly readily modifiable exposures and behaviors, is required to identify effective strategies against viral infection and transmission. Methods We conducted a world-wide mobile application-based prospective cohort study available to English speaking adults with a smartphone. We collected self-reported characteristics, exposures, and behaviors, as well as smartphone-based geolocation data. Our main outcome was incident symptoms of viral infection, defined as fevers and chills plus one other symptom previously shown to occur with SARS-CoV-2 infection, determined by daily surveys. Findings Among 14, 335 participants residing in all 50 US states and 93 different countries followed for a median 21 days (IQR 10–26 days), 424 (3%) developed incident viral symptoms. In pooled multivariable logistic regression models, female biological sex (odds ratio [OR] 1.75, 95% CI 1.39–2.20, p<0.001), anemia (OR 1.45, 95% CI 1.16–1.81, p = 0.001), hypertension (OR 1.35, 95% CI 1.08–1.68, p = 0.007), cigarette smoking in the last 30 days (OR 1.86, 95% CI 1.35–2.55, p<0.001), any viral symptoms among household members 6–12 days prior (OR 2.06, 95% CI 1.67–2.55, p<0.001), and the maximum number of individuals the participant interacted with within 6 feet in the past 6–12 days (OR 1.15, 95% CI 1.06–1.25, p<0.001) were each associated with a higher risk of developing viral symptoms. Conversely, a higher subjective social status (OR 0.87, 95% CI 0.83–0.93, p<0.001), at least weekly exercise (OR 0.57, 95% CI 0.47–0.70, p<0.001), and sanitizing one’s phone (OR 0.79, 95% CI 0.63–0.99, p = 0.037) were each associated with a lower risk of developing viral symptoms. Interpretation While several immutable characteristics were associated with the risk of developing viral symptoms, multiple immediately modifiable exposures and habits that influence risk were also observed, potentially identifying readily accessible strategies to mitigate risk in the COVID-19 era.
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Affiliation(s)
- Gregory M. Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
| | - Jeffrey E. Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Noah D. Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Eric Vittinghoff
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Vivian Yang
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Sean Joyce
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Robert Avram
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Geoffrey H. Tison
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - David Wen
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Helena Eitel
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark J. Pletcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, California, United States of America
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Yaffe K, Kaup AR, Bahorik AL, Butcher X, Attarha M, Marcus GM, Pletcher MJ, Olgin JE. Web‐based assessment of cardiovascular risk factors and cognition in older adults: Findings from the Brain eHealth feasibility study. Alzheimers Dement 2020. [DOI: 10.1002/alz.041212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Yaffe
- Department of Neurology University of California, San Francisco San Francisco CA USA
- San Francisco VA Health Care System San Francisco CA USA
- Department of Epidemiology & Biostatistics University of California San Francisco San Francisco CA USA
- Department of Psychiatry University of California San Francisco San Francisco CA USA
| | - Allison R Kaup
- University of California San Francisco San Francisco CA USA
- The Neurology Center of Southern California San Diego CA USA
| | | | | | | | - Gregory M Marcus
- Department of Epidemiology & Biostatistics University of California San Francisco San Francisco CA USA
- Department of Medicine University of California, San Francisco San Francisco CA USA
| | - Mark J Pletcher
- Department of Epidemiology & Biostatistics University of California San Francisco San Francisco CA USA
- Department of Medicine University of California, San Francisco San Francisco CA USA
| | - Jeffrey E Olgin
- Department of Epidemiology & Biostatistics University of California San Francisco San Francisco CA USA
- Department of Medicine University of California, San Francisco San Francisco CA USA
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