Memory B cells found to potently neutralize SARS-CoV-2 Omicron variant

By Neha MathurReviewed by Aimee MolineuxFeb 4 2022

In a recent study posted to the bioRxiv* pre-print server, a team of researchers captured memory B cells from a cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent or messenger ribonucleic acid (mRNA)-vaccinated individuals to study the evolution of B cell-mediated antibody responses to the N-terminal domain (NTD) in humans.

To date, research studies have demonstrated that all the anti-NTD neutralizing antibodies primarily target a single supersite. In several SARS-CoV-2 variants of concern (VOCs), including Beta, Gamma, and Omicron, residues at these supersites are found to be mutated. Thus, NTD supersite mutations most likely contribute to the poor neutralizing activity against Omicron.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Although poor anti-Omicron neutralizing activity is observed in vaccinated and convalescent individuals, vaccination elicits adequate NAbs in high amounts to confer protection against severe disease following Omicron infection. Thus, it is crucial to determine whether anti-NTD Omicron neutralizing epitopes exist and how memory B cell-induced anti-NTD immune responses evolve temporally.

About the study

In the present study, researchers examined a longitudinal cohort comprising of SARS-CoV-2-infected individuals who contracted infections between April 1 and May 8, 2020, in the pre-Omicron era. The researchers collected blood samples from these individuals at two different time points, at 1.3 and 12 months after contracting the infection. Some of the individuals  had received an mRNA vaccine approximately 40 days before the 12-month study visit.

The researchers measured antibody reactivity in test samples to the isolated Wuhan-Hu-1 and Omicron NTD by enzyme-linked immunosorbent assay (ELISA). In convalescent individuals, although anti-Wuhan-Hu-1 NTD IgG reactivity was not significantly different between the 1.3- and 12-month time points, Omicron NTD IgG reactivity dipped substantially between the two-time points. Notably, vaccination increased IgG ELISA reactivity to both Wuhan-Hu-1 and Omicron NTDs.

A combination of soluble Wuhan-Hu-1 and Gamma NTD proteins were used as bait to identify memory B cells producing antibodies specific for the anti-NTD domain. The anti-NTD antibodies represent a small subset of total anti-S antibodies. The researchers obtained 914 anti-NTD antibody sequences from three unvaccinated and three vaccinated convalescent individuals assayed at the two different time points.

Expanded clones of memory B cells accounted for 22% and 27% of all antibodies at the 1.3- and 12-month time points, respectively. Of these 90 B cell clones, 30 were conserved between time points, but most of them were unique to one of the two-time points, indicating that the antibody response continued to evolve with persisting clonal expansion.

Of all the antibodies cloned from the 1.3-month time point, 82%, 69%, and 52% bound to the Wuhan-Hu-1, Delta, and Omicron variants, respectively. The fraction of binding antibodies to Wuhan-Hu-1 and Delta NTD improved significantly after 12 months.

Finally, the researchers used biolayer interferometry (BLI) to determine whether antibody affinity increased between the two-time points and observed that anti-NTD antibodies evolved to higher affinity during the 12 months following infection irrespective of subsequent vaccination.

Findings

The SARS-CoV-2 neutralization assay showed that 103 out of 275 anti-NTD antibodies neutralized at least one of the pseudoviruses (Wuhan-Hu-1, Gamma, and PMS20) with an IC50 of less than 1000 ng/ml.

Of these, 14 were specific for Wuhan-Hu-1, 20 were limited to Gamma, 13 were PMS20-specific, and the remaining 56 neutralized two or more viruses. The antibodies targeting the NTD supersite were enriched in VH1-24, VH3-30, and VH3-33, and these three VH genes accounted for 59 of the 103 antibodies tested.

Of these six broad antibodies, four neutralized SARS-CoV-2 Alpha, Beta, Delta, Iota, and Omicron pseudoviruses, albeit at relatively high neutralizing concentrations. However, neutralization remained incomplete even at very high antibody concentrations.

The results of microneutralization experiments using authentic SARS-CoV-2-WA1/2020 confirmed that some naturally arising memory anti-NTD antibodies produced in response to Wuhan-Hu-1 infection and immunization are insensitive to the mutations found in Omicron and other VOCs.

Further, BLI experiments showed six distinct complementation groups among the 43 antibodies with the highest neutralizing activity. Groups I and II antibodies appeared to target the previously defined supersite on NTD. The group III antibody, C1717 showed broad neutralization against all SARS-CoV-2 VOCs. Altogether, 16 out of the 43 anti-NTD neutralizing antibodies tested neutralized PMS20 or Omicron, but not Wuhan-Hu-1. This suggested that the B cell memory compartment produced in response to Wuhan-Hu-1 infection contained antibodies that did not neutralize the Wuhan-Hu-1 strain and instead neutralized PMS20 and Omicron.

Conclusions

The present study demonstrated that of all the SARS-CoV-2 neutralizing antibodies identified to date, including the ones in clinical use, Omicron evades most of them. Therefore, future studies should probe new epitopes conserved among SARS-CoV-2 variants and that are potentially targeted by the broad-spectrum neutralizing antibodies.

More importantly, the findings showed that infection or vaccination-induced memory B cell populations diversify to contain high-affinity antibodies that can potently neutralize numerous SARS-CoV-2 variants, including Omicron.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.