Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets

Abstract

Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.

Identification of Human SARS-CoV-2 Monoclonal Antibodies from Convalescent Patients Using EBV Immortalization

“…In order to facilitate the screening of clones, several groups have shown that it is possible to measure their frequency in different donors and also purify these cells using tagged recombinant proteins to facilitate specific mAb isolation [ 5 , 25 ]. We attempted to do this using the first commercially available tagged SARS-CoV-2 spike or nucleocapsid recombinant proteins, but we could not identify a specific signal (data not shown).…”

“…Other strategies exist to isolate human antigen-specific mAbs from immunized donors, such as the direct sequencing of VH and VL domains by RNA sequencing (scRNA seq) of purified single antigen-specific memory B cells or antibody-secreting plasma cells [ 1 , 25 , 28 , 29 , 30 , 31 , 32 , 33 ]. These, however, are time-consuming, require subcloning of VH/VL sequences in plasmid vectors, transfection in mammalian cells, and purification of recombinant mAbs before functional assays can be performed.…”

“…These, however, are time-consuming, require subcloning of VH/VL sequences in plasmid vectors, transfection in mammalian cells, and purification of recombinant mAbs before functional assays can be performed. These methods, therefore, require more specialized laboratories with already established high throughput techniques [ 5 , 25 , 32 , 33 ].…”

Bridging the B Cell Gap: Novel Technologies to Study Antigen-Specific Human B Cell Responses

“…Notably, LIBRA-seq can also reveal broadly reactive BCRs, as B cells may bind to multiple DNA-barcoded recombinant proteins, such as distinct hemagglutinin (HA) proteins from influenza viruses. Therefore, LIBRA-seq allows for the rapid characterization of B cell responses to novel vaccine immunogens or antigens following infection, which can yield the discovery of previously unknown broadly reactive antibodies or tie B cell differentiation to specificity [ 32 ]. This powerful technology was also used to uncover antigen-specific memory B cell heterogeneity following severe acute respiratory syndrome coronavirus-2 infection [ 32 ].…”

“…Therefore, LIBRA-seq allows for the rapid characterization of B cell responses to novel vaccine immunogens or antigens following infection, which can yield the discovery of previously unknown broadly reactive antibodies or tie B cell differentiation to specificity [ 32 ]. This powerful technology was also used to uncover antigen-specific memory B cell heterogeneity following severe acute respiratory syndrome coronavirus-2 infection [ 32 ]. Moreover, LIBRA-seq has been used to reveal that AtM cells are present in both antigen-naïve individuals as well as those experiencing chronic Plasmodium falciparum infections [ 17 ].…”