Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and privat

Wu, Daichao; Kolesnikov, Alexander; Yin, Rui; Guest, Johnathan D.; Gowthaman, Ragul; Shmelev, Anton; Serdyuk, Yana; Dianov, Dmitry V.; Efimov, Grigory A.; Pierce, Brian G.; Mariuzza, Roy A.

doi:10.1038/s41467-021-27669-8

Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and privat

Journal Article · 01 January 2022 · Nat. Commun.

DOI:https://doi.org/10.1038/s41467-021-27669-8· OSTI ID:1844631

Wu, Daichao; Kolesnikov, Alexander; Yin, Rui; Guest, Johnathan D.; Gowthaman, Ragul; Shmelev, Anton; Serdyuk, Yana; Dianov, Dmitry V.; Efimov, Grigory A.; Pierce, Brian G.; Mariuzza, Roy A.

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; FOREIGN; National Institutes of Health (NIH)

OSTI ID:: 1844631

Journal Information:: Nat. Commun., Vol. 13

Country of Publication:: United States

Language:: ENGLISH

References (73)

The Novel Coronavirus Originating in Wuhan, China: Challenges for Global Health Governance Phelan, Alexandra L.; Katz, Rebecca; Gostin, Lawrence O. JAMA, Vol. 323, Issue 8 https://doi.org/10.1001/jama.2020.1097	journal	February 2020
A new coronavirus associated with human respiratory disease in China Wu, Fan; Zhao, Su; Yu, Bin Nature, Vol. 579, Issue 7798 https://doi.org/10.1038/s41586-020-2008-3	journal	February 2020
A Novel Coronavirus from Patients with Pneumonia in China, 2019 Zhu, Na; Zhang, Dingyu; Wang, Wenling New England Journal of Medicine, Vol. 382, Issue 8 https://doi.org/10.1056/NEJMoa2001017	journal	February 2020
Immunological considerations for COVID-19 vaccine strategies Jeyanathan, Mangalakumari; Afkhami, Sam; Smaill, Fiona Nature Reviews Immunology, Vol. 20, Issue 10 https://doi.org/10.1038/s41577-020-00434-6	journal	September 2020
Convergent antibody responses to SARS-CoV-2 in convalescent individuals Robbiani, Davide F.; Gaebler, Christian; Muecksch, Frauke Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2456-9	journal	June 2020
SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls Le Bert, Nina; Tan, Anthony T.; Kunasegaran, Kamini Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2550-z	journal	July 2020
Two X‐linked agammaglobulinemia patients develop pneumonia as COVID‐19 manifestation but recover Soresina, Annarosa; Moratto, Daniele; Chiarini, Marco Pediatric Allergy and Immunology, Vol. 31, Issue 5 https://doi.org/10.1111/pai.13263	journal	May 2020
Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19 Thevarajan, Irani; Nguyen, Thi H. O.; Koutsakos, Marios Nature Medicine, Vol. 26, Issue 4 https://doi.org/10.1038/s41591-020-0819-2	journal	March 2020
Viral and host factors related to the clinical outcome of COVID-19 Zhang, Xiaonan; Tan, Yun; Ling, Yun Nature, Vol. 583, Issue 7816 https://doi.org/10.1038/s41586-020-2355-0	journal	May 2020
Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19 Peng, Yanchun; Mentzer, Alexander J.; Liu, Guihai Nature Immunology, Vol. 21, Issue 11 https://doi.org/10.1038/s41590-020-0782-6	journal	September 2020
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection Minervina, Anastasia A.; Komech, Ekaterina A.; Titov, Aleksei eLife, Vol. 10 https://doi.org/10.7554/eLife.63502	journal	January 2021
Sex differences in immune responses that underlie COVID-19 disease outcomes Takahashi, Takehiro; Ellingson, Mallory K.; Wong, Patrick Nature, Vol. 588, Issue 7837 https://doi.org/10.1038/s41586-020-2700-3	journal	August 2020
Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19 Sekine, Takuya; Perez-Potti, André; Rivera-Ballesteros, Olga Cell, Vol. 183, Issue 1 https://doi.org/10.1016/j.cell.2020.08.017	journal	October 2020
A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice Roberts, Anjeanette; Deming, Damon; Paddock, Christopher D. PLoS Pathogens, Vol. 3, Issue 1 https://doi.org/10.1371/journal.ppat.0030005	journal	January 2007
T Cell Responses to Whole SARS Coronavirus in Humans Li, Chris Ka-fai; Wu, Hao; Yan, Huiping The Journal of Immunology, Vol. 181, Issue 8 https://doi.org/10.4049/jimmunol.181.8.5490	journal	October 2008
T Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice Zhao, Jincun; Zhao, Jingxian; Perlman, Stanley Journal of Virology, Vol. 84, Issue 18 https://doi.org/10.1128/JVI.01049-10	journal	September 2010
SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 ⁺ T cell responses Agerer, Benedikt; Koblischke, Maximilian; Gudipati, Venugopal Science Immunology, Vol. 6, Issue 57 https://doi.org/10.1126/sciimmunol.abg6461	journal	March 2021
Lessons for COVID-19 Immunity from Other Coronavirus Infections Sariol, Alan; Perlman, Stanley Immunity, Vol. 53, Issue 2 https://doi.org/10.1016/j.immuni.2020.07.005	journal	August 2020
Lack of Peripheral Memory B Cell Responses in Recovered Patients with Severe Acute Respiratory Syndrome: A Six-Year Follow-Up Study Tang, Fang; Quan, Yan; Xin, Zhong-Tao The Journal of Immunology, Vol. 186, Issue 12 https://doi.org/10.4049/jimmunol.0903490	journal	May 2011
Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection Ng, Oi-Wing; Chia, Adeline; Tan, Anthony T. Vaccine, Vol. 34, Issue 17 https://doi.org/10.1016/j.vaccine.2016.02.063	journal	April 2016
Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection Dan, Jennifer M.; Mateus, Jose; Kato, Yu Science, Vol. 371, Issue 6529 https://doi.org/10.1126/science.abf4063	journal	January 2021
Origin and differentiation of human memory CD8 T cells after vaccination Akondy, Rama S.; Fitch, Mark; Edupuganti, Srilatha Nature, Vol. 552, Issue 7685 https://doi.org/10.1038/nature24633	journal	December 2017
Robust SARS-CoV-2-specific T cell immunity is maintained at 6 months following primary infection Zuo, Jianmin; Dowell, Alexander C.; Pearce, Hayden Nature Immunology, Vol. 22, Issue 5 https://doi.org/10.1038/s41590-021-00902-8	journal	March 2021
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans Sahin, Ugur; Muik, Alexander; Vogler, Isabel Nature, Vol. 595, Issue 7868 https://doi.org/10.1038/s41586-021-03653-6	journal	May 2021
SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection Altmann, Daniel M.; Boyton, Rosemary J. Science Immunology, Vol. 5, Issue 49 https://doi.org/10.1126/sciimmunol.abd6160	journal	July 2020
SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors Shomuradova, Alina S.; Vagida, Murad S.; Sheetikov, Savely A. Immunity, Vol. 53, Issue 6 https://doi.org/10.1016/j.immuni.2020.11.004	journal	December 2020
Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals Grifoni, Alba; Weiskopf, Daniela; Ramirez, Sydney I. Cell, Vol. 181, Issue 7 https://doi.org/10.1016/j.cell.2020.05.015	journal	June 2020
SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition Nelde, Annika; Bilich, Tatjana; Heitmann, Jonas S. Nature Immunology, Vol. 22, Issue 1 https://doi.org/10.1038/s41590-020-00808-x	journal	September 2020
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases Tarke, Alison; Sidney, John; Kidd, Conner K. Cell Reports Medicine, Vol. 2, Issue 2 https://doi.org/10.1016/j.xcrm.2021.100204	journal	February 2021
SARS-CoV-2–specific CD8+ T cell responses in convalescent COVID-19 individuals Kared, Hassen; Redd, Andrew D.; Bloch, Evan M. Journal of Clinical Investigation, Vol. 131, Issue 5 https://doi.org/10.1172/JCI145476	journal	March 2021
CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity Nguyen, Thi H. O.; Rowntree, Louise C.; Petersen, Jan Immunity, Vol. 54, Issue 5 https://doi.org/10.1016/j.immuni.2021.04.009	journal	May 2021
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19 Grifoni, Alba; Sidney, John; Vita, Randi Cell Host & Microbe, Vol. 29, Issue 7 https://doi.org/10.1016/j.chom.2021.05.010	journal	July 2021
Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans Mateus, Jose; Grifoni, Alba; Tarke, Alison Science, Vol. 370, Issue 6512 https://doi.org/10.1126/science.abd3871	journal	August 2020
SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19 Braun, Julian; Loyal, Lucie; Frentsch, Marco Nature, Vol. 587, Issue 7833 https://doi.org/10.1038/s41586-020-2598-9	journal	July 2020
Pre-existing immunity to SARS-CoV-2: the knowns and unknowns Sette, Alessandro; Crotty, Shane Nature Reviews Immunology, Vol. 20, Issue 8 https://doi.org/10.1038/s41577-020-0389-z	journal	July 2020
A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Chi, Xiangyang; Yan, Renhong; Zhang, Jun Science, Vol. 369, Issue 6504 https://doi.org/10.1126/science.abc6952	journal	June 2020
Structural basis of a shared antibody response to SARS-CoV-2 Yuan, Meng; Liu, Hejun; Wu, Nicholas C. Science, Vol. 369, Issue 6507 https://doi.org/10.1126/science.abd2321	journal	July 2020
An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain Wu, Nicholas C.; Yuan, Meng; Liu, Hejun Cell Reports, Vol. 33, Issue 3 https://doi.org/10.1016/j.celrep.2020.108274	journal	October 2020
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies Barnes, Christopher O.; Jette, Claudia A.; Abernathy, Morgan E. Nature, Vol. 588, Issue 7839 https://doi.org/10.1038/s41586-020-2852-1	journal	October 2020
Structural basis for self-recognition by autoimmune T-cell receptors Yin, Yiyuan; Li, Yili; Mariuzza, Roy A. Immunological Reviews, Vol. 250, Issue 1 https://doi.org/10.1111/imr.12002	journal	October 2012
A Jurkat 76 based triple parameter reporter system to evaluate TCR functions and adoptive T cell strategies Rosskopf, Sandra; Leitner, Judith; Paster, Wolfgang Oncotarget, Vol. 9, Issue 25 https://doi.org/10.18632/oncotarget.24807	journal	April 2018
Normalized Synergy Predicts That CD8 Co-Receptor Contribution to T Cell Receptor (TCR) and pMHC Binding Decreases As TCR Affinity Increases in Human Viral-Specific T Cells Williams, Chad M.; Schonnesen, Alexandra A.; Zhang, Shu-Qi Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00894	journal	July 2017
Data, disease and diplomacy: GISAID's innovative contribution to global health: Data, Disease and Diplomacy Elbe, Stefan; Buckland-Merrett, Gemma Global Challenges, Vol. 1, Issue 1 https://doi.org/10.1002/gch2.1018	journal	January 2017
Detailed motifs for peptide binding to HLA-A∗0201 derived from large random sets of peptides using a cellular binding assay Drijfhout, Jan W.; Brandt, Remco M. P.; D'Amaro, Joe Human Immunology, Vol. 43, Issue 1 https://doi.org/10.1016/0198-8859(94)00151-F	journal	May 1995
How tcrs bind Mhcs, Peptides, and Coreceptors Rudolph, Markus G.; Stanfield, Robyn L.; Wilson, Ian A. Annual Review of Immunology, Vol. 24, Issue 1 https://doi.org/10.1146/annurev.immunol.23.021704.115658	journal	April 2006
A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes Pierce, Brian G.; Weng, Zhiping Protein Science, Vol. 22, Issue 1 https://doi.org/10.1002/pro.2181	journal	December 2012
Computational Alanine Scanning of Protein-Protein Interfaces Kortemme, T.; Kim, D. E.; Baker, D. Science Signaling, Vol. 2004, Issue 219 https://doi.org/10.1126/stke.2192004pl2	journal	February 2004
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor Pierce, Brian G.; Hellman, Lance M.; Hossain, Moushumi PLoS Computational Biology, Vol. 10, Issue 2 https://doi.org/10.1371/journal.pcbi.1003478	journal	February 2014
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data Reynisson, Birkir; Alvarez, Bruno; Paul, Sinu Nucleic Acids Research, Vol. 48, Issue W1 https://doi.org/10.1093/nar/gkaa379	journal	May 2020
Determinants of public T cell responses Li, Hanjie; Ye, Congting; Ji, Guoli Cell Research, Vol. 22, Issue 1 https://doi.org/10.1038/cr.2012.1	journal	January 2012
Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination Venturi, V.; Kedzierska, K.; Price, D. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 49 https://doi.org/10.1073/pnas.0608907103	journal	November 2006
Genetic and Structural Basis for Selection of a Ubiquitous T Cell Receptor Deployed in Epstein-Barr Virus Infection Miles, John J.; Bulek, Anna M.; Cole, David K. PLoS Pathogens, Vol. 6, Issue 11 https://doi.org/10.1371/journal.ppat.1001198	journal	November 2010
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 Wang, Pengfei; Nair, Manoj S.; Liu, Lihong Nature, Vol. 593, Issue 7857 https://doi.org/10.1038/s41586-021-03398-2	journal	March 2021
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals Tarke, Alison; Sidney, John; Methot, Nils Cell Reports Medicine, Vol. 2, Issue 7 https://doi.org/10.1016/j.xcrm.2021.100355	journal	July 2021
An Alternative Conformation of the T-Cell Receptor α Constant Region van Boxel, Gijs I.; Holmes, Samantha; Fugger, Lars Journal of Molecular Biology, Vol. 400, Issue 4 https://doi.org/10.1016/j.jmb.2010.05.053	journal	July 2010
Structural basis of assembly of the human T cell receptor–CD3 complex Dong, De; Zheng, Lvqin; Lin, Jianquan Nature, Vol. 573, Issue 7775 https://doi.org/10.1038/s41586-019-1537-0	journal	August 2019
Neutralizing Activity of BNT162b2-Elicited Serum Liu, Yang; Liu, Jianying; Xia, Hongjie New England Journal of Medicine, Vol. 384, Issue 15 https://doi.org/10.1056/NEJMc2102017	journal	April 2021
Durability of Responses after SARS-CoV-2 mRNA-1273 Vaccination Widge, Alicia T.; Rouphael, Nadine G.; Jackson, Lisa A. New England Journal of Medicine, Vol. 384, Issue 1 https://doi.org/10.1056/NEJMc2032195	journal	January 2021
Immunogenicity of Ad26.COV2.S vaccine against SARS-CoV-2 variants in humans Alter, Galit; Yu, Jingyou; Liu, Jinyan Nature, Vol. 596, Issue 7871 https://doi.org/10.1038/s41586-021-03681-2	journal	June 2021
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Pinto, Dora; Park, Young-Jun; Beltramello, Martina Nature, Vol. 583, Issue 7815 https://doi.org/10.1038/s41586-020-2349-y	journal	May 2020
Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses Nathan, Anusha; Rossin, Elizabeth J.; Kaseke, Clarety Cell, Vol. 184, Issue 17 https://doi.org/10.1016/j.cell.2021.06.029	journal	August 2021
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
Likelihood-enhanced fast rotation functions Storoni, Laurent C.; McCoy, Airlie J.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 3 https://doi.org/10.1107/S0907444903028956	journal	February 2004
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
T Cell Receptor Signaling Is Limited by Docking Geometry to Peptide-Major Histocompatibility Complex Adams, Jarrett J.; Narayanan, Samanthi; Liu, Baoyu Immunity, Vol. 35, Issue 5 https://doi.org/10.1016/j.immuni.2011.09.013	journal	November 2011
The Shaping of T Cell Receptor Recognition by Self-Tolerance Gras, Stephanie; Burrows, Scott R.; Kjer-Nielsen, Lars Immunity, Vol. 30, Issue 2 https://doi.org/10.1016/j.immuni.2008.11.011	journal	February 2009
Atypical TRAV1-2− T cell receptor recognition of the antigen-presenting molecule MR1 Awad, Wael; Meermeier, Erin W.; Sandoval-Romero, Maria L. Journal of Biological Chemistry, Vol. 295, Issue 42 https://doi.org/10.1074/jbc.RA120.015292	journal	October 2020
Structure of Staphylococcal Enterotoxin E in Complex with TCR Defines the Role of TCR Loop Positioning in Superantigen Recognition Rödström, Karin E. J.; Regenthal, Paulina; Lindkvist-Petersson, Karin PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0131988	journal	July 2015
CoV3D: a database of high resolution coronavirus protein structures Gowthaman, Ragul; Guest, Johnathan D.; Yin, Rui Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa731	journal	September 2020
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
Global Epidemiology of Bat Coronaviruses Wong, Antonio; Li, Xin; Lau, Susanna Viruses, Vol. 11, Issue 2 https://doi.org/10.3390/v11020174	journal	February 2019
Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses Letko, Michael; Marzi, Andrea; Munster, Vincent Nature Microbiology, Vol. 5, Issue 4 https://doi.org/10.1038/s41564-020-0688-y	journal	February 2020

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