Importance of cross-neutralizing antibodies against SARS-CoV-2 variants

By Dr. Shital Sarah Ahaley Ph.DNov 21 2021Reviewed by Danielle Ellis, B.Sc.

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are highly infectious and can evade immunity induced by natural infection and vaccination.

A new study published in the journal mBio investigates different antibodies from convalescent donors that bind three separate domains of the SARS-CoV-2 spike. The results of this study suggest that the individuals exposed to the SARS-CoV-2 from the first wave have neutralizing antibodies against current variants.

Introduction

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, several variants of concern (VOCs) have emerged. These variants are known to cause breakthrough infections, i.e., they can circumvent the protective effects of vaccination or infection-induced natural immunity. The neutralizing antibodies elicited by natural infection target the SARS-CoV-2 spike protein. Currently available COVID-19 vaccines also induce a neutralizing antibody response against the spike protein. The VOCs have mutations within the different regions of the spike protein.

Convalescent sera antibody levels and neutralization capabilities

The scientists collected blood samples from 10 convalescent donors around 49 days after symptom onset to analyze the specificity of individual memory B cells. Serum antibody reactivity was measured against spike proteins from the wildtype and D614G, B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.526 and B.1.617.1 variants and then compared.

Serum antibody levels from the 10 patients against wildtype and D614G spike antigens were similar. However, the antibody levels were reduced against the spike proteins of B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.526 and B.1.617.1 relative to the wildtype spike proteins.

Similarly, antibody levels against the receptor-binding domains (RBDs) of B.1.1.7, B.1.351 and P.1 were reduced relative to the wildtype RBD. However, there was a less than 2-fold decrease in antibody binding against single mutants of the RBD.

The sera retained similar neutralizing levels against the wildtype and the B.1.1.7 and P.1 SARS-CoV-2 variants. However, there was a reduction in neutralization against B.1.617.1 and B.1.617.2 compared to the wildtype.

These data indicate that serum antibodies elicited by natural infection were able to neutralize B.1.1.7, P.1 and wildtype viruses equally. Most donors lost neutralizing potential against B.1.617 lineage viruses.

Thus, convalescent-phase sera have reduced antibody titers but retain neutralization capabilities against circulating SARS-CoV-2 VOCs.

Monoclonal antibodies against distinct parts of the spike protein

The scientists then generated monoclonal antibodies (mAbs) from spike binding B cells isolated from 10 convalescent subjects. They sorted B cells binding to spike and/or RBD probes and performed single-cell RNA sequencing (RNA-seq) and B cell receptor sequencing.

The percentage of spike non-RBD binding B cells was 4-fold higher than that of RBD binding B cells. This means that natural infection preferentially induced B cell responses against regions on the spike outside the RBD.

The scientists generated 43 mAbs from all 10 donors specific for the WT spike protein. They investigated specific domain targeting by these mAbs using an enzyme-linked immunosorbent assay (ELISA). Eighteen out of 43 mAbs were neutralizing.

The mAbs binding the RBD and NTD-B were neutralizing and mAbs binding NTD-A and S2 were non-neutralizing. Eight mAbs were potently neutralizing antibodies and three out of seven NTD-B mAbs had moderate neutralization potency.

Thus, mAbs against the RBD were the predominant source of neutralizing antibodies induced by wildtype SARS-CoV-2 infection.

Cross-reactive mAbs

The scientists tested non-RBD-targeting mAbs for binding to a panel of SARS-CoV-2 variants. All non-RBD spike-reactive antibodies showed similar binding to the D614G spike.

All mAbs targeting NTD-A and S2 maintained similar binding to the spike of the B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.526, and B.1.617.1 variants.

The NTD-B mAbs showed significantly reduced binding to the spike of B.1.1.7, B.1.351, B.1.617.2, and B.1.617.1 while showing similar binding to B.1.526 and a minor reduction in binding to the spike of P.1.

The antibodies against NTD-B showed cross-neutralization capacity and thus may provide protection against some emerging VOCs such as B.1.1.7 and P.1.

The scientists tested RBD-targeting mAbs for binding to RBD mutants that had a single mutation. They also tested mAb binding to the RBDs of SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV) to investigate cross-reactivity to other coronaviruses.

Six mAbs could not be classified because they either lost binding to multiple mutant classes or bound equally to all RBD mutants but did not bind to SARS-CoV-1 or MERS-CoV.

A subset of RBD-binding mAbs retained neutralization activity against VOCs. None of the neutralizing mAbs induced by natural wildtype infection neutralized all emerging SARS-CoV-2 variants. However, one mAb neutralized each VOC, suggesting that the convalescent donors generated a diverse cross-neutralizing antibody response. Therefore, antibodies targeting multiple regions on the spike protein are important against emerging VOCs.

The majority of antibodies isolated from donors with high antibody levels had lower neutralizing potency than antibodies derived from donors who had lower antibody levels and less severity.

Conclusion

SARS-CoV-2 infection induces cross-neutralizing immunity against circulating VOCs. Most probably, this is due to antibodies targeting many different regions of the spike protein.

This study suggests that different cross-neutralizing antibodies that bind specific sites on the spike protein should be induced to protect against SARS-CoV-2 variants and limit the virus from escaping any single antibody target.