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.

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.

Evidence suggests that immunogenicity to mRNA-based SARS-CoV-2 vaccination in immunosuppressed patients may be reduced. This study assessed the response to 2 doses of mRNA-based SARS-CoV-2 vaccine among 133 participants with underlying chronic inflammatory disease, many of whom were receiving glucocorticoids, B-cell depletion therapy, or other immunosuppressant therapy.

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...

Summary Influenza viruses remain a major public health threat. Seasonal influenza vaccination in humans primarily stimulates pre-existing memory B cells, leading to a transient wave of circulating antibody-secreting plasmablasts 1 – 3 . This recall response contributes to “original antigenic sin,” the selective boosting of antibody specificities from prior exposures to influenza virus antigens 4 . It remains unclear whether such vaccination can also induce germinal centre (GC) reactions in the draining lymph node (LN) where diversification and maturation of recruited B cells can occur 5 . Here we used ultrasound-guided fine needle aspiration to serially sample the draining LNs and investigate the dynamics and specificity of GC B cell responses after influenza vaccination in humans. We show that influenza vaccine-binding GC B cells can be detected as early as 1 week after vaccination. In 3 out of 8 participants, we detected vaccine-binding GC B cells up to 9 weeks after vaccination. Between 12% and 88% of the responding GC B cell clones overlapped with those detected among early circulating plasmablasts. These shared B cell clones had high frequencies of somatic hypermutation (SHM) and encoded broadly cross-reactive monoclonal antibodies (mAbs). In contrast, vaccine-induced B cell clones detected only in the GC compartment exhibited significantly lower SHM frequencies and predominantly encoded strain-specific mAbs, suggesting a naïve B cell origin. Electron microscopy-based epitope mapping revealed that some of these strain-specific mAbs recognized epitopes that were not targeted by the early plasmablast response. Our results indicate that influenza virus vaccination of humans can elicit a GC reaction to which B cell clones targeting novel epitopes are more likely to be recruited, thereby broadening the spectrum of vaccine-induced protective antibodies against this rapidly mutating pathogen.