Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children

SARS-CoV-2 infection triggers adaptive immune responses from both T and B cells. However, most studies focus on peripheral blood, which may not fully reflect immune responses in lymphoid tissues at the site of infection. To evaluate both local and systemic adaptive immune responses to SARS-CoV-2, we collected peripheral blood, tonsils, and adenoids from 110 children undergoing tonsillectomy/adenoidectomy during the COVID-19 pandemic. In order to investigate the adaptive immune response locally, we measured the neutralizing antibodies against to multiple SARS-CoV-2 virus variants and performed high dimensional flow cytometry and CITEseq including TCR and BCR analysis for deeper characterization of the immune response to SARS-CoV-2. In our CITE-seq analyses, we sorted SARS-CoV-2 S1 (spike 1) binding (Spike1+) and non-binding (Spike1-) CD19+ B cells from tonsils, adenoids, and PBMCs from two subjects with a history of COVID-19 and one uninfected control. To assess T cells at the single cell level, we sorted CD95+ CD4+ and CD95+ CD8+ T cells, identified expanded T cell clonotypes, and then compared the CDR3 sequences to those previously reported to recognize SARS-CoV-2 antigens. Our results provide evidence for persistent tissue-specific immunity to SARS-CoV-2 in the upper respiratory tract of children weeks to months after acute infection. Overall design: Adenoid cells, tonsil cells, and PBMC from 2 COVID-19 convalescent children and 1 uninfected pediatric control were profiled using multi-modal single cell RNAseq including surface protein staining (customized BioLegend TotalSeq-C lyophilized panel), mRNA expression, T cell receptor V(D)J genes, and B cell receptor V(D)J genes using the 10x Genomics Chromium system. The assignment of individual cells to a donor and tissue was done antibody hashtags. CNMC 89 - COVID-19 convalescent child CNMC 71 - COVID-19 convalescent child CNMC 99 - uninfected pediatric control