In a recent study published in Science Immunology, researchers used antigen mapping to quantify and visualize antigenic differences between multiple variants of coronavirus 2 (SARS-CoV-2) of severe acute respiratory syndrome.
Study: Antigenic mapping of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically different. Image credit: Naeblys / Shutterstock
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The continued occurrence of SARS-CoV-2 variants of concern (VOCs), such as Omicron, could affect the efficacy of coronavirus 2019 vaccines (COVID-19). Therefore, it is important to evaluate the antigenic properties of future SARS-CoV-2 VOCs to inform future vaccination strategies. In addition, only a handful of studies have investigated the antigenic characteristics of the Omicron BA.2 variant, which differs substantially from its predecessor BA.1 and is currently replacing it in several countries.
About the study
In the present study, the authors investigated the degree to which BNT162b2 COVID-19 vaccine-induced sera neutralized Omicron BA.2. They obtained sera from 10 individuals who had received one, two or three doses of vaccine.
In addition, the researchers used antigenic mapping to investigate the antigenic relationships between the first SARS-CoV-2 variants, i.e., D614G, Alpha, Beta, Gamma, Delta, Zeta, Mu, and Omicron BA.1 sub-lineages. and BA.2. They used the Syrian golden hamster model to generate antisera against all these variants. High viral ribonucleic acid (RNA) titers in nasal washes at one dpi and high homologous antibody titers at 26 dpi confirmed that all test animals were successfully infected.
The plaque reduction neutralization titer (PRNT) assay shows a 50% reduction in virus-infected cells (PRNT50). The team performed a PRNT assay on authentic SARS-CoV-2 and pseudotyped viruses to generate antigen maps. As a precautionary step, the researchers sequenced viral stocks and original respiratory samples to confirm the absence of mutations acquired in culture. In addition, they again sequenced swabs seven days after infection (dpi) to confirm that SARS-CoV-2 did not mutate for the duration of the study.
The researchers cultured the D614G, Alpha, Beta, Kappa, Delta, and Omicron BA.1 spike variants in Vero-E6 cells to perform initial neutralization assays. All homologous neutralized serums at high titers except Omicron BA.1. All sera showed cross-neutralization titers reduced again to 43-fold against Omicron. In contrast, Omicron BA.1-infected hamster sera showed a two- to 81-fold reduction in cross-neutralization titers.
The team also performed pseudovirus neutralization assays on the Calu-3 cell line. They constructed antigenic maps from the neutralization data of Calu-3 and VeroE6 cells. SARS-CoV-2 enters this cell line via the serine protease-mediated entry pathway, while taking the cathepsin-mediated endocytic entry pathway into VeroE6 cells.
Study results
The same antigens were plotted in a one-time dilution of each other in Calu-3 and VeroE6 cells. Therefore, the type of cell line used for the neutralization assay did not change the topology of the antigen map. In addition, there was a significant correlation between the gross neutralizing titers of the five variants of Calu-3 and VeroE6 cells.
In particular, in antigen maps generated with authentic SARS-CoV-2 and pseudovirus, antigen positions did not differ more than twice. Although all variants of SARS-CoV-2 were grouped closely together, Omicron BA.1 acquired a position of 10 to 38 times dilutions away from the nearest virus, showing its different antigenic properties. The antigen map generated using the extended neutralization dataset also showed that Omicron BA.1 and BA.2 remained distant from the antigen map, with BA.2 located closer to the main cluster.
Authentic pseudoviruses with the E484K mutation (Beta, Gamma, Zeta, and Mu) were grouped in the upper right of the ancestral D614G strain. On the other hand, those with L452R / Q replacements were grouped on the left. The Beta and Gamma variants, which have the K417N / T mutation in addition to the E484K mutation, were grouped on the antigenic map.
Conclusions
The present study demonstrated that Omicron BA.1 and BA.2 have different antigenic properties, however, both escape vaccine-induced antibody responses.
A previous study by Wilks and colleagues has shown a similar clustering of SARS-CoV-2 variants on antigen maps, indicating that hamsters and humans generate similar antibody responses. Wilkins’ maps also showed some discrepancies; subsequently, their map showed a distance ~ twice as large between D614G and the Beta, Gamma, and Mu variants compared to the antigenic map of the present study. The differences may be due to lower titers observed in naturally infected humans compared to experimentally infected hamsters.
It is difficult to obtain human serum after primary SARS-CoV-2 infection. The current study presented hamster antisera as a useful substitute for generating antigen maps and evaluating antigen relationships between SARS-CoV-2 variants.