Distinctive serotypes of SARS-related coronaviruses defined by convalescent sera from unvaccinated individuals

Abstract

Multiple Omicron sub-lineages have emerged, with Omicron XBB and XBB.1.5 subvariants becoming the dominant variants globally at the time of this study. The key feature of new variants is their ability to escape humoral immunity despite the fact that there are limited genetic changes from their preceding variants. This raises the question of whether Omicron should be regarded as a separate serotype from viruses serologically clustered with the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Here, we present cross-neutralization data based on a pseudovirus neutralization test using convalescent sera from naïve individuals who had recovered from primary infection by SARS-CoV-1 and SARS-CoV-2 strains/variants including the ancestral virus and variants Beta, Delta, Omicron BA.1, Omicron BA.2 and Omicron BA.5. The results revealed no significant cross-neutralization in any of the three-way testing for SARS-CoV-1, ancestral SARS-CoV-2 and SARS-CoV-2 Omicron subvariants. The data argue for the assignment of three distinct serotypes for the currently known human-infecting SARS-related coronaviruses.

Keywords: Omicron; SARS-CoV-1; SARS-CoV-2; convalescent sera; primary infection; serotype.

Figure 1.. Prevalence of major Omicron variants over time

(A) Prevalence of Omicron (BA.1, BA.2, BA.2.75, BA.5, BQ.1.1, XBB and XBB.1.5) in Israel, Singapore, South Africa, the United States and worldwide over the last 15 months (since December 2021). (B) Mutations on the spike genes in Omicron (BA.1, BA.2, BA.2.75, BA.5, BQ.1.1, XBB and XBB.1.5). Data were retrieved from GISAID (https://www.gisaid.org/, 28 March 2023) via the outbreak.info API.

Figure 2.. Neutralization titers against 11 different pseudoviruses with spike proteins derived from ancestral SARS-CoV-2, Beta, Delta, Omicron BA.1, BA.2, BA.5, and SARS-CoV-1

The neutralization titer 50% (NT50) values were determined using a pseudovirus neutralization test in plasma samples derived from naïve-infected individuals who had recovered from (A) Ancestral, (B) Beta, (C) Delta, (D) SARS-CoV-1, (E) Omicron BA.1, (F) Omicron BA.2 and (G) Omicron BA.5. Geometric mean NT50 was indicated on each of the dot plot. The red line indicates threshold of neutralization for each virus, and the samples under this threshold were regarded as negative. Paired two-sided Wilcoxon rank-sum tests were used. For each comparison, the infected virus strain was set as the reference group. All statistical analyses were performed using GraphPad Prism 9. A P value less than 0.05 indicates statistical significance. The *, **, ***, and **** indicate P values less than 0.05, 0.01, 0.001 and 0.0001, respectively. (H) Antigenic cartography was generated by the NT50 in pseudoviruses (color circles) from all serum panels examined (naïve Ancestral, n = 20; naïve Beta, n = 10; naïve delta, n = 10; naïve Omicron BA.1, n = 11; naïve Omicron BA.2, n = 10; naïve Omicron BA.5, n = 5; naïve SARS-CoV-1, n = 14). The x and y axes represent the antigenic distance, with the space of the grey grid lines showing 1 antigenic unit (two-fold dilution in titer). (I) The antigenic distances between viruses were shown in the heatmap.

Figure 3.. Neutralization titers against 11 different pseudoviruses with spike proteins derived from ancestral SARS-CoV-2, Omicron (BA.1, BA.2, BA.2 L452R, BA.2 F486V, BA.5, BA.4.6.1, BA.2.75.1, XBB, and BQ.1.1) and SARS-CoV-1

The neutralization titer 50% (NT50) values were determined using pseudovirus neutralization test in plasma samples derived from individuals who had received two (A) or three (B) doses of BNT162b2. A geometric mean NT50 value was indicated on each plot. The red line indicates threshold of neutralization for each virus, and the samples under this threshold were regarded as negative. Paired two-sided Wilcoxon rank-sum tests were used. The ancestral virus was set as the reference group. All statistical analyses were performed using GraphPad Prism 9. A P value less than 0.05 indicates statistical significance. The *, **, ***, and **** indicate P values less than 0.05, 0.01, 0.001 and 0.0001, respectively. The antigenic map was generated using the NT50 in pseudoviruses from serum samples derived from individuals who received two (C) and three (D) doses of BNT162b2. The x and y axes represent the antigenic distance, with the space of the grey grid lines showing 1 antigenic unit (two-fold dilution in titer).

Figure 4.. Antigenic characterization of ancestral SARS-CoV-2, Omicron (BA.1, BA.2, BA.2 F486V, BA.2 L452R, BA.5, BA.4.6.1, BQ.1.1, XBB), and SARS-CoV-1 using BNT162b2 vaccinated sera

The heatmap indicates antigenic unit (AU) distance between viruses determined using serum samples derived from individuals who had been receiving (A) two doses of BNT162b2 and (B) three doses of BNT162b2.