Human coronavirus OC43-elicited CD4


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
26 Jan 2024
Historique:
received: 18 08 2023
accepted: 10 01 2024
medline: 27 1 2024
pubmed: 27 1 2024
entrez: 26 1 2024
Statut: epublish

Résumé

SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1

Identifiants

pubmed: 38278784
doi: 10.1038/s41467-024-45043-2
pii: 10.1038/s41467-024-45043-2
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

787

Subventions

Organisme : NIAID NIH HHS
ID : U01 AI149644
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI142790
Pays : United States

Informations de copyright

© 2024. The Author(s).

Références

Noh, J. Y., Jeong, H. W. & Shin, E. C. SARS-CoV-2 mutations, vaccines, and immunity: implication of variants of concern. Signal Transduct. Target. Ther. 6, 203 (2021).
pubmed: 34023862 pmcid: 8140323 doi: 10.1038/s41392-021-00623-2
Andrews, N. et al. Covid-19 vaccine effectiveness against the omicron (B.1.1.529) variant. New Engl. J. Med. 386, 1532–1546 (2022).
pubmed: 35249272 doi: 10.1056/NEJMoa2119451
Geers, D. et al. SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees. Sci. Immunol. 6, eabj1750 (2021).
pubmed: 34035118 pmcid: 9268159 doi: 10.1126/sciimmunol.abj1750
Nasreen, S. et al. Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario. Nat. Microbiol. 7, 379–385 (2022).
pubmed: 35132198 doi: 10.1038/s41564-021-01053-0
Wratil, P. R. et al. Three exposures to the spike protein of SARS-CoV-2 by either infection or vaccination elicit superior neutralizing immunity to all variants of concern. Nat. Med. 28, 496–503 (2022).
pubmed: 35090165 doi: 10.1038/s41591-022-01715-4
Sakurai, A. et al. Natural history of asymptomatic SARS-CoV-2 infection. New Engl. J. Med. 383, 885–886 (2020).
pubmed: 32530584 doi: 10.1056/NEJMc2013020
Spudich, S. & Nath, A. Nervous system consequences of COVID-19. Science 375, 267–269 (2022).
pubmed: 35050660 doi: 10.1126/science.abm2052
Xie, Y., Bowe, B. & Al-Aly, Z. Burdens of post-acute sequelae of COVID-19 by severity of acute infection, demographics and health status. Nat. Commun. 12, 6571 (2021).
pubmed: 34772922 pmcid: 8589966 doi: 10.1038/s41467-021-26513-3
Xie, Y., Xu, E., Bowe, B. & Al-Aly, Z. Long-term cardiovascular outcomes of COVID-19. Nat. Med. 28, 583–590 (2022).
pubmed: 35132265 pmcid: 8938267 doi: 10.1038/s41591-022-01689-3
Guan, W. J. et al. Clinical characteristics of coronavirus disease 2019 in China. New Engl. J. Med. 382, 1708–1720 (2020).
pubmed: 32109013 doi: 10.1056/NEJMoa2002032
Al-Aly, Z., Xie, Y. & Bowe, B. High-dimensional characterization of post-acute sequelae of COVID-19. Nature 594, 259–264 (2021).
pubmed: 33887749 doi: 10.1038/s41586-021-03553-9
Muscogiuri, G. et al. Low-grade inflammation, CoVID-19, and obesity: clinical aspect and molecular insights in childhood and adulthood. Int. J. Obes. 46, 1254–1261 (2022).
doi: 10.1038/s41366-022-01111-5
Ng, W. H. et al. Comorbidities in SARS-CoV-2 patients: a systematic review and meta-analysis. mBio 12, e03647–20 (2021).
pubmed: 33563817 pmcid: 7885108 doi: 10.1128/mBio.03647-20
Price-Haywood, E. G., Burton, J., Fort, D. & Seoane, L. Hospitalization and mortality among black patients and white patients with Covid-19. New Engl. J. Med. 382, 2534–2543 (2020).
pubmed: 32459916 doi: 10.1056/NEJMsa2011686
O’Driscoll, M. et al. Age-specific mortality and immunity patterns of SARS-CoV-2. Nature 590, 140–145 (2021).
pubmed: 33137809 doi: 10.1038/s41586-020-2918-0
Klang, E. et al. Severe obesity as an independent risk factor for covid-19 mortality in hospitalized patients younger than 50. Obesity (Silver Spring) 28, 1595–1599 (2020).
pubmed: 32445512 doi: 10.1002/oby.22913
Jin, J. M. et al. Gender differences in patients with COVID-19: focus on severity and mortality. Front. Public Health 8, 152 (2020).
pubmed: 32411652 pmcid: 7201103 doi: 10.3389/fpubh.2020.00152
Mateus, J. et al. Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science 370, 89–94 (2020).
pubmed: 32753554 pmcid: 7574914 doi: 10.1126/science.abd3871
Dykema, A. G. et al. Functional characterization of CD4+ T cell receptors crossreactive for SARS-CoV-2 and endemic coronaviruses. J. Clin. Invest. 131, e146922 (2021).
pubmed: 33830946 pmcid: 8121515 doi: 10.1172/JCI146922
Woldemeskel, B. A. et al. CD4+ T cells from COVID-19 mRNA vaccine recipients recognize a conserved epitope present in diverse coronaviruses. J. Clin. Invest. 132, e156083 (2022).
pubmed: 35061630 pmcid: 8884904 doi: 10.1172/JCI156083
Le Bert, N. et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 584, 457–462 (2020).
pubmed: 32668444 doi: 10.1038/s41586-020-2550-z
Tan, H. X. et al. Adaptive immunity to human coronaviruses is widespread but low in magnitude. Clin. Transl. Immunol. 10, e1264 (2021).
doi: 10.1002/cti2.1264
Grifoni, A. et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell 181, 1489–1501.e1415 (2020).
pubmed: 32473127 pmcid: 7237901 doi: 10.1016/j.cell.2020.05.015
Ni, L. et al. Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals. Immunity 52, 971–977.e973 (2020).
pubmed: 32413330 pmcid: 7196424 doi: 10.1016/j.immuni.2020.04.023
Peng, Y. et al. Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat. Immunol. 21, 1336–1345 (2020).
pubmed: 32887977 pmcid: 7611020 doi: 10.1038/s41590-020-0782-6
Weiskopf, D. et al. Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome. Sci. Immunol. 5, eabd2071 (2020).
pubmed: 32591408 pmcid: 7319493 doi: 10.1126/sciimmunol.abd2071
Kundu, R. et al. Cross-reactive memory T cells associate with protection against SARS-CoV-2 infection in COVID-19 contacts. Nat. Commun. 13, 80 (2022).
pubmed: 35013199 pmcid: 8748880 doi: 10.1038/s41467-021-27674-x
Lineburg, K. E. et al. CD8(+) T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Immunity 54, 1055–1065.e1055 (2021).
pubmed: 33945786 pmcid: 8043652 doi: 10.1016/j.immuni.2021.04.006
Braun, J. et al. SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature 587, 270–274 (2020).
pubmed: 32726801 doi: 10.1038/s41586-020-2598-9
Garcia-Jimenez, A. F. et al. Cross-reactive cellular, but not humoral, immunity is detected between OC43 and SARS-CoV-2 NPs in people not infected with SARS-CoV-2: Possible role of cT(FH) cells. J. Leukoc. Biol. 112, 339–346 (2022).
pubmed: 35384035 doi: 10.1002/JLB.4COVCRA0721-356RRR
Westphal, T. et al. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4(+) T-cell response with pre-primed responses directed against common cold coronaviruses. Front. Immunol. 14, 1182504 (2023).
pubmed: 37215095 pmcid: 10196118 doi: 10.3389/fimmu.2023.1182504
Diniz, M. O. et al. Airway-resident T cells from unexposed individuals cross-recognize SARS-CoV-2. Nat. Immunol. 23, 1324–1329 (2022).
pubmed: 36038709 pmcid: 9477726 doi: 10.1038/s41590-022-01292-1
Mesel-Lemoine, M. et al. A human coronavirus responsible for the common cold massively kills dendritic cells but not monocytes. J. Virol. 86, 7577–7587 (2012).
pubmed: 22553325 pmcid: 3416289 doi: 10.1128/JVI.00269-12
Gorse, G. J., Patel, G. B., Vitale, J. N. & O’Connor, T. Z. Prevalence of antibodies to four human coronaviruses is lower in nasal secretions than in serum. Clin. Vaccine Immunol. 17, 1875–1880 (2010).
pubmed: 20943876 pmcid: 3008199 doi: 10.1128/CVI.00278-10
Ellis, P., Somogyvari, F., Virok, D. P., Noseda, M. & McLean, G. R. Decoding Covid-19 with the SARS-CoV-2 Genome. Curr. Genet. Med. Rep. 9, 1–12 (2021).
pubmed: 33457109 pmcid: 7794078 doi: 10.1007/s40142-020-00197-5
Loyal, L. et al. Cross-reactive CD4(+) T cells enhance SARS-CoV-2 immune responses upon infection and vaccination. Science 374, eabh1823 (2021).
pubmed: 34465633 pmcid: 10026850 doi: 10.1126/science.abh1823
Mateus, J. et al. Low-dose mRNA-1273 COVID-19 vaccine generates durable memory enhanced by cross-reactive T cells. Science374, eabj9853 (2021).
pubmed: 34519540 pmcid: 8542617 doi: 10.1126/science.abj9853
Bacher, P. et al. Low-avidity CD4(+) T cell responses to SARS-CoV-2 in unexposed individuals and humans with severe COVID-19. Immunity 53, 1258–1271.e1255 (2020).
pubmed: 33296686 pmcid: 7689350 doi: 10.1016/j.immuni.2020.11.016
Augusto, D. G. et al. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 620, 128–136 (2023).
pubmed: 37468623 pmcid: 10396966 doi: 10.1038/s41586-023-06331-x
Gouma, S. et al. Health care worker seromonitoring reveals complex relationships between common coronavirus antibodies and COVID-19 symptom duration. JCI Insight 6, e150449 (2021).
pubmed: 34237028 pmcid: 8410018 doi: 10.1172/jci.insight.150449
Mallajosyula, V. et al. CD8(+) T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients. Sci. Immunol. 6, eabg5669 (2021).
pubmed: 34210785 pmcid: 8975171 doi: 10.1126/sciimmunol.abg5669
Bonifacius, A. et al. COVID-19 immune signatures reveal stable antiviral T cell function despite declining humoral responses. Immunity 54, 340–354.e346 (2021).
pubmed: 33567252 pmcid: 7871825 doi: 10.1016/j.immuni.2021.01.008
Zellweger, R. M., Prestwood, T. R. & Shresta, S. Enhanced infection of liver sinusoidal endothelial cells in a mouse model of antibody-induced severe dengue disease. Cell Host Microbe 7, 128–139 (2010).
pubmed: 20153282 pmcid: 2824513 doi: 10.1016/j.chom.2010.01.004
Zellweger, R. M. et al. CD8+ T cells can mediate short-term protection against heterotypic dengue virus reinfection in mice. J. Virol. 89, 6494–6505 (2015).
pubmed: 25855749 pmcid: 4474296 doi: 10.1128/JVI.00036-15
Balsitis, S. J. et al. Lethal antibody enhancement of dengue disease in mice is prevented by Fc modification. PLoS Pathog. 6, e1000790 (2010).
pubmed: 20168989 pmcid: 2820409 doi: 10.1371/journal.ppat.1000790
Wen, J. et al. Dengue virus-reactive CD8(+) T cells mediate cross-protection against subsequent Zika virus challenge. Nat. Commun. 8, 1459 (2017).
pubmed: 29129917 pmcid: 5682281 doi: 10.1038/s41467-017-01669-z
Wen, J. et al. CD4(+) T cells cross-reactive with dengue and zika viruses protect against zika virus infection. Cell Rep. 31, 107566 (2020).
pubmed: 32348763 pmcid: 7261136 doi: 10.1016/j.celrep.2020.107566
Regla-Nava, J. A. et al. Cross-reactive Dengue virus-specific CD8(+) T cells protect against Zika virus during pregnancy. Nat. Commun. 9, 3042 (2018).
pubmed: 30072692 pmcid: 6072705 doi: 10.1038/s41467-018-05458-0
Katzelnick, L. C. et al. Zika virus infection enhances future risk of severe dengue disease. Science 369, 1123–1128 (2020).
pubmed: 32855339 pmcid: 8274975 doi: 10.1126/science.abb6143
Katzelnick, L. C. et al. Antibody-dependent enhancement of severe dengue disease in humans. Science358, 929–932 (2017).
pubmed: 29097492 pmcid: 5858873 doi: 10.1126/science.aan6836
Salje, H. et al. Reconstruction of antibody dynamics and infection histories to evaluate dengue risk. Nature 557, 719–723 (2018).
pubmed: 29795354 pmcid: 6064976 doi: 10.1038/s41586-018-0157-4
Fowler, A. M. et al. Maternally acquired zika antibodies enhance dengue disease severity in mice. Cell Host Microbe 24, 743–750.e745 (2018).
pubmed: 30439343 pmcid: 6250068 doi: 10.1016/j.chom.2018.09.015
Gordon, A. et al. Prior dengue virus infection and risk of Zika: a pediatric cohort in Nicaragua. PLoS Med. 16, e1002726 (2019).
pubmed: 30668565 pmcid: 6342296 doi: 10.1371/journal.pmed.1002726
Rodriguez-Barraquer, I. et al. Impact of preexisting dengue immunity on Zika virus emergence in a dengue endemic region. Science 363, 607–610 (2019).
pubmed: 30733412 pmcid: 8221194 doi: 10.1126/science.aav6618
Pedroso, C. et al. Cross-protection of dengue virus infection against congenital zika syndrome, Northeastern Brazil. Emerg. Infect. Dis. 25, 1485–1493 (2019).
pubmed: 31075077 pmcid: 6649334 doi: 10.3201/eid2508.190113
Sridhar, S. et al. Effect of dengue serostatus on dengue vaccine safety and efficacy. New Engl. J. Med. 379, 327–340 (2018).
pubmed: 29897841 doi: 10.1056/NEJMoa1800820
Sharp, T. M. et al. Knowledge gaps in the epidemiology of severe dengue impede vaccine evaluation. Lancet Infect. Dis. 22, e42–e51 (2022).
pubmed: 34265259 doi: 10.1016/S1473-3099(20)30871-9
Katzelnick, L. C., Bos, S. & Harris, E. Protective and enhancing interactions among dengue viruses 1-4 and Zika virus. Curr. Opin. Virol. 43, 59–70 (2020).
pubmed: 32979816 pmcid: 7655628 doi: 10.1016/j.coviro.2020.08.006
Valentine, K. M., Croft, M. & Shresta, S. Protection against dengue virus requires a sustained balance of antibody and T cell responses. Curr. Opin. Virol. 43, 22–27 (2020).
pubmed: 32798886 pmcid: 7655611 doi: 10.1016/j.coviro.2020.07.018
Ngono, A. E. & Shresta, S. Immune response to dengue and zika. Annu. Rev. Immunol. 36, 279–308 (2018).
pubmed: 29345964 pmcid: 5910217 doi: 10.1146/annurev-immunol-042617-053142
Hassert, M., Brien, J. D. & Pinto, A. K. Mouse models of heterologous flavivirus immunity: a role for cross-reactive T cells. Front. Immunol. 10, 1045 (2019).
pubmed: 31143185 pmcid: 6520664 doi: 10.3389/fimmu.2019.01045
Gonzalez-Galarza, F. F. et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. 48, D783–D788 (2020).
pubmed: 31722398
Solberg, O. D. et al. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum. Immunol. 69, 443–464 (2008).
pubmed: 18638659 pmcid: 2632948 doi: 10.1016/j.humimm.2008.05.001
Bastard, P. et al. Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths. Sci. Immunol. 6, eabl4340 (2021).
pubmed: 34413139 pmcid: 8521484 doi: 10.1126/sciimmunol.abl4340
Bastard, P. et al. Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science 370, eabd4585 (2020).
pubmed: 32972996 pmcid: 7857397 doi: 10.1126/science.abd4585
Koning, R., Bastard, P., Casanova, J. L., Brouwer, M. C. & van de Beek, D. with the Amsterdam UMCC-BI. Autoantibodies against type I interferons are associated with multi-organ failure in COVID-19 patients. Intensive Care Med. 47, 704–706 (2021).
pubmed: 33835207 pmcid: 8034036 doi: 10.1007/s00134-021-06392-4
Troya, J. et al. Neutralizing autoantibodies to type I IFNs in >10% of patients with severe COVID-19 pneumonia hospitalized in Madrid, Spain. J. Clin. Immunol. 41, 914–922 (2021).
pubmed: 33851338 pmcid: 8043439 doi: 10.1007/s10875-021-01036-0
Vazquez, S. E. et al. Neutralizing autoantibodies to type I interferons in COVID-19 convalescent donor plasma. J. Clin. Immunol. 41, 1169–1171 (2021).
pubmed: 34009544 pmcid: 8132742 doi: 10.1007/s10875-021-01060-0
Wang, E. Y. et al. Diverse functional autoantibodies in patients with COVID-19. Nature 595, 283–288 (2021).
pubmed: 34010947 doi: 10.1038/s41586-021-03631-y
Zhang, Q. et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 370, eabd4570 (2020).
pubmed: 32972995 pmcid: 7857407 doi: 10.1126/science.abd4570
Elong Ngono, A. et al. Protective role of cross-reactive CD8 T cells against dengue virus infection. EBioMedicine 13, 284–293 (2016).
pubmed: 27746192 pmcid: 5264312 doi: 10.1016/j.ebiom.2016.10.006
Weiskopf, D. et al. Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondary infection. J. Virol. 88, 11383–11394 (2014).
pubmed: 25056881 pmcid: 4178794 doi: 10.1128/JVI.01108-14
Weiskopf, D. et al. Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design. J. Immunol. 187, 4268–4279 (2011).
pubmed: 21918184 doi: 10.4049/jimmunol.1101970
Wen, J. et al. Identification of Zika virus epitopes reveals immunodominant and protective roles for dengue virus cross-reactive CD8(+) T cells. Nat. Microbiol. 2, 17036 (2017).
pubmed: 28288094 pmcid: 5918137 doi: 10.1038/nmicrobiol.2017.36
Vita, R. et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47, D339–D343 (2019).
pubmed: 30357391 doi: 10.1093/nar/gky1006
Leist, S. R. et al. A mouse-adapted SARS-CoV-2 induces acute lung injury and mortality in standard laboratory mice. Cell 183, 1070–1085.e1012 (2020).
pubmed: 33031744 pmcid: 7510428 doi: 10.1016/j.cell.2020.09.050
Liu, Y. et al. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature 602, 294–299 (2022).
pubmed: 34818667 doi: 10.1038/s41586-021-04245-0
Pan, T. et al. Infection of wild-type mice by SARS-CoV-2 B.1.351 variant indicates a possible novel cross-species transmission route. Signal Transduct. Target Ther. 6, 420 (2021).
pubmed: 34907154 pmcid: 8669038 doi: 10.1038/s41392-021-00848-1
Ferretti, A. P. et al. Unbiased screens show CD8(+) T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2 that largely reside outside the spike protein. Immunity 53, 1095–1107.e1093 (2020).
pubmed: 33128877 pmcid: 7574860 doi: 10.1016/j.immuni.2020.10.006
Nguyen, T. H. O. et al. CD8(+) T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity. Immunity 54, 1066–1082.e1065 (2021).
pubmed: 33951417 pmcid: 8049468 doi: 10.1016/j.immuni.2021.04.009
Schulien, I. et al. Characterization of pre-existing and induced SARS-CoV-2-specific CD8(+) T cells. Nat. Med. 27, 78–85 (2021).
pubmed: 33184509 doi: 10.1038/s41591-020-01143-2
Sekine, T. et al. Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. Cell 183, 158–168.e114 (2020).
pubmed: 32979941 pmcid: 7427556 doi: 10.1016/j.cell.2020.08.017
Painter, M. M. et al. Rapid induction of antigen-specific CD4(+) T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination. Immunity 54, 2133–2142.e2133 (2021).
pubmed: 34453880 pmcid: 8361141 doi: 10.1016/j.immuni.2021.08.001
Dan, J. M. et al. Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science 371, eabf4063 (2021).
pubmed: 33408181 doi: 10.1126/science.abf4063
Hicks, J. et al. Serologic cross-reactivity of SARS-CoV-2 with endemic and seasonal betacoronaviruses. J. Clin. Immunol. 41, 906–913 (2021).
pubmed: 33725211 pmcid: 7962425 doi: 10.1007/s10875-021-00997-6
Saletti, G. et al. Older adults lack SARS CoV-2 cross-reactive T lymphocytes directed to human coronaviruses OC43 and NL63. Sci. Rep. 10, 21447 (2020).
pubmed: 33293664 pmcid: 7722724 doi: 10.1038/s41598-020-78506-9
Nickbakhsh, S. et al. Epidemiology of seasonal coronaviruses: establishing the context for the emergence of coronavirus disease 2019. J. Infect. Dis. 222, 17–25 (2020).
pubmed: 32296837 pmcid: 7184404 doi: 10.1093/infdis/jiaa185
Killerby, M. E. et al. Human coronavirus circulation in the United States 2014-2017. J. Clin. Virol. 101, 52–56 (2018).
pubmed: 29427907 pmcid: 7106380 doi: 10.1016/j.jcv.2018.01.019
Snyder, T. M. et al. Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels. medRxiv https://doi.org/10.1101/2020.07.31.20165647 (2020).
Tarke, A. et al. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep. Med. 2, 100204 (2021).
pubmed: 33521695 pmcid: 7837622 doi: 10.1016/j.xcrm.2021.100204
Saini, S. K. et al. SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8(+) T cell activation in COVID-19 patients. Sci. Immunol. 6, eabf7550 (2021).
pubmed: 33853928 pmcid: 8139428 doi: 10.1126/sciimmunol.abf7550
Quadeer, A. A., Ahmed, S. F. & McKay, M. R. Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform. Cell reports. Medicine 2, 100312 (2021).
pubmed: 34056627 pmcid: 8139281
Nelde, A. et al. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nat. Immunol. 22, 74–85 (2021).
pubmed: 32999467 doi: 10.1038/s41590-020-00808-x
Grifoni, A. et al. A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host Microbe 27, 671–680.e672 (2020).
pubmed: 32183941 pmcid: 7142693 doi: 10.1016/j.chom.2020.03.002
Kared, H. et al. SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals. J. Clin. Invest. 131, e145476 (2021).
pubmed: 33427749 pmcid: 7919723 doi: 10.1172/JCI145476
Ng, O. W. et al. Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection. Vaccine 34, 2008–2014 (2016).
pubmed: 26954467 pmcid: 7115611 doi: 10.1016/j.vaccine.2016.02.063
Prakash, S. et al. Genome-wide B cell, CD4(+), and CD8(+) T cell epitopes that are highly conserved between human and animal coronaviruses, identified from SARS-CoV-2 as targets for preemptive pan-coronavirus vaccines. J. Immunol. 206, 2566–2582 (2021).
pubmed: 33911008 doi: 10.4049/jimmunol.2001438
Shen, Y et al. Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population. bioRxiv https://doi.org/10.1101/2022.03.30.486345 (2022).
Keller, M. D. et al. SARS-CoV-2-specific T cells are rapidly expanded for therapeutic use and target conserved regions of the membrane protein. Blood 136, 2905–2917 (2020).
pubmed: 33331927 pmcid: 7746091 doi: 10.1182/blood.2020008488
Tan, A. T. et al. Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients. Cell Rep. 34, 108728 (2021).
pubmed: 33516277 pmcid: 7826084 doi: 10.1016/j.celrep.2021.108728
Crotty, S. T follicular helper cell differentiation, function, and roles in disease. Immunity 41, 529–542 (2014).
pubmed: 25367570 pmcid: 4223692 doi: 10.1016/j.immuni.2014.10.004
Ueno, H., Banchereau, J. & Vinuesa, C. G. Pathophysiology of T follicular helper cells in humans and mice. Nat Immunol. 16, 142–152 (2015).
pubmed: 25594465 pmcid: 4459756 doi: 10.1038/ni.3054
Heide, J. et al. Broadly directed SARS-CoV-2-specific CD4+ T cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19. PLoS Pathog. 17, e1009842 (2021).
pubmed: 34529740 pmcid: 8445433 doi: 10.1371/journal.ppat.1009842
Karsten, H. et al. High-resolution analysis of individual spike peptide-specific CD4(+) T-cell responses in vaccine recipients and COVID-19 patients. Clin. Transl. Immunol. 11, e1410 (2022).
doi: 10.1002/cti2.1410
Corey, L. et al. SARS-CoV-2 variants in patients with immunosuppression. New Engl. J. Med. 385, 562–566 (2021).
pubmed: 34347959 doi: 10.1056/NEJMsb2104756
Redd, A. D. et al. CD8+ T-cell responses in COVID-19 convalescent individuals target conserved epitopes from multiple prominent SARS-CoV-2 circulating variants. Open Forum Infect. Dis. 8, ofab143 (2021).
pubmed: 34322559 pmcid: 8083629 doi: 10.1093/ofid/ofab143
Naranbhai, V. et al. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 185, 1041–1051.e1046 (2022).
pubmed: 35202566 pmcid: 8810349 doi: 10.1016/j.cell.2022.01.029
Keeton, R. et al. T cell responses to SARS-CoV-2 spike cross-recognize Omicron. Nature 603, 488–492 (2022).
pubmed: 35102311 pmcid: 8930768 doi: 10.1038/s41586-022-04460-3
Gao, Y. et al. Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant. Nat. Med. 28, 472–476 (2022).
pubmed: 35042228 pmcid: 8938268 doi: 10.1038/s41591-022-01700-x
GeurtsvanKessel, C. H. et al. Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Sci. Immunol. 7, eabo2202 (2022).
pubmed: 35113647 doi: 10.1126/sciimmunol.abo2202
Sun, J. et al. Generation of a broadly useful model for COVID-19 pathogenesis, vaccination, and treatment. Cell 182, 734–743.e735 (2020).
pubmed: 32643603 pmcid: 7284240 doi: 10.1016/j.cell.2020.06.010
McMahan, K. et al. Correlates of protection against SARS-CoV-2 in rhesus macaques. Nature 590, 630–634 (2021).
pubmed: 33276369 doi: 10.1038/s41586-020-03041-6
Soresina, A. et al. Two X-linked agammaglobulinemia patients develop pneumonia as COVID-19 manifestation but recover. Pediatr. Allergy Immunol. 31, 565–569 (2020).
pubmed: 32319118 pmcid: 7264678 doi: 10.1111/pai.13263
Bange, E. M. et al. CD8(+) T cells contribute to survival in patients with COVID-19 and hematologic cancer. Nat. Med. 27, 1280–1289 (2021).
pubmed: 34017137 pmcid: 8291091 doi: 10.1038/s41591-021-01386-7
Zhuang, Z. et al. Mapping and role of T cell response in SARS-CoV-2-infected mice. J. Exp. Med. 218, e20202187 (2021).
pubmed: 33464307 pmcid: 7814348 doi: 10.1084/jem.20202187
Israelow, B. et al. Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2. Sci. Immunol. 6, eabl4509 (2021).
pubmed: 34623900 pmcid: 9047536 doi: 10.1126/sciimmunol.abl4509
Rydyznski Moderbacher, C. et al. Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity. Cell 183, 996–1012.e1019 (2020).
pubmed: 33010815 pmcid: 7494270 doi: 10.1016/j.cell.2020.09.038
Nesterenko, P. A. et al. HLA-A(*)02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses. Cell Rep. 37, 110167 (2021).
pubmed: 34919800 pmcid: 8660260 doi: 10.1016/j.celrep.2021.110167
Le Bert, N. et al. Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection. J. Exp. Med. 218, e20202617 (2021).
pubmed: 33646265 pmcid: 7927662 doi: 10.1084/jem.20202617
Tan, C. C. S. et al. Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses. Infect. Genet. Evol. 95, 105075 (2021).
pubmed: 34509646 pmcid: 8428999 doi: 10.1016/j.meegid.2021.105075
Eggenhuizen, P. J. et al. Heterologous immunity between SARS-CoV-2 and pathogenic bacteria. Front. Immunol. 13, 821595 (2022).
pubmed: 35154139 pmcid: 8829141 doi: 10.3389/fimmu.2022.821595
Low, J. S. et al. Clonal analysis of immunodominance and cross-reactivity of the CD4 T cell response to SARS-CoV-2. Science 372, 1336–1341 (2021).
pubmed: 34006597 doi: 10.1126/science.abg8985
Sagar, M. et al. Recent endemic coronavirus infection is associated with less-severe COVID-19. J. Clin. Invest. 131, e143380 (2021).
pubmed: 32997649 pmcid: 7773342 doi: 10.1172/JCI143380
Humbert, M. et al. Functional SARS-CoV-2 cross-reactive CD4(+) T cells established in early childhood decline with age. Proc. Natl Acad. Sci. USA 120, e2220320120 (2023).
pubmed: 36917669 pmcid: 10041119 doi: 10.1073/pnas.2220320120
Zhao, J. et al. Airway memory CD4(+) T cells mediate protective immunity against emerging respiratory coronaviruses. Immunity 44, 1379–1391 (2016).
pubmed: 27287409 pmcid: 4917442 doi: 10.1016/j.immuni.2016.05.006
Poston, D. et al. Absence of severe acute respiratory syndrome coronavirus 2 neutralizing activity in prepandemic sera from individuals with recent seasonal coronavirus infection. Clin. Infect. Dis. 73, e1208–e1211 (2021).
pubmed: 33270134 doi: 10.1093/cid/ciaa1803
Ercanoglu, M. S. et al. No substantial preexisting B cell immunity against SARS-CoV-2 in healthy adults. iScience 25, 103951 (2022).
pubmed: 35224466 pmcid: 8857777 doi: 10.1016/j.isci.2022.103951
Pinto, D. et al. Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 373, 1109–1116 (2021).
pubmed: 34344823 pmcid: 9268357 doi: 10.1126/science.abj3321
Sun, X. et al. Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Nat. Microbiol. 7, 1063–1074 (2022).
pubmed: 35773398 doi: 10.1038/s41564-022-01155-3
Dacon, C. et al. Broadly neutralizing antibodies target the coronavirus fusion peptide. Science 377, 728–735 (2022).
pubmed: 35857439 doi: 10.1126/science.abq3773
Low, J. S. et al. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science 377, 735–742 (2022).
pubmed: 35857703 doi: 10.1126/science.abq2679
Anderson, E. M. et al. Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection. Cell 184, 1858–1864.e1810 (2021).
pubmed: 33631096 pmcid: 7871851 doi: 10.1016/j.cell.2021.02.010
Ng, K. W. et al. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 370, 1339–1343 (2020).
pubmed: 33159009 pmcid: 7857411 doi: 10.1126/science.abe1107
Poston, D et al. Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection. medRxiv https://doi.org/10.1101/2020.10.08.20209650 (2020).
Premkumar, L. et al. The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients. Sci. Immunol. 5, eabc8413 (2020).
pubmed: 32527802 pmcid: 7292505 doi: 10.1126/sciimmunol.abc8413
Grifoni, A. et al. Prior dengue virus exposure shapes T cell immunity to Zika Virus in humans. J. Virol. 91, e01469–17 (2017).
pubmed: 28978707 pmcid: 5709580 doi: 10.1128/JVI.01469-17
Wragg, K. M. et al. Establishment and recall of SARS-CoV-2 spike epitope-specific CD4(+) T cell memory. Nat. Immunol. 23, 768–780 (2022).
pubmed: 35314848 doi: 10.1038/s41590-022-01175-5
Francis, J. M. et al. Allelic variation in class I HLA determines CD8(+) T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2. Sci. Immunol. 7, eabk3070 (2022).
pubmed: 34793243
Heitmann, J. S. et al. A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity. Nature 601, 617–622 (2022).
pubmed: 34814158 doi: 10.1038/s41586-021-04232-5
Bastard, P. Why do people die from COVID-19? Science 375, 829–830 (2022).
pubmed: 35201875 doi: 10.1126/science.abn9649
Minervina, A. A. et al. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells. medRxiv https://doi.org/10.1101/2021.07.12.21260227 (2022).
Choi, H. et al. Protective immunity by an engineered DNA vaccine for Mayaro virus. PLoS Negl. Trop. Dis. 13, e0007042 (2019).
pubmed: 30730897 pmcid: 6366747 doi: 10.1371/journal.pntd.0007042
Vijgen, L. et al. Development of one-step, real-time, quantitative reverse transcriptase PCR assays for absolute quantitation of human coronaviruses OC43 and 229E. J. Clin. Microbiol. 43, 5452–5456 (2005).
pubmed: 16272469 pmcid: 1287813 doi: 10.1128/JCM.43.11.5452-5456.2005
Mendoza, E. J., Manguiat, K., Wood, H. & Drebot, M. Two detailed plaque assay protocols for the quantification of infectious SARS-CoV-2. Curr. Protoc. Microbiol. 57, ecpmc105 (2020).
pubmed: 32475066 doi: 10.1002/cpmc.105
Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 25, 2000045 (2020).
pubmed: 31992387 pmcid: 6988269 doi: 10.2807/1560-7917.ES.2020.25.3.2000045
Alexandersen, S., Chamings, A. & Bhatta, T. R. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat. Commun. 11, 6059 (2020).
pubmed: 33247099 pmcid: 7695715 doi: 10.1038/s41467-020-19883-7
Elong Ngono, A. et al. Mapping and role of the CD8(+) T cell response during primary Zika virus infection in mice. Cell Host Microbe 21, 35–46 (2017).
pubmed: 28081442 doi: 10.1016/j.chom.2016.12.010
Gruber, A. D. et al. Standardization of reporting criteria for lung pathology in SARS-CoV-2-infected hamsters: what matters? Am. J. Respir. Cell Mol. Biol. 63, 856–859 (2020).
pubmed: 32897757 pmcid: 7790148 doi: 10.1165/rcmb.2020-0280LE
Alves, R. SOURCE_DATA_NCOMMS-23-38557B_part9 [Data set]. Zenodo https://doi.org/10.5281/zenodo.10397796 , (2023).

Auteurs

Rúbens Prince Dos Santos Alves (RP)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Julia Timis (J)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Robyn Miller (R)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Kristen Valentine (K)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Paolla Beatriz Almeida Pinto (PBA)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Andrew Gonzalez (A)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Jose Angel Regla-Nava (JA)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico.

Erin Maule (E)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Michael N Nguyen (MN)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Norazizah Shafee (N)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Sara Landeras-Bueno (S)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Eduardo Olmedillas (E)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.

Brett Laffey (B)

Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.

Katarzyna Dobaczewska (K)

Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.

Zbigniew Mikulski (Z)

Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.

Sara McArdle (S)

Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.

Sarah R Leist (SR)

Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Kenneth Kim (K)

Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA.

Ralph S Baric (RS)

Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Erica Ollmann Saphire (E)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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.

Annie Elong Ngono (A)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA. aelong@lji.org.

Sujan Shresta (S)

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA. sujan@lji.org.

Classifications MeSH