A recent study published in the journal Proceedings of the National Academy of Sciences presented an antigenic map of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants constructed from hamster sera.
The 2019 coronavirus disease (COVID-19) pandemic has caused more than 775 million cases and more than 7 million deaths worldwide. Vaccination has significantly reduced disease burden and mortality rates. Nevertheless, the antigenic variability of SARS-CoV-2 due to substitutions in its spike protein has led to escape from neutralizing antibodies induced by vaccines or infections.
Omicron variants of SARS-CoV-2 show strong immune escape compared to previous variants, which has led to the development of bivalent vaccines containing additional antigens. Initial efforts to track the antigenic evolution of SARS-CoV-2 were based on primary infection or human vaccination sera. However, the use of primary infection sera is becoming increasingly difficult.
The antigenic map was constructed using the Racmacs package, ensuring robustness to missing data and noise.
Study: Antigenic mapping using variant-specific hamster sera reveals significant antigenic variation among Omicron subvariants. Image credit: Lightspring / Shutterstock
The study and findings
In the present study, the researchers constructed the antigenic map of SARS-CoV-2 variants using hamster sera. First, female Syrian hamsters were infected with SARS-CoV-2 B.1, Alpha, Beta, Delta, Omicron BA.1, BA.2, BA.2.12, BA.5 and XBB.2 and a mechanical B. 1 variant with E484K replacement (B.1+E484K). Hamsters were infected twice to increase serum neutralization. Sera were collected two weeks after the second infection.
In addition, sera from unvaccinated humans infected with D614G, Alpha, or Beta were used to examine whether reactivity patterns in hamster sera were similar to those in human sera. Sera were titrated by plaque reduction neutralization assay in Vero E6 cells against different live SARS-CoV-2 isolates. All hamsters had high antibody titers and those infected with the same isolate had uniform patterns of reactivity.
Titers between the BA.4 and BA.5 isolates and the two BA.2 isolates were comparable. Sera from those infected with pre-Omicron variants were at least reactive to each non-homologous pre-Omicron variant. Titers of pre-Omicron sera were lower against Omicron variants BA.1, BA.2 and BA.4/5. D614G sera were unreactive or had low titers against Omicron variants BN.1.3.1, BQ.1.18, XBB.2 and BF.7.
Antigenic map showing antigenic relationships between SARS-CoV-2 variants and sera. The distances between each variant and serum correspond to the fold of the maximum titer for each serum. Viruses are shown as circles, sera as squares, with sera colored in the color of their homologous variant (blue: D614G, green: Alpha, dark-yellow: Beta, orange: Delta, green-blue: Mu, cyan: B .1 +E484K, red: BA.1, orchid: BA.2 (2×, on top of each other), pink: BA.4 and BA.5, ocher: BQ.1.18, brown: BF.7, sea green : XBB.2, light-orchid: BN.1.3.1, dark blue: EG.4.1, yellow: JN.1). The side length of each grid square corresponds to a two-fold dilution of serum in the neutralization assay. Map rotation is arbitrary and here is oriented to match previously published maps.
Omicron sera showed undetectable or low titers against pre-Omicron variants. In addition, sera BA.1 and BA.2 showed reactivity against BA.2 and BA.1, respectively, but had low or undetectable titers against Omicron JN.1, EG.5.1, XBB.2, BN.1.3. 1 , variants BQ.1.18 and BF.7. BA.5 sera had high titers against variants BQ.1.18, BA.5, BF.7, EG.5.1 and XBB.2 but not against JN.1, BA.1, BN.1.3.1 or BA. 2.
XBB.2 sera showed high titers against the homologous variant XBB.2, with some reactivity against JN.1, BA.5 and EG.5.1. Primary titers and fold changes showed significant antigenic distance between the Omicron and pre-Omicron variants. In addition, antigenic diversity was significantly high among Omicron variants.
The antigenic map showed that many Omicron subvariants are often as antigenically different from each other as the wild type is from Omicron BA.1, highlighting the substantial diversity among Omicron subvariants.
The team developed an antigenic map of the titers and noted a cluster of pre-Omicron variants and a loose clustering of Omicron variants. The antigenic distance between Omicron variants was almost similar to that between BA.1 and pre-Omicron variants. BQ.1.18, BF.7 and BA.4/5 formed a relatively tight cluster.
The JN.1 variant was the most distant from the D614G strain and was placed at a distance from the EG.5.1 and XBB.2 variants. Interestingly, JN.1 and BN.1.3.1 had close antigenic similarity. Notably, the largest antigenic distances were due to the inclusion of titers against XBB.2, BA.1, BA.2 and BA.5, as their exclusion caused close clustering of Omicron variants. This meant that Omicron sera (not pre-Omicron sera) were required to detect differences between Omicron variants.
The study findings were compared with previous antigenic maps, highlighting differences in the placement of certain Omicron subvariants.
The team also investigated the type and minimum number of sera necessary for proper antigenic triangulation of maps. This analysis excluded titers between sera XBB.2 and BA.5 and variants JN.1, EG.5.1, BN.1.3.1, XBB.2, BQ.1.18 and BF.7. Antigenic maps were generated from random sample combinations of sera groups and sera. BA.1 and BA.2 serogroups were required for adequate placement of the Omicron variants and thus were always included.
Subsampling from pre-Omicron sera pools yielded antigenic maps similar to those constructed from all sera. However, reducing the number of sera per serogroup negatively affected the map topology, although the number of pre-Omicron serogroups could be reduced. Finally, a comparison of titers between hamster and human sera revealed that titers in hamster sera were higher in magnitude, with less fold change and more compact topology.
conclusions
Overall, the study presented an antigenic map of SARS-CoV-2 variants using hamster sera, revealing the clustering of pre-Omicron variants and the distinct location of Omicron variants. The Omicron JN.1 variant was the most distant from the D614G strain. This antigenic map was similar to a previously reported map constructed from hamster sera, although with some differences. Overall, the findings highlight the utility and suitability of monospecific hamster sera.
The study notes potential limitations, including variability in individual responses and the effect of the prime-boost immunization strategy on antibody specificity and affinity.
