Science - USA (2020-10-02)

3. I. Martincorenaet al.,Science 362 , 911–917 (2018).


4. C. Tomasetti, B. Vogelstein, G. Parmigiani,Proc. Natl. Acad.
   Sci. U.S.A. 110 , 1999–2004 (2013).


5. M. R. Stratton, P. J. Campbell, P. A. Futreal,Nature 458 ,
   719 – 724 (2009).


6. M. Greaves, C. C. Maley,Nature 481 , 306–313 (2012).


7. K. A. Hoadleyet al.,Cell 173 , 291–304.e6 (2018).


8. I. Martincorenaet al.,Science 348 , 880–886 (2015).


9. A. Yokoyamaet al.,Nature 565 , 312–317 (2019).


10. H. Lee-Sixet al.,Nature 574 , 532–537 (2019).


11. S. F. Brunneret al.,Nature 574 , 538–542 (2019).


12. L. Mooreet al.,Nature 580 , 640–646 (2020).


13. K. Yoshidaet al.,Nature 578 , 266–272 (2020).


14. T. Baeet al.,Science 359 , 550–555 (2018).


15. M. A. Lodatoet al.,Science 359 , 555–559 (2018).


16. Y. S. Juet al.,Nature 543 , 714–718 (2017).


17. H. Lee-Sixet al.,Nature 561 , 473–478 (2018).


18. K. Yizhaket al.,Science 364 , eaaw0726 (2019).


19. P. E. García-Nieto, A. J. Morrison, H. B. Fraser,Genome Biol.
    20 , 298 (2019).


20. D. E. Brashet al.,Proc. Natl. Acad. Sci. U.S.A. 88 , 10124– 10128
    (1991).


21. A. Ziegleret al.,Nature 372 , 773–776 (1994).


22. S. C. Baker, J. Southgate, inElectrospinning for Tissue
    Regeneration, L. A. Bosworth, S. Downes, Eds. (Woodhead
    Publishing Series in Biomaterials, Woodhead Publishing, 2011),
    pp. 225–241.


23. C. Varleyet al.,Exp. Cell Res. 306 , 216–229 (2005).


24. G. Guoet al.,Nat. Genet. 45 , 1459–1463 (2013).


25. A. G. Robertsonet al.,Cell 171 , 540–556.e25 (2017).


26. Cancer Genome Atlas Research Network,Nature 507 , 315– 322
    (2014).


27. J. Michl, M. J. Ingrouille, M. S. Simmonds, M. Heinrich,
    Nat. Prod. Rep. 31 , 676–693 (2014).


28. U. Mengs,Arch. Toxicol. 61 , 504–505 (1988).


29. A. W. T. Nget al.,Sci. Transl. Med. 9 , eaan6446 (2017).


30. Y. Duet al.,Eur. Urol. 71 , 841–843 (2017).


31. S. L. Poonet al.,Genome Med. 7 , 38 (2015).


32. L. B. Alexandrovet al.,Nature 500 , 415–421 (2013).


33. L. B. Alexandrovet al.,Nature 578 , 94–101 (2020).


34. C. H. Chenet al.,Int. J. Cancer 133 , 14–20 (2013).


35. Cancer Genome Atlas Network,Nature 487 , 330– 337
    (2012).


36. C. Kandothet al.,Nature 497 , 67–73 (2013).


37. S. Nik-Zainalet al.,Cell 149 , 994–1007 (2012).


38. I. Martincorenaet al.,Cell 171 , 1029–1041.e21 (2017).


39. M. B. H. Thomsenet al.,Sci. Rep. 7 , 11702 (2017).


40. T. Majewskiet al.,Cell Rep. 26 , 2241–2256.e4 (2019).


41. A. R. J. Lawsonet al.,Science 370 , 75–82 (2020).
    42.L.Vaclavik,A.J.Krynitsky,J.I.Rader,Food Addit. Contam.
    Part A Chem. Anal. Control Expo. Risk Assess. 31 , 784– 791
    (2014).


42. H. Y. Yang, P. C. Chen, J. D. Wang,BioMed Res. Int. 2014 ,
    569325 (2014).


43. T. P. Cheung, C. Xue, K. Leung, K. Chan, C. G. Li,Clin. Toxicol.
    44 , 371–378 (2006).


44. M. N. Lai, S. M. Wang, P. C. Chen, Y. Y. Chen, J. D. Wang,
    J. Natl. Cancer Inst. 102 , 179–186 (2010).


45. K. Shinet al.,Nat. Cell Biol. 16 , 469–478 (2014).


46. J. J. Salket al.,Cell Rep. 28 , 132–144.e3 (2019).


47. R. Liet al., supplementary of UTUC-Normal, Version V1,
    Zenodo (2020); https://doi.org/10.5281/zenodo.3966801.


48. R. Liet al., supplementary of UTUC-Normal 2, Version V1,
    Zenodo (2020); https://doi.org/10.5281/zenodo.3726413.

ACKNOWLEDGMENTS
We thank all the patients for their consent and participation in this
study. We thank X. M. Wang from Peking University for the helpful
discussion on mutational signature analysis. We thank T. S. Sun
from Peking University for helping create the bladder cartoon.
Funding:This work was financially supported by the National Key
Research and Development Program (2018YFA0902802), the
National Science and Technology Major Project (2018ZX10302205
and 2019YFC1315702), the National Natural Science Foundation of
China (31722003, 31770925, and 81802533), the Guangdong
Province Key Research and Development Program
(2019B020226002), and the Beijing Municipal Science and
Technology Commission (Z191100006619010). R.L. was funded by
the BoYa Postdoctoral Fellowship of Peking University.Author
contributions:F.B., T.X., R.L., Y.D., Z.C., and D.X. designed the
experiments. R.L. led the data analysis with help from Z.C. and Z.L. Y.D.,
T.L., and X.C. collected the samples with help from G.W. Y.D.,
M.L., and G.W. performed pathological examinations. Z.C. and D.X.

performed experiments with help from S.J. and Y.D. R.L. and F.B.

wrote the manuscript with help from Y.D.Competing interests:

The authors declare no competing interests.Data and materials

availability:The sequencing raw data generated in this study have

been deposited in the Genome Sequence Archive (GSA) in BIG

Data Center (https://bigd.big.ac.cn), Beijing Institute of Genomics

(BIG), Chinese Academy of Sciences, under accession number

HRA000137 (https://bigd.big.ac.cn/gsa-human/s/A88e89NG).

Data from the Chinese bladder cancer study that were used in the

MutSigCV analysis are deposited in the Sequence Read Archive

(SRA) (www.ncbi.nlm.nih.gov/sra) under accession number

SRA063495 ( 24 ). The input data for Sequenza, ReCapSeq,

ABSOLUTE, mutational signature analysis, Dirichlet process

analysis, and VCF files of all somatic mutations; the raw outputs

from Sequenza, ABSOLUTE, and Dirichlet process analysis;

and the code for Dirichlet process analysis are all available at

Zenodo ( 48 , 49 ).

SUPPLEMENTARY MATERIALS

science.sciencemag.org/content/370/6512/82/suppl/DC1

Materials and Methods

Figs. S1 to S11

Tables S1 to S15

References ( 50 – 65 )

MDAR Reproducibility Checklist

30 December 2019; accepted 4 August 2020

10.1126/science.aba7300

CORONAVIRUS

Selective and cross-reactive SARS-CoV-2 T cell

epitopes in unexposed humans

Jose Mateus^1 , Alba Grifoni^1 , Alison Tarke^1 , John Sidney^1 , Sydney I. Ramirez1,3, Jennifer M. Dan1,3,

Zoe C. Burger^3 , Stephen A. Rawlings^3 , Davey M. Smith^3 , Elizabeth Phillips^2 , Simon Mallal^2 ,

Marshall Lammers^1 , Paul Rubiro^1 , Lorenzo Quiambao^1 , Aaron Sutherland^1 , Esther Dawen Yu^1 ,

Ricardo da Silva Antunes^1 , Jason Greenbaum^1 , April Frazier^1 , Alena J. Markmann^4 ,

Lakshmanane Premkumar^5 , Aravinda de Silva^5 , Bjoern Peters1,3, Shane Crotty1,3,

Alessandro Sette1,3*†, Daniela Weiskopf^1 *†

Many unknowns exist about human immune responses to the severe acute respiratory syndrome

coronavirus 2 (SARS-CoV-2) virus. SARS-CoV-2–reactive CD4+T cells have been reported in

unexposed individuals, suggesting preexisting cross-reactive T cell memory in 20 to 50% of people.

However, the source of those T cells has been speculative. Using human blood samples derived

before the SARS-CoV-2 virus was discovered in 2019, we mapped 142 T cell epitopes across the

SARS-CoV-2 genome to facilitate precise interrogation of the SARS-CoV-2–specific CD4+T cell

repertoire. We demonstrate a range of preexisting memory CD4+T cells that are cross-reactive

with comparable affinity to SARS-CoV-2 and the common cold coronaviruses human coronavirus

(HCoV)-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Thus, variegated T cell memory to

coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity

observed in coronavirus disease 2019 (COVID-19) disease.

T

he emergence of severe acute respiratory

syndrome coronavirus 2 (SARS-CoV-2)

in late 2019 and its subsequent global

spread has led to millions of infections

and substantial morbidity and mortal-

ity ( 1 ). Coronavirus disease 2019 (COVID-19),

the clinical disease caused by SARS-CoV-2 in-

fection, can range from mild, self-limiting dis-

ease to acute respiratory distress syndrome

and death ( 2 ). The mechanisms underlying

the spectrum of COVID-19 disease severity

states and the nature of protective immunity

against COVID-19 remain unclear.

Studies investigating the human immune

response against SARS-CoV-2 have begun to

characterize SARS-CoV-2 antigen-specific

T cell responses ( 3 – 8 ), and multiple studies

have described marked activation of T cell

subsets in acute COVID-19 patients ( 9 – 13 ).

Unexpectedly, antigen-specific T cell studies

performed with five different cohorts reported

that 20 to 50% of people who had not been

exposed to SARS-CoV-2 had significant T cell

reactivity directed against peptides correspond-

ing to SARS-CoV-2 sequences ( 3 – 7 ). The studies

were from geographically diverse cohorts

(the United States, the Netherlands, Germany,

Singapore, and the United Kingdom), and the

general pattern observed was that the T cell

reactivity found in unexposed individuals was

predominantly mediated by CD4+T cells. It

was speculated that this phenomenon might

be due to preexisting memory responses against

humanÒcommon coldÓcoronaviruses (HCoVs)

such as HCoV-OC43, HCoV-HKU1, HCoV-NL63,

and HCoV-229E. These HCoVs share partial

sequence homology with SARS-CoV-2, are

SCIENCEsciencemag.org 2 OCTOBER 2020•VOL 370 ISSUE 6512 89

(^1) Center for Infectious Disease and Vaccine Research, La Jolla
Institute for Immunology, La Jolla, CA 92037, USA.^2 Institute
for Immunology and Infectious Diseases, Murdoch University,
Perth, WA 6150, Australia.^3 Department of Medicine, Division
of Infectious Diseases and Global Public Health, University of
California, San Diego, La Jolla, CA 92037, USA.^4 Department
of Medicine, Division of Infectious Diseases, University of
North Carolina School of Medicine, Chapel Hill, NC 27599,
USA.^5 Department of Microbiology and Immunology,
University of North Carolina School of Medicine, Chapel
Hill, NC 27599, USA.
*Corresponding author. Email: [email protected] (A.S.); daniela@lji.
org (D.W.)†These authors contributed equally to this work.
RESEARCH | RESEARCH ARTICLES