Omicron BA.1 breakthrough infection in vaccinated individuals recall memory B cells to confer immunity

In a recent study posted to the bioRxiv* server, a team of researchers followed up with individuals vaccinated with a coronavirus disease 2019 (COVID-19) vaccine based on the messenger ribonucleic acid (mRNA) platform up to six months following Omicron BA.1 breakthrough infection to trace the evolution of their antibody immunity. In particular, they observed how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD)-specific neutralizing antibody (nAb) responses in these vaccinated individuals evolved over time.

Background

Currently available COVID-19 vaccines induce high levels of protection against pre-Omicron variants (e.g., Delta). However, Omicron sublineages, including BA.2, BA.2.12.1, BA.4/5, BA.2.75, BA.2.75.2, and BA.4.6, have drifted far away antigenically and developed extensive immune evasiveness. More infective sub-variants continue to emerge and replace prior sub-variants.

Although some Omicron spike (S)-based booster mRNA vaccines have received emergency use authorization (EUA) to counter the high prevalence of Omicron breakthrough infections, the data supporting their immunogenicity and efficacy in humans remains limited. There is a need to understand whether a secondary exposure to antigenically divergent variants, such as Omicron BA.1, triggers SARS-CoV-2-specific B cell memory. If yes, how this immunity evolves alongside SARS-CoV-2 RBD-specific antibodies remains to be determined.

About the study

In the present study, researchers created a cohort comprising seven mRNA-1273 vaccinated donors to profile their SARS-CoV-2-specific serological and memory B responses up to six months following Omicron BA.1 breakthrough infection. Initially, they characterized their antibody response for 14 to 27 days after BA.1 breakthrough infection. Next, they obtained blood samples from six of the seven participants to study the evolution of this response over four to six months post breakthrough infection.

Further, the team tested the neutralizing activity of these plasma samples against multiple SARS-CoV-2 variants, including D614G ancestral strain, Beta, Delta, and Omicron BA.1, BA.2, BA.4/5, and BA.2.75, using a murine-leukemia virus (MLV)-based pseudovirus assay. In addition, they screened more antigenically divergent SARS-CoV.

The researchers used flow cytometry (FC) to determine the magnitude and cross-reactivity of the SARS-CoV-2-specific B cell response. The B cell staining involved the use of differentially labeled RBD tetramers from Wuhan-Hu1 and BA.1. Further, the team single-cell sorted 71 to 110 class-switched RBD reactive B cells from four vaccinated donors – IML4042, IML4043, IML4044, and IML4045 between 139 and 170 days following BA.1 infection.

From 363 natively paired full-length immunoglobulins G (IgGs), they randomly selected one to two antibodies belonging to each convergent germline to perform deep mutational scanning (DMS) analysis. This screening involved a library encoding all possible amino acid substitutions from BA.1. These analyses helped the researchers compare the molecular characteristics of antibodies isolated at early and late periods points following BA. 1 infection.

Study findings         

From the study cohort, three mRNA-vaccinated donors experienced a BA.1 breakthrough infection after two doses of mRNA-1273, while the remaining three contracted this infection following a booster dose.

Despite the waning of nAb titers over time, sera of all vaccinated donors had detectable neutralizing activity against all of the SARS-CoV-2 variants tested at the five to six months, with median titers ranging from 117 to 552. Notably, nAb titers remained within three-fold of that for D614G for all SARS-CoV-2 variants except Omicron BA.4/5, which showed the highest degree of immune escape (5.5-fold reduction compared to D614G), as also observed in previous studies. However, cross-neutralizing activity or serum neutralization breadth remained the same over time against all SARS-CoV-2 variants, except for SARS-CoV.

Total RBD reactive B cells and WT/BA.1 cross-reactive B cells comprised a median of 0.44% and 0.37% of class-switched IgG+ or IgA+ B cells, respectively, at five to six months time points. Thus, 86% of these B cells displayed BA.1/WT cross-reactivity, compared with 75% at one month post-infection. WT-specific B cells decreased from 25% to 11% between one and five to six months-timepoint.

Due to the waning phenomenon, there was a moderate but marked decline in the frequencies of WT/BA.1 cross-reactive B cell during early and late study time points. At the later time point, the authors also noted the emergence of a BA.1-specific B cell population in three of the six vaccinated donors, though the magnitude of this response varied between 1% and 18%. Omicron BA.1 breakthrough infection induced a WT/BA.1 cross-reactive B cell response at early time points post-infection, and this response only modestly declined in six months.

Similar to the antibodies isolated at the early time point, 73 to 97% of newly isolated antibodies primarily recognized both WT and BA.1 RBDs. Additionally, they exhibited clonal diversity and preferred VH germline genes, IGHV1-46, 1-69, 3-13, 3-53, 3-66, 3-9, and 4-31. The magnitude of somatic hypermutations (SHMs) in the cross-reactive nAbs increased from a median of 9 VH nucleotide substitutions at one month to 11 VH nucleotide substitutions by five to six months, indicating affinity maturation in secondary germinal centers (GCs).

These antibodies displayed 1.7-fold improved binding to BA.1 and two-fold reduced binding affinity to the WT RBD relative to early antibodies, indicating affinity maturation towards BA.1 at the expense of WT affinity. These late antibodies showed more balanced affinity profiles than the early antibodies (73% vs. 24%). Notably, convergent nAb classes dominated the BA.1 breakthrough response at early and late time points.

BA.2.75 and BA.4/5 RBDs had increased binding resistance to IGHV3-53/66 antibodies, providing a molecular explanation for the high degree of antigenic convergence of recent Omicron sub-variants and their increased immune evasion potential relative to BA.1. Thus, engineering S-based immunogens inducing diverse nAbs targeting numerous co-dominant epitopes could help limit convergent immune pressure, thereby constraining viral evolution. Also, this could be the key to “variant-proof” COVID-19 vaccines.

Conclusions

To summarize, BA.1 breakthrough infection in mRNA-vaccinated individuals triggered nAbs with a good neutralizing breadth and mature B cell (MBC) responses that persisted for a minimum of six months. Perhaps, this explains how BA.1 breakthrough infection protects infections from BA.1, BA.2, and BA.5 for at least five to six months. The recall of cross-reactive vaccine-induced MBCs with SHMs mediates this MBC response following breakthrough infection, which evolves to enhance breadth and potency for at least six months. A second heterologous exposure further broadens the serological repertoire by activating these affinity matured MBCs.

Overall, the study data indicated that infection or vaccination with antigenically divergent SARS-CoV-2 variants, such as Omicron BA.1, could confer protection by broadening pre-existing B cell memory or a recall of MBCs.

*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.

Written by

Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.