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Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
by
Swadling, Leo
, Schmidt, Nathalie M.
, Jensen, Melanie P.
, Moon, James C.
, Boyton, Rosemary J.
, Treibel, Thomas A.
, McKnight, Áine
, McCoy, Laura E.
, Joy, George
, Valdes, Ana M.
, Johnson, Marina
, Le Bert, Nina
, Balloux, Francois
, Tan, Cedric C. S.
, Davies, Jessica
, Maini, Mala K.
, Chandran, Aneesh
, Goldblatt, David
, Manisty, Charlotte
, Pade, Corinna
, Jeffery-Smith, Anna
, Aidoo-Micah, Gloryanne
, Altmann, Daniel M.
, Shaw, Emily
, Gibbons, Joseph M.
, van Dorp, Lucy
, Amin, Oliver E.
, Tham, Christine Y. L.
, Bertoletti, Antonio
, Noursadeghi, Mahdad
, Tan, Anthony T.
, Diniz, Mariana O.
, Rosenheim, Joshua
, Chain, Benjamin M.
, Kucykowicz, Stephanie
in
13/1
/ 13/106
/ 13/31
/ 631/250/1619/554
/ 631/250/2152/1566/1571
/ 631/250/254
/ 631/326/596/4130
/ 82/75
/ Antibodies
/ Asymptomatic Infections
/ Cell Proliferation
/ Cohort Studies
/ Conservation
/ Conserved sequence
/ Coronaviridae
/ Coronaviruses
/ COVID-19
/ COVID-19 - immunology
/ COVID-19 - virology
/ Cytomegalovirus
/ Diagnostic tests
/ DNA-directed RNA polymerase
/ DNA-Directed RNA Polymerases - immunology
/ DNA-Directed RNA Polymerases - metabolism
/ Epitopes
/ Epstein-Barr virus
/ Evolution, Molecular
/ Female
/ Health Personnel
/ Hepatitis
/ Humanities and Social Sciences
/ Humans
/ Immunological memory
/ Infections
/ Influenza
/ Laboratories
/ Lymphocytes
/ Lymphocytes T
/ Male
/ Medical personnel
/ Membrane Proteins - immunology
/ Memory cells
/ Memory T Cells - cytology
/ Memory T Cells - immunology
/ multidisciplinary
/ Multienzyme Complexes - immunology
/ Neutralization
/ Nucleotide sequence
/ Pandemics
/ Peptides
/ Polymerase chain reaction
/ Proteins
/ Respiratory diseases
/ RNA polymerase
/ SARS-CoV-2 - enzymology
/ SARS-CoV-2 - growth & development
/ SARS-CoV-2 - immunology
/ Science
/ Science (multidisciplinary)
/ Seroconversion
/ Severe acute respiratory syndrome coronavirus 2
/ Subclinical infection
/ Transcription
/ Transcription, Genetic - immunology
/ Viral diseases
2022
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Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
by
Swadling, Leo
, Schmidt, Nathalie M.
, Jensen, Melanie P.
, Moon, James C.
, Boyton, Rosemary J.
, Treibel, Thomas A.
, McKnight, Áine
, McCoy, Laura E.
, Joy, George
, Valdes, Ana M.
, Johnson, Marina
, Le Bert, Nina
, Balloux, Francois
, Tan, Cedric C. S.
, Davies, Jessica
, Maini, Mala K.
, Chandran, Aneesh
, Goldblatt, David
, Manisty, Charlotte
, Pade, Corinna
, Jeffery-Smith, Anna
, Aidoo-Micah, Gloryanne
, Altmann, Daniel M.
, Shaw, Emily
, Gibbons, Joseph M.
, van Dorp, Lucy
, Amin, Oliver E.
, Tham, Christine Y. L.
, Bertoletti, Antonio
, Noursadeghi, Mahdad
, Tan, Anthony T.
, Diniz, Mariana O.
, Rosenheim, Joshua
, Chain, Benjamin M.
, Kucykowicz, Stephanie
in
13/1
/ 13/106
/ 13/31
/ 631/250/1619/554
/ 631/250/2152/1566/1571
/ 631/250/254
/ 631/326/596/4130
/ 82/75
/ Antibodies
/ Asymptomatic Infections
/ Cell Proliferation
/ Cohort Studies
/ Conservation
/ Conserved sequence
/ Coronaviridae
/ Coronaviruses
/ COVID-19
/ COVID-19 - immunology
/ COVID-19 - virology
/ Cytomegalovirus
/ Diagnostic tests
/ DNA-directed RNA polymerase
/ DNA-Directed RNA Polymerases - immunology
/ DNA-Directed RNA Polymerases - metabolism
/ Epitopes
/ Epstein-Barr virus
/ Evolution, Molecular
/ Female
/ Health Personnel
/ Hepatitis
/ Humanities and Social Sciences
/ Humans
/ Immunological memory
/ Infections
/ Influenza
/ Laboratories
/ Lymphocytes
/ Lymphocytes T
/ Male
/ Medical personnel
/ Membrane Proteins - immunology
/ Memory cells
/ Memory T Cells - cytology
/ Memory T Cells - immunology
/ multidisciplinary
/ Multienzyme Complexes - immunology
/ Neutralization
/ Nucleotide sequence
/ Pandemics
/ Peptides
/ Polymerase chain reaction
/ Proteins
/ Respiratory diseases
/ RNA polymerase
/ SARS-CoV-2 - enzymology
/ SARS-CoV-2 - growth & development
/ SARS-CoV-2 - immunology
/ Science
/ Science (multidisciplinary)
/ Seroconversion
/ Severe acute respiratory syndrome coronavirus 2
/ Subclinical infection
/ Transcription
/ Transcription, Genetic - immunology
/ Viral diseases
2022
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Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
by
Swadling, Leo
, Schmidt, Nathalie M.
, Jensen, Melanie P.
, Moon, James C.
, Boyton, Rosemary J.
, Treibel, Thomas A.
, McKnight, Áine
, McCoy, Laura E.
, Joy, George
, Valdes, Ana M.
, Johnson, Marina
, Le Bert, Nina
, Balloux, Francois
, Tan, Cedric C. S.
, Davies, Jessica
, Maini, Mala K.
, Chandran, Aneesh
, Goldblatt, David
, Manisty, Charlotte
, Pade, Corinna
, Jeffery-Smith, Anna
, Aidoo-Micah, Gloryanne
, Altmann, Daniel M.
, Shaw, Emily
, Gibbons, Joseph M.
, van Dorp, Lucy
, Amin, Oliver E.
, Tham, Christine Y. L.
, Bertoletti, Antonio
, Noursadeghi, Mahdad
, Tan, Anthony T.
, Diniz, Mariana O.
, Rosenheim, Joshua
, Chain, Benjamin M.
, Kucykowicz, Stephanie
in
13/1
/ 13/106
/ 13/31
/ 631/250/1619/554
/ 631/250/2152/1566/1571
/ 631/250/254
/ 631/326/596/4130
/ 82/75
/ Antibodies
/ Asymptomatic Infections
/ Cell Proliferation
/ Cohort Studies
/ Conservation
/ Conserved sequence
/ Coronaviridae
/ Coronaviruses
/ COVID-19
/ COVID-19 - immunology
/ COVID-19 - virology
/ Cytomegalovirus
/ Diagnostic tests
/ DNA-directed RNA polymerase
/ DNA-Directed RNA Polymerases - immunology
/ DNA-Directed RNA Polymerases - metabolism
/ Epitopes
/ Epstein-Barr virus
/ Evolution, Molecular
/ Female
/ Health Personnel
/ Hepatitis
/ Humanities and Social Sciences
/ Humans
/ Immunological memory
/ Infections
/ Influenza
/ Laboratories
/ Lymphocytes
/ Lymphocytes T
/ Male
/ Medical personnel
/ Membrane Proteins - immunology
/ Memory cells
/ Memory T Cells - cytology
/ Memory T Cells - immunology
/ multidisciplinary
/ Multienzyme Complexes - immunology
/ Neutralization
/ Nucleotide sequence
/ Pandemics
/ Peptides
/ Polymerase chain reaction
/ Proteins
/ Respiratory diseases
/ RNA polymerase
/ SARS-CoV-2 - enzymology
/ SARS-CoV-2 - growth & development
/ SARS-CoV-2 - immunology
/ Science
/ Science (multidisciplinary)
/ Seroconversion
/ Severe acute respiratory syndrome coronavirus 2
/ Subclinical infection
/ Transcription
/ Transcription, Genetic - immunology
/ Viral diseases
2022
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Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
Journal Article
Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
2022
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Overview
Individuals with potential exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) do not necessarily develop PCR or antibody positivity, suggesting that some individuals may clear subclinical infection before seroconversion. T cells can contribute to the rapid clearance of SARS-CoV-2 and other coronavirus infections
1
–
3
. Here we hypothesize that pre-existing memory T cell responses, with cross-protective potential against SARS-CoV-2 (refs.
4
–
11
), would expand in vivo to support rapid viral control, aborting infection. We measured SARS-CoV-2-reactive T cells, including those against the early transcribed replication–transcription complex (RTC)
12
,
13
, in intensively monitored healthcare workers (HCWs) who tested repeatedly negative according to PCR, antibody binding and neutralization assays (seronegative HCWs (SN-HCWs)). SN-HCWs had stronger, more multispecific memory T cells compared with a cohort of unexposed individuals from before the pandemic (prepandemic cohort), and these cells were more frequently directed against the RTC than the structural-protein-dominated responses observed after detectable infection (matched concurrent cohort). SN-HCWs with the strongest RTC-specific T cells had an increase in
IFI27
, a robust early innate signature of SARS-CoV-2 (ref.
14
), suggesting abortive infection. RNA polymerase within RTC was the largest region of high sequence conservation across human seasonal coronaviruses (HCoV) and SARS-CoV-2 clades. RNA polymerase was preferentially targeted (among the regions tested) by T cells from prepandemic cohorts and SN-HCWs. RTC-epitope-specific T cells that cross-recognized HCoV variants were identified in SN-HCWs. Enriched pre-existing RNA-polymerase-specific T cells expanded in vivo to preferentially accumulate in the memory response after putative abortive compared to overt SARS-CoV-2 infection. Our data highlight RTC-specific T cells as targets for vaccines against endemic and emerging
Coronaviridae
.
Seronegative healthcare workers with an innate signature of infection preferentially expand pre-existing T cells targeting the conserved replication transcription complex of SARS-CoV-2 in abortive infection.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ 13/106
/ 13/31
/ 82/75
/ COVID-19
/ DNA-Directed RNA Polymerases - immunology
/ DNA-Directed RNA Polymerases - metabolism
/ Epitopes
/ Female
/ Humanities and Social Sciences
/ Humans
/ Male
/ Membrane Proteins - immunology
/ Multienzyme Complexes - immunology
/ Peptides
/ Proteins
/ SARS-CoV-2 - growth & development
/ Science
/ Severe acute respiratory syndrome coronavirus 2
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