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Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J, Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ. Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection. Nat Immunol 2023; 24:1711-1724. [PMID: 37735592 DOI: 10.1038/s41590-023-01613-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific cluster of differentiation (CD)4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production and primary responses to nonspike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.
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Affiliation(s)
- Mark M Painter
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Timothy S Johnston
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jefferson J S Santos
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Juliana S Qin
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Bria Fulmer
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Justine C Williams
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michelle L McKeague
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ahmad Goode
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sean Nasta
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ashwin N Skelly
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura E Felley
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Joellen Weaver
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sherea Long
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Macy Kee
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Cynthia Clendenin
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn Medicine Biobank, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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Painter MM, Johnston TS, Lundgreen KA, Santos JJS, Qin JS, Goel RR, Apostolidis SA, Mathew D, Fulmer B, Williams JC, McKeague ML, Pattekar A, Goode A, Nasta S, Baxter AE, Giles JR, Skelly AN, Felley LE, McLaughlin M, Weaver J, Kuthuru O, Dougherty J, Adamski S, Long S, Kee M, Clendenin C, da Silva Antunes R, Grifoni A, Weiskopf D, Sette A, Huang AC, Rader DJ, Hensley SE, Bates P, Greenplate AR, Wherry EJ. Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies. bioRxiv 2023:2023.02.05.527215. [PMID: 36798171 PMCID: PMC9934532 DOI: 10.1101/2023.02.05.527215] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened Spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific CD4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production, and primary responses to non-Spike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.
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Affiliation(s)
- Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Timothy S Johnston
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jefferson J S Santos
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Juliana S Qin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Bria Fulmer
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Justine C Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Michelle L McKeague
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ajinkya Pattekar
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ahmad Goode
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sean Nasta
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ashwin N Skelly
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laura E Felley
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maura McLaughlin
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Joellen Weaver
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oliva Kuthuru
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Jeanette Dougherty
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sharon Adamski
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Sherea Long
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Macy Kee
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Cynthia Clendenin
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander C Huang
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA, USA
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