Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq

Abstract

B cell response plays a critical role against SARS-CoV-2 infection. However, little is known about the diversity and frequency of the paired SARS-CoV-2 antigen-specific BCR repertoire after SARS-CoV-2 infection. Here, we performed single-cell RNA sequencing and VDJ sequencing using the memory and plasma B cells isolated from five convalescent COVID-19 patients, and analyzed the spectrum and transcriptional heterogeneity of antibody immune responses. Via linking BCR to antigen specificity through sequencing (LIBRA-seq), we identified a distinct activated memory B cell subgroup (CD11chighCD95high) had a higher proportion of SARS-CoV-2 antigen-labeled cells compared with memory B cells. Our results revealed the diversity of paired BCR repertoire and the non-stochastic pairing of SARS-CoV-2 antigen-specific immunoglobulin heavy and light chains after SARS-CoV-2 infection. The public antibody clonotypes were shared by distinct convalescent individuals. Moreover, several antibodies isolated by LIBRA-seq showed high binding affinity against SARS-CoV-2 receptor-binding domain (RBD) or nucleoprotein (NP) via ELISA assay. Two RBD-reactive antibodies C14646P3S and C2767P3S isolated by LIBRA-seq exhibited high neutralizing activities against both pseudotyped and authentic SARS-CoV-2 viruses in vitro. Our study provides fundamental insights into B cell response following SARS-CoV-2 infection at the single-cell level.

Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine

“…IgA-switched Spike-specific B cells were also increased post-vaccination ( Fig. 1 F), which can be linked to the simultaneous expansion of plasmablasts observed in these subjects, as these B cell subsets are known to be primarily IgA + when in steady-state circulation [ 19 , 31 ].…”

“…Matching B cell heavy chain V and J genes and assessing sequence similarity in the heavy chain CDR3 (CDRH3) region are criteria typically used to identify similar B cell clonotypes in different subject cohorts [ 19 , 21 , 22 , 32 , [34] , [35] , [36] , [37] , [38] ]. Clonotypes from both naïve BNT162b2 vaccinees [ 21 , 22 , 32 ] and convalescent unvaccinated individuals [ 19 , [34] , [35] , [36] , [37] , [38] ] have been found to be homologous with published antibodies and/or amongst different individuals based on the above criteria, showing convergent development of conserved variable region genes and sequences that work to target SARS-CoV-2. Many of these clonotypes have been identified to specifically target RBD, with subsets of these antibody clones shown to be neutralizing [ 32 , 34 , 36 ].…”

“…Interestingly, one of the B cell subsets expanded post-vaccination was IgA + B cells, a population thought to primarily line mucosal sites. As mRNA vaccines are not mucosal vaccines, an increase in IgA + B cells was unexpected, but may also be linked to a simultaneous increase in plasmablast populations, which are known to be IgA+ in circulation [ 19 , 31 ]. Further research into this expanded subset of cells could reveal informative details on the breadth of immunological stimulation by BNT162b2.…”

“…Many studies have separately assessed the effects of both natural SARS-CoV-2 infection [ [17] , [18] , [19] , [20] ] and prophylactic mRNA vaccination [ 17 , [20] , [21] , [22] , [23] ] on B cell populations by single-cell RNA sequencing. These next-generation sequencing technologies have facilitated the elucidation of clonality amongst specific B cell subsets [ 17 , 20 ], as well as the detection of sequence homologies amongst published SARS-CoV-2 clonotypes [ 21 ] within and between subject cohorts.…”

Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

“…LIBRA-seq has also been used to delineate cross-reactive antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with distinct epitopes and Fc effector functions 177 as well as rapid profiling of SARS-CoV-2 specific memory B cells. 178 …”