Study shows hybrid immunity or vaccine boosters elicit plasma neutralizing activity against Omicron sublineages

By Neha MathurOct 24 2022Reviewed by Danielle Ellis, B.Sc.

In a recent study published in Science, researchers evaluated imprinted antibody responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages.

Background

SARS-CoV-2 Omicron sublineages represent an antigenic shift. They harbor unique spike (S) mutations that facilitate their escape from neutralizing antibodies (nAbs) induced by prior infection by a different strain or vaccination. For instance, both Omicron BA.1 and BA.2 subvariants have unique amino acid mutations, which impart distinctive antigenic properties.

These nAbs primarily target mutations harbored in the N-terminal and receptor-binding domains (NTD and RBD) of BA.1 S, rationalizing the markedly reduced plasma-neutralizing activity of previously infected or vaccinated subjects, especially those who have not received booster doses. It also helps Omicron escape from most clinically used monoclonal antibodies (mAbs). Subsequently, even though milder, Omicron is causing an increasing number of breakthrough infections than infections in immunologically naive individuals.

About the study

In the present study, researchers first evaluated the magnitude of immune evasion associated with the Omicron sublineages using plasma from six cohorts of individuals. These cohorts had people previously infected in 2020 with the Wuhan-Hu1-like SARS-CoV-2 strain and then vaccinated with a two-dose or three-dose vaccination regimen(s). Other cohorts had people who were triply vaccinated and yet contracted a Delta or an Omicron BA.1 breakthrough infection, plus those vaccinated and boosted but never infected.

Further, the team investigated the cross-reactivity of RBD-directed antibodies produced by in vitro stimulated memory B cells collected 200 days after infection or vaccination and circulating plasma cells collected soon after infection. For this analysis, the researchers used blood samples from individuals infected before Omicron emerged and subsequently vaccinated, plus people who suffered an Omicron primary infection or breakthrough infection. Notably, in regions where the researchers collected samples, Omicron infections occurred between January and March 2022, and 90% of cases were due to Omicron BA.1/BA.2.

Next, the team determined the site specificity of RBD-directed antibodies secreted by stimulated memory B cells against structurally characterized mAbs. Furthermore, the team assessed IgG and IgA binding titers in nasal swabs of subjects who experienced a BA.1 breakthrough infection or vaccinated-only individuals to evaluate their mucosal antibody responses.

Results

The study demonstrated that exposure to antigenically farther Omicron sublineages primarily recalled existing memory B cells specific for epitopes shared by multiple SARS-CoV-2 variants. They did not prime naïve B cells recognizing Omicron-specific epitopes at least up to six months after breakthrough infection.

Immune imprinting is a beneficial phenomenon that preferentially boosts antibody responses against epitopes shared with the original strain. So the researchers expected that infected and vaccinated individuals could trigger cross-reactive responses to SARS-CoV-2 S epitopes. On the contrary,  prior antigenic exposure hindered antibody responses to some Omicron S-specific epitopes. Omicron breakthrough infections could not even elicit high cross-reactive nAbs against sarbecoviruses.

The authors noted that it most likely happened because of the low frequency of memory B cells encoding for nAbs targeting shared antigenic sites between pre-Omicron variants (e.g., Wuhan-Hu-1), Omicron, and SARS-CoV. For instance, mutations in the RBD antigenic site II in Omicron BA.1/BA.2 inhibited the neutralizing activity of pan-sarbecovirus nAbs, such as S2X259 and ADG2. Thus, these Omicron sublineages resisted neutralization by some of these mAbs. Intriguingly, the conservation of RBD antigenic sites across sarbecoviruses partially restricted immune pressure and contributed to viral fitness.

The researchers also identified an ultrapotent mAb S2X324 that remained unaffected by S mutations of all Omicron sublineages. It exhibited neutralization potency against Omicron BA.1, BA.2, BA.3, BA.4, BA.5, BA.2.12.1 and BA.2.75. In addition, it cross-reacted with all SARS-CoV-2 variants except BA.2.75 and neutralized them with half maximal inhibitory concentration (IC50) values below 10 ng/ml.

S2X324 also cross-reacted with the sarbecovirus clade 1b but did not recognize more evolutionarily distant sarbecoviruses. Furthermore, S2X324 inhibited binding of the SARS-CoV-2 RBD to human angiotensin-converting enzyme 2 (ACE2) in a concentration-dependent manner, as measured by competition enzyme-linked immunosorbent assay. Further, it induced slow premature shedding of the S1 subunit of the S protein.

The researchers determined a cryo-electron microscopy structure of the Omicron BA.1 S bound to the S2X324 Fab fragment at 3.1 Å resolution, which showed that S2X324-mediated inhibition of SARS-CoV-2 involved blockage of ACE2 binding.

Conclusions

Understanding how prior antigen exposure via vaccination or infection could shape the immune response to subsequent infection(s) with a different SARS-CoV-2 variant could help develop strategies to combat the ongoing COVID-19 pandemic.

So far, all studies have focused exclusively on serum antibodies and systemic cell-mediated immunity to combat COVID-19. However, the respiratory mucosal surface first interacts with SARS-CoV-2, which enters via the upper respiratory tract. This raises the possibility of exploring mucosal immunity for beneficial therapeutic or prophylactic purposes.

The current study finding that SARS-CoV-2 breakthrough infections elicit neutralizing activity in the nasal mucosa is a significant one. It points to the feasibility of developing vaccines that could be intranasally administered, that is, at the site of SARS-CoV-2 entry. Recently, a preclinical assessment of a broad-spectrum sarbecovirus vaccine demonstrated the induction of lung-resident protective mucosal humoral and cellular immunity in the nasal mucosa. Indeed, these observations would aid the development and evaluation of the next generation of COVID-19 vaccines, possibly those that could be intranasally administered.