Longitudinal single-cell analysis of SARS-CoV-2–reactive B cells uncovers persistence of early-formed, antigen-specific clones

Abstract

Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from severe COVID-19 patients every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE)-Seq, B cell receptor (BCR)-Seq with oligotagged antigen baits. While the proportion of Spike Receptor Binding Domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike-and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen specific cells, which was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to one year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen specific B cell responses in longitudinally sampled COVID-19 infected patients.

Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques

“…The analysis demonstrates that many of the lineages were traceable at all interrogated time points, demonstrating early elicitation followed by extensive clonal diversi cation of these lineages. B cell lineage persistence was also previously reported from SARS-CoV-2-infected individuals based on the analysis of mAbs or single B cell sequencing data from sequential time points [50][51][52] . A limitation with these approaches is the number of cells and compartments that can be sampled.…”

Sort-Seq: immune repertoire-based scRNA-Seq systematization

“…“Eff-mem IFN response” cluster is nearly absent in healthy donors’ blood but is well-detectable in moderate and severe COVID patients ( Supplementary Fig. 4), probably representing the typical behavior of Th cells in acute viral infection 30 . Tfh subset is found in two dissimilar clusters differing in the expression of CXCR5 and CXCR3.…”

Comparable CD8+ T‐cell responses to SARS‐CoV‐2 vaccination in single‐cell transcriptomics of recently allogeneic transplanted patients and healthy individuals

“…[16][17][18]23 After SARS-CoV-2 infection however, antigen specificity was determined to be a strong driver for IGHV gene usage, with VH1-24, VH3-30, and VH3-33 being the preferentially utilized genes with spike specificity. [22][23][24] Although ASCT responders showed an increase in the usage of the IGHV gene VH3-33 after vaccination, this change did not reach significance (Figure 3F). TCRα and TCRß usage after vaccination was analyzed in ASCT patients and showed TRAV1-2, TRAV12-3, TRAV24, TRAV26-2, TRAV8-6, TRBV27, TRBV30, TRBV5-4, TRBV7-3, and TRBV9 to be preferentially used after vaccination.…”

“…Apart from ASCT patients, single‐cell RNA sequencing (scRNA‐seq) and bulk sequencing strategies have been applied to dissect immune responses to SARS‐CoV‐2 infection and vaccination, providing in‐depth insights into changes in immune cell abundances and gene expression 15–21 . Complimented by B cell receptor (BCR) and T cell receptor (TCR) sequencing, analysis of B‐ and T‐cell receptor repertoires and dynamics of specific clonotypes have been performed and a considerable number of SARS‐CoV‐2‐specific TCR and antibody sequences have been described 22–26 . Despite a common vaccination antigen, only a fraction of these responses can be attributed to public TCRs and BCRs, whereas a large proportion of the SARS‐CoV‐2‐specific response is accounted for by private clonotypes.…”