Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease

10.1016/j.immuni.2021.05.010

Immunity

Contributing to research themes:

Abstract

The kinetics of the immune changes in COVID-19 across severity groups have not been rigorously assessed. Using immunophenotyping, RNA sequencing and serum cytokine analysis, we analyzed serial samples from 207 SARS-CoV2-infected individuals with a range of disease severities over 12 weeks from symptom onset. An early robust bystander CD8+ T cell immune response, without systemic inflammation, characterized asymptomatic or mild disease. Hospitalized individuals had delayed bystander responses and systemic inflammation that was already evident near symptom onset, indicating that immunopathology may be inevitable in some individuals. Viral load did not correlate with this early pathological response, but did correlate with subsequent disease severity. Immune recovery is complex, with profound persistent cellular abnormalities in severe disease correlating with altered inflammatory responses, with signatures associated with increased oxidative phosphorylation replacing those driven by cytokines tumor necrosis factor (TNF) and interleukin (IL)-6. These late immunometabolic and immune defects may have clinical implications.

Author list:

Affiliations

  1. Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
  2. Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
  3. MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
  4. Cancer Research UK – Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
  5. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
  6. Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
  7. Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK 8 Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK 9 Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK 10 Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK 11 NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK 12 NHS Blood and Transplant, Cambridge, UK 13 The Australian National Phenome Centre, Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK 15 R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands
  8. Heart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
  9. Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
  10. Department of Biomedicine, University and University Hospital Basel, 4031 Basel, Switzerland
  11. Botnar Research Centre for Child Health (BRCCH) University Basel & ETH Zurich, 4058 Basel, Switzerland

 

Authors

Laura Bergamaschi1,2,20 Federica Mescia1,2,20 Lorinda Turner1,2,20 Aimee L.Hanson1,2,20 Prasanti Kotagiri1,2,20 Benjamin J. DunmoreHélène RuffieuxAloka De Sa12 Oisín HuhnMichael D. Morgan4,5 Pehuen Pereyra Gerber12 Mark R. Wills1,2 Stephen Baker1,2 Fernando J.Calero‐NietoRainer DoffingerGordon Dougan1,2 Anne ElmerIan G. GoodfellowRavindra K. Gupta1,2 Myra HosmilloKelvin Hunter1,2 Nathalie Kingston10,11 Paul J.Lehner1,2 Nicholas J. Matheson1,2,12Jeremy K. Nicholson13 Anna M. Petrunkina1,2 Sylvia RichardsonCaroline SaundersJames E.D. Thaventhiran1,2,14 Erik J.M. Toonen15 Michael P. WeekesCambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Berthold GöttgensMark Toshner2,16,17 Christoph Hess1,2,18,19 John R. Bradley2,11 Paul A. Lyons1,2 Kenneth G.C. Smith1,2,21