Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

doi:10.1038/s41590-020-0782-6

. 2020 Nov;21(11):1336-1345.

doi: 10.1038/s41590-020-0782-6. Epub 2020 Sep 4.

Broad and strong memory CD4⁺ and CD8⁺ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

Yanchun Peng^#^{1

2}, Alexander J Mentzer^#^{3

4

5}, Guihai Liu^#^{2

4

6}, Xuan Yao^#^{1

2

4}, Zixi Yin^#^{1

2}, Danning Dong^#^{2

4

7}, Wanwisa Dejnirattisai^#⁴, Timothy Rostron⁸, Piyada Supasa⁴, Chang Liu^{2

4}, César López-Camacho^{3

4}, Jose Slon-Campos⁴, Yuguang Zhao⁴, David I Stuart^{2

3

4

9}, Guido C Paesen³, Jonathan M Grimes^{3

4

9}, Alfred A Antson¹⁰, Oliver W Bayfield¹⁰, Dorothy E D P Hawkins¹⁰, De-Sheng Ker¹⁰, Beibei Wang^{2

4}, Lance Turtle^{11

12}, Krishanthi Subramaniam¹², Paul Thomson¹², Ping Zhang⁴, Christina Dold^{13

14}, Jeremy Ratcliff⁴, Peter Simmonds⁴, Thushan de Silva¹⁵, Paul Sopp⁸, Dannielle Wellington^{1

2}, Ushani Rajapaksa^{2

4}, Yi-Ling Chen¹, Mariolina Salio¹, Giorgio Napolitani¹, Wayne Paes⁴, Persephone Borrow⁴, Benedikt M Kessler^{2

4}, Jeremy W Fry¹⁶, Nikolai F Schwabe¹⁶, Malcolm G Semple^{12

17}, J Kenneth Baillie¹⁸, Shona C Moore¹², Peter J M Openshaw¹⁹, M Azim Ansari⁴, Susanna Dunachie^{4

5}, Eleanor Barnes^{4

5

20}, John Frater^{4

5}, Georgina Kerr⁴, Philip Goulder^{4

5}, Teresa Lockett⁵, Robert Levin²¹, Yonghong Zhang^{2

6}, Ronghua Jing⁶, Ling-Pei Ho^{1

2

4

20}; Oxford Immunology Network Covid-19 Response T cell Consortium; ISARIC4C Investigators; Richard J Cornall^{1

4

5}, Christopher P Conlon^{2

4

5}, Paul Klenerman^{4

5

20}, Gavin R Screaton^{4

5

20}, Juthathip Mongkolsapaya^{2

4

20

22}, Andrew McMichael^{2

4}, Julian C Knight^{2

3

4

5}, Graham Ogg^{1

2

5

20}, Tao Dong^{23

24

25}

Collaborators, Affiliations

Affiliations

¹ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
² Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
³ Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
⁴ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁵ Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁶ Beijing You'an Hospital, Capital Medical University, Beijing, China.
⁷ CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Xinjiang, China.
⁸ Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
⁹ Diamond Light Source, Didcot, UK.
¹⁰ York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
¹¹ Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
¹² NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
¹³ Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁴ NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK.
¹⁵ The Florey Institute for Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK.
¹⁶ ProImmune, Oxford, UK.
¹⁷ Respiratory Medicine, Institute in The Park, Alder Hey Children's Hospital, Liverpool, UK.
¹⁸ Anaesthesia, Critical Care and Pain Medicine Division of Health Sciences, University of Edinburgh, Edinburgh, UK.
¹⁹ National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK.
²⁰ NIHR Oxford Biomedical Research Centre, Oxford, UK.
²¹ Worthing Hospital, Worthing, UK.
²² Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.
²³ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.
²⁴ Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.
²⁵ Nuffield Department of Medicine, University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.

^# Contributed equally.

PMID: 32887977
PMCID: PMC7611020
DOI: 10.1038/s41590-020-0782-6

Broad and strong memory CD4⁺ and CD8⁺ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

Yanchun Peng et al. Nat Immunol. 2020 Nov.

. 2020 Nov;21(11):1336-1345.

doi: 10.1038/s41590-020-0782-6. Epub 2020 Sep 4.

Authors

Affiliations

¹ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
² Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
³ Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
⁴ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁵ Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁶ Beijing You'an Hospital, Capital Medical University, Beijing, China.
⁷ CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Xinjiang, China.
⁸ Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
⁹ Diamond Light Source, Didcot, UK.
¹⁰ York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
¹¹ Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
¹² NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
¹³ Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁴ NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK.
¹⁵ The Florey Institute for Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK.
¹⁶ ProImmune, Oxford, UK.
¹⁷ Respiratory Medicine, Institute in The Park, Alder Hey Children's Hospital, Liverpool, UK.
¹⁸ Anaesthesia, Critical Care and Pain Medicine Division of Health Sciences, University of Edinburgh, Edinburgh, UK.
¹⁹ National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK.
²⁰ NIHR Oxford Biomedical Research Centre, Oxford, UK.
²¹ Worthing Hospital, Worthing, UK.
²² Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.
²³ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.
²⁴ Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.
²⁵ Nuffield Department of Medicine, University of Oxford, Oxford, UK. tao.dong@imm.ox.ac.uk.

^# Contributed equally.

PMID: 32887977
PMCID: PMC7611020
DOI: 10.1038/s41590-020-0782-6

Abstract

The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4⁺ and/or CD8⁺ epitopes, including six immunodominant regions. Six optimized CD8⁺ epitopes were defined, with peptide-MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8⁺ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.

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Conflict of interest statement

Competing interests The authors declare no competing interests.

Figures

**Fig. 1. Memory T cell responses specific to SARS-CoV-2 virus proteins in 42 convalescent patients infected with SARS-CoV-2.**
Of the 42 patients studied, 28 had mild symptoms while 14 showed severe symptoms. PBMCs were isolated and IFN-γ production was detected by ELISpot after incubation with SARS-CoV-2 peptides. a, Magnitude of IFN-γ T cell responses for each individual. Each bar shows the total T cell responses of each individual specific to all of the SARS-CoV-2 protein peptides tested. Each colored segment represents the source protein corresponding to peptide pools eliciting IFN-γ T cell responses. b, Breadth of T cell responses for each individual. The breadth of T cell responses was calculated by the number of peptide pools in the first-dimension (n = 29) cells that responded to spot-forming units. The experiments were repeated in 35 participants where sample availability permitted. Env: envelope protein

**Fig. 2. Comparison of the magnitude and breadth of T cell responses specific to each viral protein between convalescent patients with mild symptoms and those with severe symptoms.**
PBMCs were isolated and IFN-γ production was detected by ELISpot after incubation with SARS-CoV-2 peptides. a,b, Magnitude (a) and breadth (b) of T cell responses against each viral protein between those with mild symptoms (n = 28) and those with severe symptoms (n= 14). P values were as follows: overall: P = 0.002 for magnitude; P = 0.002 for breadth; spike: P = 0.021 for magnitude; P = 0.016 for breadth; membrane: P = 0.0003 for magnitude; P = 0.033 for breadth; ORF3a: P < 0.0001 for magnitude; P = 0.001 for breadth; ORF8: P = 0.011 for magnitude; P = 0.014 for breadth. Data are presented as medians with interquartile ranges. The Mann–Whitney U-test was used for the analysis and two-tailed P values were calculated. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.001. NS, not significant.

**Fig. 3. Correlation of T cell responses against SARS-CoV-2 with spike-, RBD- and NP-specific antibody responses.**
a-c, Spike (a), RBD (b) and NP EPTs (c) in association with overall T cell responses. Red and black data points represent patients with severe and mild symptoms, respectively. n = 42. Spearman’s rank correlation coefficients (R) are shown. d, Comparison of spike EPTs (P < 0.0001), RBD EPTs (P < 0.0001) and NP EPTs (P = 0.0004) for patients with mild symptoms (n = 28) versus severe symptoms (n = 14). Data are presented as medians with interquartile ranges and a Mann-Whitney U-test was used for comparison. Two-tailed P values were calculated. ***P < 0.001; ****P < 0.0001.

**Fig. 4. Distribution of SARS-CoV-2-specific CD4⁺ and CD8⁺ memory T cell responses.**
Cytokine-producing T cells were detected by ICS after incubation with SARS-CoV-2 peptides. a,b, Flow cytometric plots representing CD4⁺ T cells (a) and CD8⁺ T cells (b) expressing IFN-γ (x axis), TNF (y axis) and/or IL-2 (y axis) upon stimulation with the respective SARS-CoV-2 peptide pools in examples of mild (left) and severe cases (right). c, Comparison of the relative proportion of SARS-CoV-2 peptide pool-reactive CD8⁺ T cells between mild (spike, n = 11; M/NP, n = 14; ORF/Env, n = 5; overall: n = 14) and severe cases (spike, n = 7; M/NP, n = 7; ORF/Env, n = 4; overall, n = 8). P values were as follows: P = 0.0268 (spike); P = 0.02 (M/NP); P = 0.0159 (overall). The SARS-CoV-2 peptide pool-reactive CD4⁺ or CD8⁺ T cells were identified with at least one of the three cytokines (IFN-γ, TNF and IL-2) detected. Data are shown as medians with interquartile ranges. The Mann-Whitney U-test was used for the analysis. Two-tailed P values were calculated. *P < 0.05.

**Fig. 5. Cytokine profile of SARS-Cov-2-specific T cells.**
The cytokine production of SARS-Cov-2-specific T cells was assessed by ICS after incubation with SARS-CoV-2 peptides. a, Pie charts representing the relative proportions of spike-, M/NP- and ORF/env-specific CD4⁺ and CD8⁺ T cells producing one (green), two (pink) or three cytokines (black) (out of IFN-γ, TNF and IL-2). b, Comparison of the frequency of multifunctional CD8⁺ T cells targeting spike and M/NP. The open circles and squares represent T cell responses in mild cases and severe cases, respectively. P values are as follows: P = 0.0037 (mild); P = 0.3823 (severe); P = 0.0231 (overall). c, Relative frequencies of CD4⁺ and CD8⁺ T cells expressing CD107a after antigen stimulation. The data shown are from 14 patients with mild symptoms and eight patients with severe symptoms. The Mann–Whitney U-test was used for the analysis. Two-tailed P values were calculated. *P < 0.05; **P < 0.01.

**Fig. 6. Defined SARS-CoV-2-specific CD8 epitopes.**
Examples of peptide–MHC class I pentamer staining ex vivo, with PBMCs (HLA-B*0702, -B*4001, -A*1101, -A*0101 and -A*0201) or with cultured cell lines (HLA-A*0301). Eleven donors were tested with positive pentamer staining.

**Fig. 7. Memory phenotype and differentiation status of SARS-CoV-2-specific CD8⁺ T cells.**
PBMCs were isolated and stained with peptide–MHC class I pentameric complexes and markers of T cell memory and differentiation. a, Representative fluorescence-activated cell sorting plots of gating for different cell subsets. b,c, Expression of memory markers (CCR7 and CD45RA) (b) and differentiation markers (CD27 and CD28) (c) on CD8⁺ pentamer⁺ T cells. n = 7 donors. Data are presented as means ± s.e.m.

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Update of

Broad and strong memory CD4 ⁺ and CD8 ⁺ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients.
Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, Lopez-Camacho C, Slon-Campos J, Zhao Y, Stuart D, Paeson G, Grimes J, Antson F, Bayfield OW, Hawkins DE, Ker DS, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler B, Fry JW, Schwabe NF, Semple MG, Baillie KJ, Moore S, Openshaw PJ, Ansari A, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Cornall RJ, Conlon C, Klenerman P, McMichael A, Screaton G, Mongkolsapaya J, Knight JC, Ogg G, Dong T. Peng Y, et al. bioRxiv [Preprint]. 2020 Jun 8:2020.06.05.134551. doi: 10.1101/2020.06.05.134551. bioRxiv. 2020. Update in: Nat Immunol. 2020 Nov;21(11):1336-1345. doi: 10.1038/s41590-020-0782-6. PMID: 32577665 Free PMC article. Updated. Preprint.

Comment in

T cells in COVID-19 - united in diversity.
Swadling L, Maini MK. Swadling L, et al. Nat Immunol. 2020 Nov;21(11):1307-1308. doi: 10.1038/s41590-020-0798-y. Nat Immunol. 2020. PMID: 32895541 No abstract available.

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References

1. Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015;1282:1–23. - PMC - PubMed
1. Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7:439–450. - PMC - PubMed
1. Xu Z, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020;8:420–422. - PMC - PubMed
1. Guan WJ, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med. 2020;382:1708–1720. - PMC - PubMed
1. Yu J, et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science. 2020;369:806–811. - PMC - PubMed

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[1] Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015;1282:1–23. - PMC - PubMed

[2] Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015;1282:1–23. - PMC - PubMed

[3] Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7:439–450. - PMC - PubMed

[4] Perlman S, Netland J. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol. 2009;7:439–450. - PMC - PubMed

[5] Xu Z, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020;8:420–422. - PMC - PubMed

[6] Xu Z, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020;8:420–422. - PMC - PubMed

[7] Guan WJ, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med. 2020;382:1708–1720. - PMC - PubMed

[8] Guan WJ, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med. 2020;382:1708–1720. - PMC - PubMed

[9] Yu J, et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science. 2020;369:806–811. - PMC - PubMed

[10] Yu J, et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science. 2020;369:806–811. - PMC - PubMed

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Broad and strong memory CD4⁺ and CD8⁺ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

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Broad and strong memory CD4⁺ and CD8⁺ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

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