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This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

Germinal centres (GC) are lymphoid structures where B cells acquire affinity-enhancing somatic hypermutations (SHM), with surviving clones differentiating into memory B cells (MBCs) and long-lived bone marrow plasma cells (BMPCs) [1][2][3][4][5] . SARS-CoV-2 mRNA vaccination induces a persistent GC response that lasts for at least six months in humans [6][7][8] . The fate of responding GC B cells as well as the functional consequences of such persistence have not been elucidated. We detected SARS-CoV-2 spike (S)-specific MBCs in 42 individuals who had received two doses of BNT162b2, a SARS-CoV-2 mRNA vaccine six months earlier. S-specific IgG-secreting BMPCs were detected in 9 out of 11 participants. Using a combined approach of sequencing the B cell receptors of responding blood plasmablasts and MBCs, lymph node GC and plasma cells and BMPCs from eight individuals and expression of the corresponding monoclonal antibodies (mAbs), we tracked the evolution of 1540 S-specific B cell clones. We show that early blood S-specific plasmablasts -on averageexhibited the lowest SHM frequencies. In comparison, SHM frequencies of S-specific GC B cells increased by 3.5-fold within six months after vaccination. S-specific MBCs and BMPCs accumulated high levels of SHM, which corresponded with enhanced anti-S antibody avidity in blood and affinity as well as neutralization capacity of BMPC-derived mAbs. This study documents how the striking persistence of SARS-CoV-2 vaccination-induced GC reaction in humans culminates in affinity-matured long-term antibody responses that potently neutralize the virus. B cell response to mRNA vaccinationWe have previously shown that vaccination of humans with The Pfizer-BioNTech SARS-CoV-2 mRNA vaccine, BNT162b2 induces a robust but transient circulating plasmablast (PB) response and a persistent germinal centre (GC) reaction in the draining lymph nodes 6 . Whether these persistent GC responses lead to the generation of affinity-matured memory B cells (MBCs) and long-lived bone marrow-resident plasma cells (BMPCs) remains unclear. To address this question, we analyzed long-term B cell responses in the participants enrolled in our previously described observational study of 43 healthy participants (13 with a history of SARS-CoV-2 infection) who received two doses of BNT162b2 (Extended Data Tables 1) 6,7 . Long-term blood samples (n=42) and fine needle aspirates (FNAs) of the draining axillary lymph nodes (n=15) were collected 29 weeks post-vaccination (Fig. 1a). Bone marrow aspirates were collected 29 (n=11) and 40 weeks (n=2) post-vaccination, with the latter time point used only for B cell receptor (BCR) repertoire profiling (Fig. 1a). None of the participants who contributed FNA or bone marrow specimens had SARS-CoV-2 infection history. GC B cells were detected in FNAs from all 15 participants (Fig. 1b, c, left panels, Extended Data Fig. 1a, Extended Data Table 2). All 14 participants with FNAs collected prior to week 29 generated S-binding GC B cell responses of varying magnitudes (Fig 1b, c, r...

SARS-CoV-2 mRNA vaccines induce robust anti-spike (S) antibody and CD4 + T cell responses. It is not yet clear whether vaccine-induced follicular helper CD4 + T (T FH ) cell responses contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we evaluated the T cell receptor sequences and phenotype of lymph node T FH . Mining of the responding T FH T cell receptor repertoire revealed a strikingly immunodominant HLA-DPB1 ∗ 04-restricted response to S 167-180 in individuals with this allele, which is among the most common HLA alleles in humans. Paired blood and lymph node specimens show that while circulating S-specific T FH cells peak one week after the second immunization, S-specific T FH persist at nearly constant frequencies for at least six months. Collectively, our results underscore the key role that robust T FH cell responses play in establishing long-term immunity by this efficacious human vaccine.

SARS-CoV-2 mRNA vaccines generate high and persistent levels of circulating anti-spike (S) antibodies and S-specific CD4+ T cells following prime-boost vaccination. It is not yet clear whether vaccine-induced follicular helper CD4+ T (TFH) cell responses in the draining lymph nodes contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we show that frequency of TFH correlates with that of S-binding germinal center B cells. Mining of of the responding TFH T cell receptor repertoire revealed a strikingly immunodominant HLA-DPB1*04-restricted response to S167-180 in individuals with this allele, which is itself among the most common HLA alleles in humans. Analysis of paired blood and lymph node specimens show that circulating S-specific TFH cells peak one week after the second immunization while S-specific lymph node TFH persist at nearly constant frequencies for at least six months following mRNA vaccination. Collectively, our results underscore the key role that robust TFH cell responses play in establishing long-term immunity by this very efficacious human vaccine.