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bioRxiv · 10.1101/2023.08.08.552415

Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5

Kaku, Y.·Kosugi, Y.·Uriu, K.·Ito, J.·Kuramochi, J.·Sadamasu, K.·Yoshimura, K.·Asakura, H.·Nagashima, M.·The Genotype to Phenotype Japan (G2P-Japan) Consortium,·Sato, K.
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Abstract

As of July 2023, EG.5.1 (a.k.a. XBB.1.9.2.5.1), a XBB subvariant bearing the S:Q52H and S:F456L substitutions, alongside the S:F486P substitution (Figure S1A), has rapidly spread in some countries. On July 19, 2023, the WHO classified EG.5 as a variant under monitoring. First, we showed that EG.5.1 exhibits a higher effective reproduction number compared with XBB.1.5, XBB.1.16, and its parental lineage (XBB.1.9.2), suggesting that EG.5.1 will spread globally and outcompete these XBB subvariants in the near future. We then addressed whether EG.5.1 evades from the antiviral effect of the humoral immunity induced by breakthrough infection (BTI) of XBB subvariants and performed a neutralization assay using XBB BTI sera. However, the 50% neutralization titer (NT50) of XBB BTI sera against EG.5.1 was comparable to those against XBB.1.5/1.9.2 and XBB.1.16. Moreover, the sensitivity of EG.5.1 to convalescent sera of XBB.1- and XBB.1.5-infected hamsters was similar to those of XBB.1.5/1.9 and XBB.1.16. These results suggest that the increased Re of EG.5.1 is attributed to neither increased infectivity nor immune evasion from XBB BTI, and the emergence and spread of EG.5 is driven by the other pressures. We previously demonstrated that Omicron BTI cannot efficiently induce antiviral humoral immunity against the variant infected. In fact, the NT50s of the BTI sera of Omicron BA.1, BA.2, and BA.5 against the variant infected were 3.0-, 2.2-, and 3.4-fold lower than that against the ancestral B.1.1 variant, respectively. However, strikingly, we found that the NT50 of the BTI sera of XBB1.5/1.9 and XBB.1.16 against the variant infected were 8.7- and 8.3-fold lower than that against the B.1.1 variant. These results suggest that XBB BTI cannot efficiently induce antiviral humoral immunity against XBB subvariants. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/552415v1_figs1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@f95376org.highwire.dtl.DTLVardef@d66fa8org.highwire.dtl.DTLVardef@3c8841org.highwire.dtl.DTLVardef@15824c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO Virological features of EG.5.1 and XBB BTI (A) Frequency of mutations of interest in the representative XBB sublineages. Only mutations with a frequency >0.5 in at least one but not all the representative sublineages are shown. Note that the S proteins of XBB.1.5 and XBB.1.9.2 are identical. (B) Estimated epidemic dynamics of the representative XBB sublineages in countries where >50 sequences of EG.5.1, XBB.1.5, XBB.1.9.2, and XBB.1.16 were detected from April 1, 2023 to July 13, 2023. Countries are ordered according to the number of detected sequences of EG.5.1. Line, posterior mean; ribbon, 95% Bayesian confidence interval. The dynamics for EG.5.1 is highlighted by a red arrowhead. (C) Estimated relative Re of the representative XBB sublineages in the six countries. The relative Re of XBB.1.5 is set to 1 (horizontal dashed line). Violin, posterior distribution; dot, posterior mean; line, 95% Bayesian confidence interval. (D) Lentivirus-based pseudovirus assay. HOS-ACE2-TMPRSS2 cells were infected with pseudoviruses bearing each S protein. The amount of input virus was normalized to the amount of HIV-1 p24 capsid protein. The percentage infectivity of XBB.1.5/1.9.2, XBB.1.5/1.9.2+Q52H, XBB.1.5/1.9.2+F456L, and EG.5.1 compared to that of XBB.1.5/1.9.2 are shown. The horizontal dash line indicates the mean value of the percentage infectivity of the XBB.1.5/1.9.2. Assays were performed in quadruplicate. The presented data are expressed as the average {+/-} SD. Each dot indicates the result of an individual replicate. (E-G) Neutralization assay. Assays were performed with pseudoviruses harboring the S proteins of B.1.1, BA.1, BA.2, BA.5, BQ.1.1, XBB.1, XBB.1.5/1.9.2, XBB.1.16, EG.5.1, XBB.1.5/1.9.2+Q52H, and XBB.1.5/1.9.2+F456L. The following sera were used: convalescent sera from fully vaccinated individuals who had been infected with XBB.1.5 (one 3-dose vaccinated. 1 donor in total), XBB.1.9 (one 3-dose vaccinated donor, one 4-dose vaccinated donor and one 5-dose vaccinated donor. 3 donors in total), and XBB.1.16 (one 2-dose vaccinated donor, two 3-dose vaccinated donors, and one 4-dose vaccinated donor. 4 donors in total) (E); sera from hamster infected with XBB.1 (left) or XBB.1.5 (right) (F); and convalescent sera from fully vaccinated individuals who had been infected with BA.1 (thirteen 2-dose vaccinated, 13 donors in total) (left)1, BA.2 (nine 2-dose vaccinated and four 3-dose vaccinated donors. 13 donors in total) (middle)19, and BA.5 (one 2-dose vaccinated, thirteen 3-dose vaccinated donors, and one 4-dose vaccinated. 15 donors in total) (right)19 (G). Each dot indicates the result of an individual replicate. Assays for each serum sample were performed in triplicate to determine the 50% neutralization titer (NT50). Each dot represents one NT50 value, and the geometric mean and 95% confidence interval are shown. The number in parenthesis indicates the mean of NT50 values. The horizontal dash line indicates the detection limit (120-fold). In D, statistically significant differences (**, P < 0.001, ***, P < 0.0001) versus XBB.1.5/1.9.2 were determined by two-sided Students t tests. Blue asterisks indicate decreased percentage of infectivity. In E and G, statistically significant differences versus B.1.1 were determined by two-sided Wilcoxon signed-rank tests. The fold change between B.1.1 and the variant indicated is shown in red. Background information on the convalescent donors is summarized in Table S1. In F, statistically significant differences (*, P < 0.01, **, P < 0.001) between B.1.1 and XBB.1 (left) or XBB.1.5/1.9.2 (right) were determined by two-sided Wilcoxon signed-rank tests and indicated with asterisks. Red asterisks indicate decreased NT50s. C_FIG

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Kaku, Y., Kosugi, Y., Uriu, K., Ito, J., Kuramochi, J., Sadamasu, K., Yoshimura, K., Asakura, H., Nagashima, M., The Genotype to Phenotype Japan (G2P-Japan) Consortium,, Sato, K.. 2023-08-08. Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5. https://doi.org/10.1101/2023.08.08.552415

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