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Biering SB, Gomes de Sousa FT, Tjang LV, Pahmeier F, Zhu C, Ruan R, Blanc SF, Patel TS, Worthington CM, Glasner DR, Castillo-Rojas B, Servellita V, Lo NTN, Wong MP, Warnes CM, Sandoval DR, Clausen TM, Santos YA, Fox DM, Ortega V, Näär AM, Baric RS, Stanley SA, Aguilar HC, Esko JD, Chiu CY, Pak JE, Beatty PR, Harris E. SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling. Nat Commun 2022; 13:7630. [PMID: 36494335 PMCID: PMC9734751 DOI: 10.1038/s41467-022-34910-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of vascular leak are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to induce barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-β signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-β signaling axis are required for S-mediated barrier dysfunction. Notably, we show that SARS-CoV-2 infection caused leak in vivo, which was reduced by inhibiting integrins. Our findings offer mechanistic insight into SARS-CoV-2-triggered vascular leak, providing a starting point for development of therapies targeting COVID-19.
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Affiliation(s)
- Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
| | | | - Laurentia V Tjang
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Felix Pahmeier
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Chi Zhu
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Richard Ruan
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sophie F Blanc
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Trishna S Patel
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Bryan Castillo-Rojas
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Nicholas T N Lo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Marcus P Wong
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Colin M Warnes
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel R Sandoval
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Mandel Clausen
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Douglas M Fox
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Victoria Ortega
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Anders M Näär
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Charles Y Chiu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - P Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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Fields AT, Lee MC, Mayer F, Santos YA, Bainton CM, Matthay ZA, Callcut RA, Mayer N, Cuschieri J, Kober KM, Bainton RJ, Kornblith LZ. A new trauma frontier: Exploratory pilot study of platelet transcriptomics in trauma patients. J Trauma Acute Care Surg 2022; 92:313-322. [PMID: 34738997 PMCID: PMC8781218 DOI: 10.1097/ta.0000000000003450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The earliest measurable changes to postinjury platelet biology may be in the platelet transcriptome, as platelets are known to carry messenger ribonucleic acids (RNAs), and there is evidence in other inflammatory and infectious disease states of differential and alternative platelet RNA splicing in response to changing physiology. Thus, the aim of this exploratory pilot study was to examine the platelet transcriptome and platelet RNA splicing signatures in trauma patients compared with healthy donors. METHODS Preresuscitation platelets purified from trauma patients (n = 9) and healthy donors (n = 5) were assayed using deep RNA sequencing. Differential gene expression analysis, weighted gene coexpression network analysis, and differential alternative splicing analyses were performed. In parallel samples, platelet function was measured with platelet aggregometry, and clot formation was measured with thromboelastography. RESULTS Differential gene expression analysis identified 49 platelet RNAs to have differing abundance between trauma patients and healthy donors. Weighted gene coexpression network analysis identified coexpressed platelet RNAs that correlated with platelet aggregation. Differential alternative splicing analyses revealed 1,188 splicing events across 462 platelet RNAs that were highly statistically significant (false discovery rate <0.001) in trauma patients compared with healthy donors. Unsupervised principal component analysis of these platelet RNA splicing signatures segregated trauma patients in two main clusters separate from healthy controls. CONCLUSION Our findings provide evidence of finetuning of the platelet transcriptome through differential alternative splicing of platelet RNA in trauma patients and that this finetuning may have relevance to downstream platelet signaling. Additional investigations of the trauma platelet transcriptome should be pursued to improve our understanding of the platelet functional responses to trauma on a molecular level.
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3
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Biering SB, de Sousa FTG, Tjang LV, Pahmeier F, Ruan R, Blanc SF, Patel TS, Worthington CM, Glasner DR, Castillo-Rojas B, Servellita V, Lo NT, Wong MP, Warnes CM, Sandoval DR, Clausen TM, Santos YA, Ortega V, Aguilar HC, Esko JD, Chui CY, Pak JE, Beatty PR, Harris E. SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling. bioRxiv 2021:2021.12.10.472112. [PMID: 34931188 PMCID: PMC8687463 DOI: 10.1101/2021.12.10.472112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/08/2023]
Abstract
Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of this pathology are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo , independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-β signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-β signaling axis are required for S-mediated barrier dysfunction. Our findings suggest that S interactions with barrier cells are a contributing factor to COVID-19 disease severity and offer mechanistic insight into SARS-CoV-2 triggered vascular leak, providing a starting point for development of therapies targeting COVID-19 pathogenesis.
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Affiliation(s)
- Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | - Laurentia V. Tjang
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Felix Pahmeier
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Richard Ruan
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sophie F. Blanc
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Trishna S. Patel
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | - Dustin R. Glasner
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Bryan Castillo-Rojas
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Nicholas T.N. Lo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Marcus P. Wong
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Colin M. Warnes
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel R. Sandoval
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Mandel Clausen
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Yale A. Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Victoria Ortega
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Charles Y. Chui
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - P. Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Lead contact
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4
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Esteves FAM, Silva TM, Ramos TMB, Silva AM, Santos YA, Santos MMBD, Tenório GB, Almeida MIM. OTIMIZAÇÃO DO PROCESSO DE TRABALHO PARA REALIZAÇÃO DO EXAME DE HEMOGLOBINA GLICADA: UM ESTUDO DE EQUIVALÊNCIA DE SISTEMAS ANALÍTICOS UTILIZANDO A METODOLOGIA DE HPLC POR TROCA IÔNICA E DE AFINIDADE PELO BORONATO NO LABORATÓRIO PÚBLICO DA CIDADE DO RECIFE. Hematol Transfus Cell Ther 2021. [DOI: 10.1016/j.htct.2021.10.736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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5
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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6
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Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CSS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv 2021; 7:eabe5984. [PMID: 33536218 PMCID: PMC7857687 DOI: 10.1126/sciadv.abe5984] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
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Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Jing Cheng
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Sanchez-San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Tony Li
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ray Chan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia S Chu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chiara A Wabl
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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7
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Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood. Nat Commun 2020; 11:4698. [PMID: 32943630 PMCID: PMC7499171 DOI: 10.1038/s41467-020-18468-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [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: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Given the limited availability of serological testing to date, the seroprevalence of SARS-CoV-2-specific antibodies in different populations has remained unclear. Here, we report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seroreactivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors in early April 2020. We additionally describe the longitudinal dynamics of immunoglobulin-G (IgG), immunoglobulin-M (IgM), and in vitro neutralizing antibody titers in COVID-19 patients. The median time to seroconversion ranged from 10.3-11.0 days for these 3 assays. Neutralizing antibodies rose in tandem with immunoglobulin titers following symptom onset, and positive percent agreement between detection of IgG and neutralizing titers was >93%. These findings emphasize the importance of using highly accurate tests for surveillance studies in low-prevalence populations, and provide evidence that seroreactivity using SARS-CoV-2 anti-nucleocapsid protein IgG and anti-spike IgM assays are generally predictive of in vitro neutralizing capacity.
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Affiliation(s)
- Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandra Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K Hills
- 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
| | - Chuanyi M Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Laboratory Medicine Service, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M C Hakim
- Department of Medicine at ZSFG, The Division of HIV, ID & Global Medicine, San Francisco, CA, USA
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Thornborrow
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Michael P Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
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8
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Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim JM, Sujishi K, Alazzeh F, Pham L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area. medRxiv 2020:2020.05.19.20107482. [PMID: 32511477 PMCID: PMC7273245 DOI: 10.1101/2020.05.19.20107482] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 01/09/2023]
Abstract
We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.
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Affiliation(s)
- Dianna L. Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M. Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R. Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G. Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P. Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandy Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R. Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M. Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N. Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M. Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A. Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K. Hills
- 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
| | - Chuanyi M. Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Lab Medicine Service, San Francisco VA Healthcare System
| | - Jeffrey D. Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M.C. Hakim
- Department of Medicine at ZSFG, the Division of HIV, ID & Global Medicine
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Michael P. Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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