{"doi":"10.1016/j.isci.2023.106937","title":"Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection","abstract":"T cell responses precede antibody and may provide early control of infection. We analyzed the clonal basis of this rapid response following SARS-COV-2 infection. We applied T cell receptor (TCR) sequencing to define the trajectories of individual T cell clones immediately. In SARS-COV-2 PCR+ individuals, a wave of TCRs strongly but transiently expand, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains but not with circulating human coronaviruses. Many expanding CDR3s were present at high frequency in pre-pandemic repertoires. Early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the preinfection naive repertoire. High-frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.","journal":"iScience","year":2023,"id":336263,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":19,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9478,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":106072,"name":"Yanchun Peng","orcid":"0000-0003-2340-0499","position":1,"is_corresponding":false},{"id":991127,"name":"Cedric Tan","orcid":"0000-0003-3536-8465","position":2,"is_corresponding":false},{"id":991128,"name":"Michal Mark","orcid":"0000-0002-7083-4364","position":3,"is_corresponding":false},{"id":991129,"name":"Gayathri Nageswaran","orcid":"0009-0005-7449-0924","position":4,"is_corresponding":false},{"id":465014,"name":"Suzanne Byrne","orcid":"0000-0001-7059-9774","position":5,"is_corresponding":false},{"id":991130,"name":"Tahel Ronel","orcid":"0000-0002-9513-9181","position":6,"is_corresponding":false},{"id":991554,"name":"Tom Peacock","orcid":null,"position":7,"is_corresponding":false},{"id":991131,"name":"Andreas Mayer","orcid":"0000-0002-6643-7622","position":8,"is_corresponding":false},{"id":342629,"name":"Aneesh Chandran","orcid":"0000-0003-1027-2862","position":9,"is_corresponding":false},{"id":991132,"name":"Joshua Rosenheim","orcid":"0000-0003-0171-2053","position":10,"is_corresponding":false},{"id":1461,"name":"Matthew V. X. Whelan","orcid":"0000-0003-0441-3358","position":11,"is_corresponding":false},{"id":550373,"name":"Xuan Yao","orcid":"0000-0001-9237-0380","position":12,"is_corresponding":false},{"id":106073,"name":"Guihai Liu","orcid":"0009-0003-3684-4870","position":13,"is_corresponding":false},{"id":625328,"name":"Suet Ling Felce","orcid":"0000-0001-8534-1629","position":14,"is_corresponding":false},{"id":106116,"name":"Tao Dong","orcid":"0000-0003-3545-3758","position":15,"is_corresponding":false},{"id":83854,"name":"Alexander J. Mentzer","orcid":"0000-0002-4502-2209","position":16,"is_corresponding":false},{"id":83924,"name":"Julian C. 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