|
1
|
Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young KC, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2. Nat Immunol 2024; 25:218-225. [PMID: 38212464 PMCID: PMC10834368 DOI: 10.1038/s41590-023-01724-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used 'omic" assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.
Collapse
Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyrlia C Young
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - 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
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, San Francisco, CA, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, 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
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
|
2
|
Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young K, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2. bioRxiv 2023:2023.02.09.527892. [PMID: 36798286 PMCID: PMC9934605 DOI: 10.1101/2023.02.09.527892] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 02/12/2023]
Abstract
Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.
Collapse
Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Kyrlia Young
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| |
Collapse
|
|
3
|
Thaweethai T, Jolley SE, Karlson EW, Levitan EB, Levy B, McComsey GA, McCorkell L, Nadkarni GN, Parthasarathy S, Singh U, Walker TA, Selvaggi CA, Shinnick DJ, Schulte CCM, Atchley-Challenner R, Alba GA, Alicic R, Altman N, Anglin K, Argueta U, Ashktorab H, Baslet G, Bassett IV, Bateman L, Bedi B, Bhattacharyya S, Bind MA, Blomkalns AL, Bonilla H, Bush PA, Castro M, Chan J, Charney AW, Chen P, Chibnik LB, Chu HY, Clifton RG, Costantine MM, Cribbs SK, Davila Nieves SI, Deeks SG, Duven A, Emery IF, Erdmann N, Erlandson KM, Ernst KC, Farah-Abraham R, Farner CE, Feuerriegel EM, Fleurimont J, Fonseca V, Franko N, Gainer V, Gander JC, Gardner EM, Geng LN, Gibson KS, Go M, Goldman JD, Grebe H, Greenway FL, Habli M, Hafner J, Han JE, Hanson KA, Heath J, Hernandez C, Hess R, Hodder SL, Hoffman MK, Hoover SE, Huang B, Hughes BL, Jagannathan P, John J, Jordan MR, Katz SD, Kaufman ES, Kelly JD, Kelly SW, Kemp MM, Kirwan JP, Klein JD, Knox KS, Krishnan JA, Kumar A, Laiyemo AO, Lambert AA, Lanca M, Lee-Iannotti JK, Logarbo BP, Longo MT, Luciano CA, Lutrick K, Maley JH, Marathe JG, Marconi V, Marshall GD, Martin CF, Matusov Y, Mehari A, Mendez-Figueroa H, Mermelstein R, Metz TD, Morse R, Mosier J, Mouchati C, Mullington J, Murphy SN, Neuman RB, Nikolich JZ, Ofotokun I, Ojemakinde E, Palatnik A, Palomares K, Parimon T, Parry S, Patterson JE, Patterson TF, Patzer RE, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Quigley JG, Reddy U, Reece R, Reeder H, Reeves WB, Reiman EM, Rischard F, Rosand J, Rouse DJ, Ruff A, Saade G, Sandoval GJ, Schlater SM, Shepherd F, Sherif ZA, Simhan H, Singer NG, Skupski DW, Sowles A, Sparks JA, Sukhera FI, Taylor BS, Teunis L, Thomas RJ, Thorp JM, Thuluvath P, Ticotsky A, Tita AT, Tuttle KR, Urdaneta AE, Valdivieso D, VanWagoner TM, Vasey A, Verduzco-Gutierrez M, Wallace ZS, Ward HD, Warren DE, Weiner SJ, Welch S, Whiteheart SW, Wiley Z, Wisnivesky JP, Yee LM, Zisis S, Horwitz LI, Foulkes AS. Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection. JAMA 2023; 329:1934-1946. [PMID: 37278994 PMCID: PMC10214179 DOI: 10.1001/jama.2023.8823] [Citation(s) in RCA: 152] [Impact Index Per Article: 152.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/01/2023] [Indexed: 06/07/2023]
Abstract
Importance SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals. Objective To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections. Design, Setting, and Participants Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling. Exposure SARS-CoV-2 infection. Main Outcomes and Measures PASC and 44 participant-reported symptoms (with severity thresholds). Results A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years [IQR, 35-60]) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% [95% CI, 8.8%-11%]) were PASC positive at 6 months. Conclusions and Relevance A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.
Collapse
Affiliation(s)
- Tanayott Thaweethai
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| | | | | | | | - Bruce Levy
- Harvard Medical School, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Lisa McCorkell
- Patient-Led Research Collaborative, Calabasas, California
| | | | | | - Upinder Singh
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mario Castro
- University of Kansas Medical Center, Kansas City
| | | | | | - Peter Chen
- Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Helen Y Chu
- University of Washington School of Medicine, Seattle
| | | | | | | | | | | | | | | | | | | | | | | | - Cheryl E Farner
- The University of Texas Health Science Center at San Antonio
| | | | | | - Vivian Fonseca
- Tulane University Health Sciences Center, New Orleans, Louisiana
| | | | | | | | | | | | | | - Minjoung Go
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | - John Hafner
- University of Illinois Chicago College of Medicine
| | - Jenny E Han
- Emory University School of Medicine, Atlanta, Georgia
| | | | - James Heath
- Institute for Systems Biology, Seattle, Washington
| | | | - Rachel Hess
- University of Utah Schools of the Health Sciences, Salt Lake City
| | - Sally L Hodder
- West Virginia Clinical and Translational Science Institute, Morgantown
| | | | | | | | | | | | - Janice John
- Cambridge Health Alliance, Cambridge, Massachusetts
| | | | - Stuart D Katz
- New York University Grossman School of Medicine, New York
| | | | | | - Sara W Kelly
- University of Illinois College of Medicine at Peoria
| | | | - John P Kirwan
- Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | | | | | - Jerry A Krishnan
- University of Illinois Hospital and Health Sciences System, Chicago
| | - Andre Kumar
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | | | | | | | | | - Jason H Maley
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | | | | | - Yuri Matusov
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Alem Mehari
- Howard University College of Medicine, Washington, DC
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jan E Patterson
- The University of Texas Health Science Center at San Antonio
| | | | | | | | | | | | - Beth A Plunkett
- Harvard Medical School, Boston, Massachusetts
- NorthShore University HealthSystem, Evanston, Illinois
| | | | - Athena Poppas
- Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | | | - Uma Reddy
- Columbia University Irving Medical Center, New York, New York
| | - Rebecca Reece
- West Virginia University School of Medicine, Morgantown
| | | | - W B Reeves
- Department of Medicine, The University of Texas Health Science Center at San Antonio
| | | | | | | | | | - Adam Ruff
- The University of Kansas Medical Center, Kansas City
| | | | - Grecio J Sandoval
- Milken Institute of Public Health, The George Washington University, Washington, DC
| | | | | | - Zaki A Sherif
- Howard University College of Medicine, Washington, DC
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Steven J Weiner
- The George Washington University Biostatistics Center, Rockville, Maryland
| | | | | | | | | | - Lynn M Yee
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | - Andrea S Foulkes
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| |
Collapse
|