PMID- 33521695
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220211
IS  - 2666-3791 (Electronic)
IS  - 2666-3791 (Linking)
VI  - 2
IP  - 2
DP  - 2021 Feb 16
TI  - Comprehensive analysis of T cell immunodominance and immunoprevalence of 
      SARS-CoV-2 epitopes in COVID-19 cases.
PG  - 100204
LID - 10.1016/j.xcrm.2021.100204 [doi]
LID - 100204
AB  - T cells are involved in control of SARS-CoV-2 infection. To establish the 
      patterns of immunodominance of different SARS-CoV-2 antigens and precisely 
      measure virus-specific CD4(+) and CD8(+) T cells, we study epitope-specific 
      T cell responses of 99 convalescent coronavirus disease 2019 (COVID-19) cases. 
      The SARS-CoV-2 proteome is probed using 1,925 peptides spanning the entire 
      genome, ensuring an unbiased coverage of human leukocyte antigen (HLA) alleles 
      for class II responses. For HLA class I, we study an additional 5,600 predicted 
      binding epitopes for 28 prominent HLA class I alleles, accounting for wide global 
      coverage. We identify several hundred HLA-restricted SARS-CoV-2-derived epitopes. 
      Distinct patterns of immunodominance are observed, which differ for CD4(+) 
      T cells, CD8(+) T cells, and antibodies. The class I and class II epitopes are 
      combined into epitope megapools to facilitate identification and quantification 
      of SARS-CoV-2-specific CD4(+) and CD8(+) T cells.
CI  - (c) 2021 The Author(s).
FAU - Tarke, Alison
AU  - Tarke A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Department of Internal Medicine and Center of Excellence for Biomedical Research 
      (CEBR), University of Genoa, Genoa 16132, Italy.
FAU - Sidney, John
AU  - Sidney J
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Kidd, Conner K
AU  - Kidd CK
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Dan, Jennifer M
AU  - Dan JM
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Ramirez, Sydney I
AU  - Ramirez SI
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Yu, Esther Dawen
AU  - Yu ED
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Mateus, Jose
AU  - Mateus J
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - da Silva Antunes, Ricardo
AU  - da Silva Antunes R
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Moore, Erin
AU  - Moore E
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Rubiro, Paul
AU  - Rubiro P
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Methot, Nils
AU  - Methot N
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Phillips, Elizabeth
AU  - Phillips E
AD  - Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 
      Australia.
FAU - Mallal, Simon
AU  - Mallal S
AD  - Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 
      Australia.
FAU - Frazier, April
AU  - Frazier A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Rawlings, Stephen A
AU  - Rawlings SA
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Greenbaum, Jason A
AU  - Greenbaum JA
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Peters, Bjoern
AU  - Peters B
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Smith, Davey M
AU  - Smith DM
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Crotty, Shane
AU  - Crotty S
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
FAU - Weiskopf, Daniela
AU  - Weiskopf D
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Grifoni, Alba
AU  - Grifoni A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
FAU - Sette, Alessandro
AU  - Sette A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology (LJI), La Jolla, CA 92037, USA.
AD  - Division of Infectious Diseases and Global Public Health, Department of Medicine, 
      University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
LA  - eng
GR  - 75N93019C00001/AI/NIAID NIH HHS/United States
GR  - T32 AI007036/AI/NIAID NIH HHS/United States
GR  - U01 CA260541/CA/NCI NIH HHS/United States
GR  - T32 AI007384/AI/NIAID NIH HHS/United States
GR  - P30 AI036214/AI/NIAID NIH HHS/United States
GR  - K08 AI135078/AI/NIAID NIH HHS/United States
GR  - U19 AI142742/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20210126
PL  - United States
TA  - Cell Rep Med
JT  - Cell reports. Medicine
JID - 101766894
UOF - bioRxiv. 2020 Dec 09;:. PMID: 33330869
PMC - PMC7837622
OTO - NOTNLM
OT  - CD4+T cells
OT  - CD8+ T cells
OT  - COVID-19
OT  - HLA
OT  - SARS-CoV-2
OT  - T cells
OT  - epitopes
COIS- A.S. is a consultant for Gritstone, Flow Pharma, Merck, Epitogenesis, Gilead, and 
      Avalia. S.C. is a consultant for Avalia. All other authors declare no competing 
      interests. LJI has filed for patent protection for various aspects of vaccine 
      design and identification of specific epitopes.
EDAT- 2021/02/02 06:00
MHDA- 2021/02/02 06:01
PMCR- 2021/01/26
CRDT- 2021/02/01 06:03
PHST- 2020/11/18 00:00 [received]
PHST- 2020/12/17 00:00 [revised]
PHST- 2021/01/20 00:00 [accepted]
PHST- 2021/02/02 06:00 [pubmed]
PHST- 2021/02/02 06:01 [medline]
PHST- 2021/02/01 06:03 [entrez]
PHST- 2021/01/26 00:00 [pmc-release]
AID - S2666-3791(21)00015-X [pii]
AID - 100204 [pii]
AID - 10.1016/j.xcrm.2021.100204 [doi]
PST - ppublish
SO  - Cell Rep Med. 2021 Feb 16;2(2):100204. doi: 10.1016/j.xcrm.2021.100204. Epub 2021 
      Jan 26.