RNA vaccines are efficient preventive measures to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the initial two mRNA vaccine doses, the IgG response mainly consists of the pro-inflammatory subclasses IgG1 and IgG3. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. IgG4 antibodies among all spike-specific IgG antibodies rose on average from 0.04% shortly after the second vaccination to 19.27% late after the third vaccination. This induction of IgG4 antibodies was not observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. Single-cell sequencing and flow cytometry revealed substantial frequencies of IgG4-switched B cells within the spike-binding memory B-cell population (median 14.4%; interquartile range (IQR) 6.7–18.1%) compared to the overall memory B-cell repertoire (median 1.3%; IQR 0.9–2.2%) after three immunizations. Importantly, this class switch was associated with a reduced capacity of the spike-specific antibodies to mediate antibody-dependent cellular phagocytosis and complement deposition. Since Fc-mediated effector functions are critical for antiviral immunity, these findings may have consequences for the choice and timing of vaccination regimens using mRNA vaccines, including future booster immunizations against SARS-CoV-2.

The pathogenesis of severe COVID-19 reflects an inefficient immune reaction to SARS-CoV-2. Here we analyze, at the single cell level, plasmablasts egressed into the blood to study the dynamics of adaptive immune response in COVID-19 patients requiring intensive care. Before seroconversion in response to SARS-CoV-2 spike protein, peripheral plasmablasts display a type 1 interferon-induced gene expression signature; however, following seroconversion, plasmablasts lose this signature, express instead gene signatures induced by IL-21 and TGF-β, and produce mostly IgG1 and IgA1. In the sustained immune reaction from COVID-19 patients, plasmablasts shift to the expression of IgA2, thereby reflecting an instruction by TGF-β. Despite their continued presence in the blood, plasmablasts are not found in the lungs of deceased COVID-19 patients, nor does patient IgA2 binds to the dominant antigens of SARS-CoV-2. Our results thus suggest that, in severe COVID-19, SARS-CoV-2 triggers a chronic immune reaction that is instructed by TGF-β, and is distracted from itself.

TRIANNI mice carry an entire set of human immunoglobulin V region gene segments and are a powerful tool to rapidly isolate human monoclonal antibodies. After immunizing these mice with DNA encoding the spike protein of SARS‐CoV‐2 and boosting with spike protein, we identified 29 hybridoma antibodies that reacted with the SARS‐CoV‐2 spike protein. Nine antibodies neutralize SARS‐CoV‐2 infection at IC50 values in the subnanomolar range. ELISA‐binding studies and DNA sequence analyses revealed one cluster of three clonally related neutralizing antibodies that target the receptor‐binding domain and compete with the cellular receptor hACE2. A second cluster of six clonally related neutralizing antibodies bind to the N‐terminal domain of the spike protein without competing with the binding of hACE2 or cluster 1 antibodies. SARS‐CoV‐2 mutants selected for resistance to an antibody from one cluster are still neutralized by an antibody from the other cluster. Antibodies from both clusters markedly reduced viral spread in mice transgenic for human ACE2 and protected the animals from SARS‐CoV‐2‐induced weight loss. The two clusters of potent non‐competing SARS‐CoV‐2 neutralizing antibodies provide potential candidates for therapy and prophylaxis of COVID‐19. The study further supports transgenic animals with a human immunoglobulin gene repertoire as a powerful platform in pandemic preparedness initiatives. This article is protected by copyright. All rights reserved

The human immune response to SARS-CoV-2 infection is highly variable, with less than 10% of infections resulting in severe COVID-19 requiring intensive care unit (ICU) treatment. Here we have analyzed the dynamics of the adaptive immune response in COVID-19 ICU patients at the level of single cell transcriptomes and B cell and T cell receptor (BCR, TCR) repertoires. Early after ICU admission, before seroconversion in response to SARS-CoV-2 spike protein, patients generate activated peripheral B cells with a type 1 interferon-induced gene expression signature. After seroconversion, patients display circulating activated B cells expressing an IL-21-induced gene expression signature and mainly IgG1 and IgA1, two isotypes induced by IL-21 and TGF-β, respectively. In sustained COVID-19, the persistent immune reaction is shifted to IgA2-expressing activated peripheral B cells, displaying somatic hypermutation, and expressing TGF-β-induced signature genes, like IgA germline transcripts. The switch from an IgG1 to an IgA2-dominated B cell response correlates with the appearance of SARS-CoV-2 reactive follicular T helper cells expressing IL-21 and/or TGF-β in the blood. Despite the continued presence of IgA2-expressing B cells and IgA antibodies in the blood of progressed COVID-19 patients, IgA2 secreting cells were scarce in the lungs of deceased COVID-19 patients. In summary, in severely affected COVID-19 patients SARS-CoV-2 triggers chronic immune reactions which are controlled by TGF-β, with most of the activated B cells being no longer specific for the SARS-CoV-2 spike protein and its receptor binding domain, nor for nucleoprotein. TGF-β may candidate as a target to ameliorate detrimental immunopathology in those patients.

In the version of this article initially published, the middle name of Katharina Marie Habenicht was misspelled (Maria), and has been amended in the HTML and PDF versions of the article.