Highlights
- •
Measuring immunity to SARS-CoV-2 is key for understanding COVID-19 and vaccine development
- •
Epitope pools detect CD4+ and CD8+ T cells in 100% and 70% of convalescent COVID patients
- •
T cell responses are focused not only on spike but also on M, N, and other ORFs
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T cell reactivity to SARS-CoV-2 epitopes is also detected in non-exposed individuals
Summary
Graphical Abstract
Keywords
Introduction
- Guo X.
- Guo Z.
- Duan C.
- Chen Z.
- Wang G.
- Lu Y.
- Li M.
- Lu J.
- Okba N.M.A.
- Raj V.S.
- Widjaja I.
- GeurtsvanKessel C.H.
- de Bruin E.
- Chandler F.D.
- Park W.B.
- Kim N.J.
- Farag E.A.B.A.
- Al-Hajri M.
- et al.
- Blanco-Melo D.
- Nilsson-Payant B.E.
- Liu W.-C.
- Møller R.
- Panis M.
- Sachs D.
- Albrecht R.A.
- tenOever B.R.
- Guo T.
- Fan Y.
- Chen M.
- Wu X.
- Zhang L.
- He T.
- Wang H.
- Wan J.
- Wang X.
- Lu Z.
- Giamarellos-Bourboulis E.J.
- Netea M.G.
- Rovina N.
- Akinosoglou K.
- Antoniadou A.
- Antonakos N.
- Damoraki G.
- Gkavogianni T.
- Adami M.E.
- Katsaounou P.
- et al.
Results
SARS-CoV-2 Peptides and Predicted Class I and Class II Epitopes
- Lindestam Arlehamn C.S.
- McKinney D.M.
- Carpenter C.
- Paul S.
- Rozot V.
- Makgotlho E.
- Gregg Y.
- van Rooyen M.
- Ernst J.D.
- Hatherill M.
- et al.
Immunological Phenotypes of Recovered COVID-19 Patients
Age (years) | Unexposed (n = 20) | COVID-19 (n = 20) |
---|---|---|
20–66 (median = 31, IQR = 21) | 20–64 (median = 44, IQR = 9) | |
Gender | ||
Male (%) | 35% (7/20) | 45% (9/20) |
Female (%) | 65% (13/20) | 55% (11/20) |
Residency | ||
California (%) | 95% (19/20) | 100% (20/20) |
USA, Non-California (%) | 5% (1/20) | 0% (0/20) |
Sample Collection Date | March 2015–March 2018 | March–April 2020 |
SARS-CoV-2 PCR Positivity | N/A | 100% (16/16 tested) |
Antibody Test Positivity | N/A | 90% (18/20) |
Disease Severity | ||
Mild | N/A | 70% (14/20) |
Moderate | N/A | 20% (4/20) |
Severe | N/A | 10% (2/20) |
Critical | N/A | 0% (0/20) |
Symptoms | ||
Cough | N/A | 79% (15/19) |
Fatigue | N/A | 42% (8/19) |
Fever | N/A | 37% (7/19) |
Anosmia | N/A | 21% (4/19) |
Dyspnea | N/A | 16% (3/19) |
Diarrhea | N/A | 5% (1/19) |
Days Post Symptom Onset at Collection | N/A | 20–36 (18/20) (median = 26, IQR = 7) |
Past Medical History | ||
No known | N/A | 65% (13/20) |
Hyperlipidemia | N/A | 15% (3/20) |
Hypertension | N/A | 10% (2/20) |
Asthma | N/A | 10% (2/20) |
Known or suspected sick contact/exposure | N/A | 75% (15/20) |
Identification and Quantitation of SARS-CoV-2-Specific CD4+ T Cell Responses
- Havenar-Daughton C.
- Reiss S.M.
- Carnathan D.G.
- Wu J.E.
- Kendric K.
- Torrents de la Peña A.
- Kasturi S.P.
- Dan J.M.
- Bothwell M.
- Sanders R.W.
- et al.
- Dan J.M.
- Lindestam Arlehamn C.S.
- Weiskopf D.
- da Silva Antunes R.
- Havenar-Daughton C.
- Reiss S.M.
- Brigger M.
- Bothwell M.
- Sette A.
- Crotty S.
- Dan J.M.
- Havenar-Daughton C.
- Kendric K.
- Al-Kolla R.
- Kaushik K.
- Rosales S.L.
- Anderson E.L.
- LaRock C.N.
- Vijayanand P.
- Seumois G.
- et al.
Identification and Quantitation of SARS-CoV-2-Specific CD8+ T Cell Responses
Relationship between SARS-CoV-2-Specific CD4+ T Cell Responses and IgG and IgA Titers
Pre-existing Cross-Reactive Coronavirus-Specific T Cells
- Huang A.T.
- Garcia-Carreras B.
- Hitchings M.D.T.
- Yang B.
- Katzelnick L.
- Rattigan S.M.
- Borgert B.
- Moreno C.
- Solomon B.D.
- Rodriguez-Barraquer I.
- et al.
SARS-CoV-2 ORF Targets of CD4+ and CD8+ T Cells
Discussion
Limitations and Future Directions
STAR★Methods
Key Resources Table
REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
M5E2 (V500) [anti-CD14] | Becton Dickinson | 561391 (RRID:AB_10611856) |
HIB19 (V500) [anti-CD19] | Becton Dickinson | 561121 (RRID:AB_10562391) |
FN50 (BV605) [anti-CD4] | Becton Dickinson | 562989 (RRID:AB_2737935) |
RPA-T8 (BV650) [anti-CD8] | BioLegend | 301042 (RRID:AB_2563505) |
FN50 (PE-CF594) [anti-CD69] | Becton Dickinson | 562617 (RRID:AB_2737680) |
Ber-ACT35 (PE-Cy7) [anti-OX40] | Biolegend | 350012 (RRID:AB_10901161)a |
4B4-1 (APC) [anti-CD137] | BioLegend | 309810 (RRID:AB_830672) |
OKT3 (AF700) [anti-CD3] | Biolegend | 317340 (RRID:AB_2563408) |
G043H7 (BV421) [anti-CD45RA] | BioLegend | 353207 (RRID:AB_10915137) |
4S.B3 (FITC) [anti-IFNγ] | Thermo Fisher Scientific | 11-7319-82 (RRID: AB_465415) |
GB11 (PE) [anti-Granzyme B] | Thermo Fisher Scientific | 12-8899-41 (RRID: AB_1659718) |
Mab11 (PeCy7) [anti-TNFα] | ebioscience | 25-7349-82 (RRID:AB_469686) |
JES3-19F1 (APC) [anti-IL-10] | BioLegend | 506807 (RRID:AB_315457) |
3D12 (APC ef780) [anti-CCR7] | eBioscience | 47-1979-42 (RRID:AB_1518794) |
B56 (FITC) [anti-KI67] | Becton Dickinson | 556026 (RRID:AB_396302) |
SK3 (percp efluor710) [anti-CD4] | Invitrogen | 46-0047-42 (RRID:AB_1834401) |
GB11 (af647) [anti-GzmB] | Biolegend | 515406 (RRID:AB_2566333) |
MHM-88 (af700) [anti-IgM] | Biolegend | 314538 (RRID:AB_2566615) |
O323 (APC cy7) [anti-CD27] | Biolegend | 302816 (RRID:AB_571977) |
IA6-2 (PE) [anti-IgD] | Becton Dickinson | 555779 (RRID:AB_396114) |
HCD56 (PE Dazzle) [anti-CD56] | Biolegend | 318348 (RRID:AB_2563564) |
HIB19 (Cy5) [anti-CD19PE] | Biolegend | 302210 (RRID:AB_314240) |
HIT2 (PECy7) [anti-CD38] | Invitrogen | 25-0389-42 (RRID:AB_1724057) |
J252D4 (bv421) [anti-CXCR5] | Biolegend | 356920 (RRID:AB_2562303) |
63D3 (bv510) [anti-CD14] | Biolegend | 367123 (RRID:AB_2716228) |
HI100 (bv570) [anti-CD45RA] | Biolegend | 304132 (RRID:AB_2563813) |
G025H7 (bv605) [anti-CXCR3] | Biolegend | 353728 (RRID:AB_2563157) |
2H7 (bv650) [anti-CD20] | Biolegend | 302336 (RRID:AB_2563806) |
G043H7 (bv711) [anti-CCR7] | Biolegend | 353228 (RRID:AB_2563865) |
EH12.2H7 (bv786) [anti-PD-1] | Biolegend | 329930 (RRID:AB_2563443) |
UCHT1 (buv395) [anti-CD3] | Becton Dickinson | 563546 (RRID:AB_2744387) |
Live/dead (UV) [Zombie] | Biolegend | 423108 |
11A9 (buv496) [anti-CCR6] | Becton Dickinson | 612948 (RRID:AB_2833076) |
3G8 (buv737) [anti-CD16] | Becton Dickinson | 612786 (RRID:AB_2833077) |
SK1 (buv805) [anti-CD8] | Becton Dickinson | 612889 (RRID:AB_2833078) |
LEGENDplex 13-plex kit | Biolegend | 740809 |
Biological Samples | ||
Healthy donor blood samples | Carter BloodCare | http://www.carterbloodcare.org/ |
Healthy donor blood samples | LJI Clinical Core | https://www.iedb.org/ |
Convalescent donor blood samples | UC San Diego Health | http://www.health.ucsd.edu/ |
Chemicals, Peptides, and Recombinant Proteins | ||
Synthetic peptides | Synthetic Biomolecules (aka A&A) | http://www.syntheticbiomolecules.com/ |
SARS-CoV-2 Receptor Binding Domain (RBD) protein |
Stadlbauer et al., 2020
|
N/A |
Critical Commercial Assays | ||
CoronaCheck COVID-19 Rapid Antibody Test Kit | 20/20 BioResponse | https://coronachecktest.com/ |
Deposited Data | ||
Wuhan-Hu-1 RNA isolate | NCBI nuccore database | GenBank: MN_908947 |
ORF10 protein | NCBI protein database | NCBI: YP_009725255.1 |
Nucleocapsid phosphoprotein | NCBI protein database | NCBI: YP_009724397.2 |
ORF8 protein | NCBI protein database | NCBI: YP_009724396.1 |
ORF7a protein | NCBI protein database | NCBI: YP_009724395.1 |
ORF6 protein | NCBI protein database | NCBI: YP_009724394.1 |
membrane glycoprotein | NCBI protein database | NCBI: YP_009724393.1 |
envelope protein | NCBI protein database | NCBI: YP_009724392.1 |
ORF3a protein | NCBI protein database | NCBI: YP_009724391.1 |
surface glycoprotein | NCBI protein database | NCBI: YP_009724390.1 |
orf1ab polyprotein | NCBI protein database | NCBI: YP_009724389.1 |
Software and Algorithms | ||
IEDB |
Vita et al., 2019
|
https://www.iedb.org |
IEDB-AR (analysis resource) |
Dhanda et al., 2019
|
http://tools.iedb.org |
NetMHCpan EL 4.0 |
Jurtz et al., 2017
|
http://tools.iedb.org/mhci/ |
IEDB |
Vita et al., 2019
|
https://www.iedb.org |
Tepitool |
Paul et al., 2016
,
Paul et al., 2015
|
http://tools.iedb.org/tepitool/ |
FlowJo 10 | FlowJo | https://www.flowjo.com/ |
GraphPad Prism 8.4 | GraphPad | https://www.graphpad.com/ |
LEGENDplex v8.0 | Biolegend | https://www.biolegend.com/ |
Resource Availability
Lead Contact
Materials Availability
Data and Code Availability
Experimental Model and Subject Details
Human Subjects
Healthy Unexposed Donors
Convalescent COVID-19 Donors
Method Details
Peptide Pools
Epitope MegaPool (MP) design and preparation
Protein peptide pools
PBMC isolation
- Weiskopf D.
- Angelo M.A.
- de Azeredo E.L.
- Sidney J.
- Greenbaum J.A.
- Fernando A.N.
- Broadwater A.
- Kolla R.V.
- De Silva A.D.
- de Silva A.M.
- et al.
SARS-CoV-2 RBD ELISA
OC43 and NL63 coronavirus RBD ELISA
Flow Cytometry
Direct ex vivo PBMC immune cell phenotyping
T cell stimulations
Activation induced cell marker assay
Intracellular cytokine staining assay
Cytokine bead assays
Identification of coronavirus epitopes and associated literature references
Quantification and Statistical Analysis
Acknowledgments
Author Contributions
Declaration of Interests
Supplemental Information
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Document S1. Tables S1–S5
-
Table S6. Raw Data for Figures 2, 3, and 6
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