Human and hamster sera correlate well in identifying antigenic drift among SARS-CoV-2 variants, including JN.1

Abstract

Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with fivefold to sixfold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a fivefold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.IMPORTANCEUpdates to COVID-19 vaccine antigens depend on assessing how much vaccine antigens differ antigenically from newer SARS-CoV-2 variants. Human sera from single variant infections are ideal for discriminating antigenic differences among variants, but such primary infection sera are now rare due to high population immunity. It remains unclear whether sera from experimentally infected animals could substitute for human sera for antigenic assessments. This report shows that neutralization titers of variant-matched human and hamster primary infection sera correlate well and recognize variants similarly, indicating that hamster sera can be a proxy for human sera for antigenic assessments. We further show that human sera following an XBB.1.5 booster vaccine broadly neutralized XBB sub-lineage variants but titers were fivefold lower against the more recent JN.1 variant. These findings support updating the current COVID-19 vaccine variant composition and developing a framework for assessing antigenic differences in future variants using hamster primary infection sera.

Keywords: COVID-19 vaccines; JN.1 variant; SARS-CoV-2 variants; XBB.1.5 booster sera; antigenic assessments; antigenic maps; hamster sera; neutralization titers.

Fig 1

Neutralization titers and specificity against SARS-CoV-2 variants by hamster primary infection sera. (A) Hamster pre-Omicron primary infection sera. (B) Hamster Omicron primary infection sera. Neutralization titers against the indicated variants in hamster primary infection sera are plotted. Dots indicate the results from individual samples that are connected among titers against different variants. Neutralizations were measured in lentiviral-based pseudovirus neutralization assays. Statistical analysis was performed by Dunn’s multiple comparison tests. Neutralization titers against different variants were compared to the neutralization titers of the infecting variant in each sera panel. P values for comparisons between the groups are shown, where *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. n: sample number.

Fig 2

Neutralization titers and specificity against SARS-CoV-2 variants correlate well between human and hamster primary infection sera. Neutralization titers (GMT) against the indicated variants in human and hamster primary infection sera of the indicated SARS-CoV-2 variants infection are plotted. A Spearman correlation of neutralization titers of individual human and hamster serum samples against variants in each sera panel is analyzed. The Neutralization titers of the individual serum samples against the variants are shown in Fig. S2. A Pearson correlation among all neutralization titers (GMT) of all human and hamster sera is analyzed. Dots indicate the GMT. n: sample number. All data human primary infection sera were reported previously (26). Spike genotypes of the hamster infections and pseudoviruses used for neutralizations are listed in Table S4. Spike genotypes of the human infections are listed in Tables S7 and S8. A full comparison of the genotypes of all spikes is shown in Fig. S1.

Fig 3

Antigenic maps made with neutralization titers from human and hamster primary infection sera closely resemble one another. Antigenic maps were made using antigenic cartography with titers for primary infection sera from (A) humans and (B) hamsters. (C) Comparison of virus positions between human primary infection map and hamster primary infection map. Arrows point to virus positions from the human map to the hamster map. (D) Merged human-hamster map containing primary infection sera from both humans and hamsters. (E) Merged human-hamster map compared to the hamster primary infection map. (F) Submap including only the hamster XBB cluster. Each grid-square side corresponds to a twofold dilution in the pseudovirus neutralization assay. Antigenic distance is measured in any direction on the grid. Antigens are shown as circles and labeled. Sera are shown as squares and are colored by the infecting variant. The human primary infection map was reported previously (26).

Fig 4

Neutralization titers and specificity against SARS-CoV-2 variants in human sera after multiple antigen exposures. (A) Neutralization titers represented as 50% inhibitory dilutions (ID₅₀) against pseudoviruses bearing spike proteins from the indicated variants are plotted for the human sera after multiple antigen exposures. Dots indicate the results from individual samples that are connected among titers against different variants. (B) The comparison of neutralization titers (GMT) against the indicated variants in each sera panel. Two-way ANOVA was performed to determine the difference between two different sample groups with individual serum neutralization titers against variants. P values for the difference between the two groups are shown, where *P < 0.05, **P < 0.01, and ****P < 0.0001. n: sample number. All data on human primary infection sera were reported previously (26). All data of V3 sera, except neutralizations against the stains of XBB-lineages, were reported previously (26). Neutralization titers against D614G, BA.4/BA.5, BQ.1.1, XBB, and XBB.1.5 in the sera panels of V4 + Bi, V3 + Bi, V3 + PVI, and V4 were reported previously (29). XBB.1.5 booster group* includes six individuals without reported PVIs; three individuals with presumed BA.1 PVIs; four individuals with presumed BA.5 PVIs after three doses of the ancestral COVID-19 vaccine; and three individuals with presumed XBB PVIs after the bivalent booster. PVI infections were assigned according to the time of infections.

Fig 5

Antibody landscapes of multiple antigen exposure sera groups show that the XBB.1.5 COVID-19 booster vaccine increases magnitude and breadth of antibody titers against newer variants. (A–E) Antibody landscapes generated with (A) V3 + Bi vaccination sera, (B) V3 + PVI sera, (C) V4 vaccination sera, (D) V4 + Bi vaccination sera, and (E) XBB 1.5 booster sera*. (F) Each multiple antigen exposure serum group is stacked on top of one another for visualization. All antibody landscapes were plotted above the full hamster antigenic map seen in Fig. 3B. The x and y coordinates indicate the location of the variants in the 2D map with measured titer plotted on the z-axis in a third dimension above the antigenic map. A cone landscape was fitted and plotted above each 2D map with each landscape being fitted with its slope. Each landscape is a representation of the average of all individual landscapes within that distinct multiple antigen exposure group. The peak of the cone landscape represents the highest titer measured against any of the antigens. This peak was consistently located above D614G. Lines extending from the x- and y-axes into the z-axis represent the average log GMT against the antigen located at that x,y coordinate. Residuals between measured and predicted titers are represented by a dotted line above or below the landscape corresponding to each antigen.

Fig 6

Serum clustering visualizations showing that distances between newer variants and D614G decrease with XBB.1.5 booster. (A–E) Antigenic cartography tools were used to measure antigenic distances between D614G and other variants for different multiple antigen exposure groups. (A) V3 + Bi vaccination sera, (B) V3 + PVI sera, (C) V4 vaccination sera, (D) V4 + Bi vaccination sera, and (E) XBB.1.5 booster sera*. Lines indicate antigenic distances from ancestral D614G to a newer variant. Sera are shown as small squares and viruses as colored circles. (F) Antigenic distances between D614G and newer variants for each multiple antigen exposure group.