Distinct T Cell Functional Profiles in Sars-Cov-2 Seropositive and Seronegative Children Associated with Endemic Human Coronavirus Cross-Reactivity

SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on SARS-CoV-2 antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.Funding Information: This work is supported by the South African Medical Research Council (SA-MRC) with funds received from the South African Department of Science and Innovation (DSI), (grants 96825, SHIPNCD 76756, and DST/CON 0250/2012), the Poliomyelitis Research Foundation (21/65) and the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). SA-MRC to R.S.K. UK NIHR GECO award (GEC111 to H.J.Z), the Bill & Melinda Gates Foundation, USA (grants OPP1017641, OPP1017579 to H.J.Z). P.L.M. is supported by the South African Research Chairs Initiative of the Department of Science and Innovation and National Research Foundation of South Africa (NRF 9834), the SA-MRC SHIP programme and the Centre for the AIDS Programme of Research in South Africa (CAPRISA). C.R. is supported by the EDCTP2 program of the European Union’s Horizon 2020 programme (TMA2017SF-1951-TB-SPEC), the Wellcome Trust (226137/Z/22/Z) and the National Institutes of Health (NIH) (R21AI148027). W.A.B. is supported by the EDCTP2 program of the European Union’s Horizon 2020 programme (TMA2016SF-1535-CaTCH-22), the Wellcome Trust (226137/Z/22/Z) and the EU-Africa Concerted Action on SARS-CoV-2 Virus Variant and Immunological Surveillance (COVICIS), funded through the EU’s Horizon Europe Research and Innovation Programme (101046041). H.J.Z is supported by the SA-MRC. This work was supported by the Crick African Network (CAN), through a fellowship to K.W. This fellowship funded K.W’s salary and study consumables. The CAN receives its funding from the UK’s Global Challenges Research Fund (MR/P028071/1), and by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC1001647), the UK Medical Research Council (FC1001647), and the Wellcome Trust (FC1001647). For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. T.F.S is supported by the DSI/NRF Innovation (PDP) postdoctoral fellowship. This work was also funded by a grant from the Wellcome CIDRI through a rapid COVID grant given to L.Z. and K.W., K.W. is supported by the SA-MRC with funds received from National Treasury. L.Z. is funded by the SA-MRC through its Division of Research Capacity Development under the Mid-Career Scientist Programme from funding received from the South African National Treasury. The content hereof is the sole responsibility of the authors and do not necessarily represent the official views of the SA-MRC. L.Z. also receives support from the National Research Foundation of South Africa (NRF), as well as the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement, via the African Research Leader Award (MR/S005242/1). Declaration of Interests: The authors have no competing interests. Ethical Approval Statement: The first cohort enrolled 50 children from the Red Cross War Memorial Children’s Hospital (Cape Town, Western Cape, South Africa). This study is approved by University of Cape Town Human Research Ethics Committee as a Paediatric Immunology Biorepository (UCT HREC 112/2012) and MIS-C substudy (UCT HREC 599/2020).A further 21 children were enrolled from the Drakenstein Child Health Study (DCHS) (Cape Winelands Western Cape, South Africa), a birth cohort study. The participants from this study were recruited between 1 February 2021 and 20 May 2021, after the first and the second infection waves with Ancestral strain and Beta variant in South Africa. The study was approved by the University of Cape Town Human Research Ethics Committee and renewed annually (HREC 401/2009). Parents or legal guardians provided written informed consent for all paediatric participants. COVID-19 convalescent unvaccinated adults from a longitudinal study of healthcare workers (HCW) enrolled from Groote Schuur Hospital (Cape Town, Western Cape, South Africa) were included in the study (n=30). HCW in this cohort were recruited between July 2020 and January 2021 and were selected for inclusion based on a prior PCR-confirmed SARS-CoV-2 infection at least 3 months earlier. All participants were asymptomatic or had mild symptoms and did not require hospitalization for COVID-19 and were symptom-free at the time of sampling. Written informed consent was obtained from all participants and the study was approved by the University of Cape Town Human Research Ethics Committee (HREC 190/2020 and 209/2020).