SARS-CoV-2 Omicron breakthrough infections induce antibodies with cross-variant neutralization potential and recall memory B cells

In a recent study posted to the bioRxiv* pre-print server, researchers reported breakthrough infections (BTIs) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)’s new variant of concern (VOC), Omicron, that elicited broadly cross-reactive neutralizing antibodies (nAbs) in BNT162b2-vaccinated individuals. Additionally, BTIs by the Omicron VOC induced a robust B cell recall response.

Study: Omicron breakthrough infection drives cross-variant neutralization and memory B cell formation. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock
Study: Omicron breakthrough infection drives cross-variant neutralization and memory B cell formation. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock

Globally, over one billion people have been immunized with messenger ribonucleic acid (mRNA)-based coronavirus disease 2019 (COVID-19) vaccines, including the BNT162b2 vaccine.

The protective immunity elicited by the currently used mRNA COVID-19 vaccines wanes over time, requiring routine booster vaccinations to recall immunity and maintain efficacy against the new SARS-CoV-2 VOCs. Yet, these vaccines based on the ancestral Wuhan-Hu-1 (WA1) strain induce nAbs with the ability to combat WA1 and other SARS-CoV-2 VOCs. 

The long-lived memory B (BMEM) cellular pool is a critical determinant of an individual’s ability to respond to a reencounter with an antigen, especially for newly emerging SARS-CoV-2 variants or booster vaccination, hence could guide future vaccine development. Additionally, the continued hypermutations in the BMEM cells expand the breadth of SARS-CoV-2 VOCs’ recognition over time.

About the study

In the present study, researchers collected blood samples from the individuals who participated in the BNT162b2 vaccine trials to investigate biomarkers in four independent groups.

These individuals had i) received two- or ii) three- doses of the BNT162b2 vaccine without a prior BTI at the time of sample collection iii) two- or three doses of the BNT162b2 vaccine and had an Omicron BTI after a median of approximately five months or four weeks, respectively.

The team performed both a pseudovirus neutralization test (pVNT) and a live viral neutralization test (VNT). The former investigated the breadth of inhibition of SARS-CoV-2 entry in a propagation-deficient set-up; whereas the latter evaluated neutralization during multiple replication cycles with the nAbs maintained throughout the study period.

Lastly, the researchers employed flow cytometry (FC)-based B cell phenotyping assays on bulk peripheral blood mononuclear cells (PBMCs) for detecting VOC-specific spike (S) protein-binding B cells in sera samples.

Study findings

Omicron BTIs boosted the magnitude and breadth of nAb response in both double- and triple-vaccinated individuals, with slightly higher nAb titers and a 50% decrease in pseudovirus-infected cells’ (pVN50) geometric mean titers (GMTs) in the triple-vaccinated individuals.

Likewise, Omicron infection increased pVN50 GMTs against Omicron BA.1, BA.2 sub-variants, and Delta to 1029, 836, and 1103, respectively, in triple-vaccinated individuals compared to the corresponding pVN50 GMTs of 160, 211, and 370 in the Omicron-naïve triple-vaccinated individuals. Similarly, Omicron-naïve double- and triple-vaccinated individuals showed high neutralizing activity against other VOCs. Accordingly, 50% virus neutralization (VN50) GMTs were in the same range as against the WA1 strain. Overall, Omicron BTIs augmented immunity against various VOCs in vaccinated individuals.

Omicron BTIs expanded the already existing BMEM cell repertoire rather than inducing Omicron-specific BMEM cells, formed in response to previous exposure to the WA1 S protein in the vaccinated individuals, with particularly striking effects in the double-vaccinated individuals. Omicron-convalescent double-vaccinated individuals had a higher frequency of BMEM cells and higher nAb titers against all SARS-CoV-2 VOCs than triple-vaccinated individuals.

Omicron BTIs substantially boosted the receptor-binding domain (RBD)-specific BMEM cells than BMEM cells that recognized S protein-specific epitopes outside the RBD. Interestingly, the SARS-CoV-2 S RBD harbors multiple nAb binding sites, including some regions unaffected by Omicron mutations, e.g., position L452.

The FC results showed that sera from Omicron-convalescents robustly neutralized SARS-CoV-1, indicating that Omicron BTIs in vaccinated individuals stimulated BMEM cells that formed nAbs against S protein epitopes conserved across SARS-CoV-1 and SARS-CoV-2 families.

The live SARS-CoV-2 VNT results showed that among BNT162b2 double- and triple-vaccinated individuals, Omicron BTIs were associated with robustly increased neutralizing activity against the Omicron BA.1 sub-variant.

Conclusions

Taken together, the study data points to designing a vaccine adapted to the Omicron S protein rather than boosters with the existing WA1 S to recall the B-cell memory repertoire. This pre-formed B-cell memory pool could be further remodeled, by exposure to heterologous S proteins, to generate nAbs with the potential to neutralize SARS-CoV-2 variants that evade immunity.

Recent studies have reported broadly active nAbs in SARS-CoV-1-infected individuals vaccinated with BNT162b2. Notably, the C-terminal of Omicron S houses its conserved subdominant neutralizing epitopes. Future studies mapping monoclonal antibodies derived from Omicron-specific BMEM cells could shed light on how such pan-sarbecoviruses' immune responses are triggered.

*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.

Journal reference:
Neha Mathur

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.

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