Antibody evasiveness of SARS-CoV-2 subvariants KP.3.1.1 and XEC

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and spread, and it remains critical to understand the functional consequences of mutations in dominant viral variants. The recombinant JN.1 subvariant XEC recently replaced KP.3.1.1 to become the most prevalent subvariant worldwide. Here, we measure the in vitro neutralization of KP.3.1.1 and XEC by human sera, monoclonal antibodies, and the soluble human ACE2 (hACE2) receptor relative to the parental subvariants KP.3 and JN.1. KP.3.1.1 and XEC are slightly more resistant (1.3- to 1.6-fold) than KP.3 to serum neutralization and antigenically similar. Both also demonstrate greater resistance to neutralization by select monoclonal antibodies and soluble hACE2, all of which target the top of the viral spike. Our findings suggest that the upward motion of the receptor-binding domain in the spike may be partially hindered by the N-terminal domain mutations in KP.3.1.1 and XEC, allowing these subvariants to better evade serum antibodies that target the viral spike in the up position and to have a growth advantage.

Keywords: ACE2 inhibition; CP: Immunology; CP: Microbiology; JN.1 subvariants; KP.3.1.1; SARS-CoV-2; XEC; antibody evasion; mRNA vaccines; monoclonal antibodies; serum neutralization.

Graphical abstract

Figure 1

Characterization of SARS-CoV-2 JN.1 sublineages, including serum neutralizing antibody evasion and antigenicity (A) Relative frequencies of dominant SARS-CoV-2 subvariants from April 2024 to February 2025; data are from GISAID. (B) Viral evolutionary pathways and spike mutations of the indicated JN.1 subvariants. (C and D) Serum neutralizing titers (ID₅₀) against VSV-based pseudoviruses bearing spike proteins from SARS-CoV-2 JN.1 sublineages for samples from cohorts JN.1 infx (C) and KP.2 MV (D). Compared with KP.3, KP.3.1.1 carries an S31Δ spike mutation in the NTD. The geometric mean ID₅₀ titer (GMT) is presented at the top. The fold change in GMT for each virus compared to KP.3 is also shown immediately above the symbols. Statistical analyses used Wilcoxon matched-pairs signed-rank tests, comparing to KP.3. n, sample size; ns, not significant. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, ^∗∗∗∗p < 0.0001. Numbers under the dotted lines denote numbers of serum samples that were under the limit of detection (ID₅₀ < 100). (E) Antigenic map generated using all neutralization data from (C) and (D). One antigenic unit (AU) represents an approximately 2-fold change in ID₅₀ titer. Serum samples and viruses are shown as squares and dots, respectively. The geometric mean antigenic distance of variants to sera is indicated in brackets.

Figure 2

mAb neutralization, hACE2 inhibition, and structural analysis of the indicated JN.1 sublineage variants (A) mAb neutralization against the indicated pseudoviruses. Antibody concentrations resulting in 50% inhibition of infectivity (IC₅₀) are presented. (B) Sensitivity of JN.1 subvariants to hACE2 inhibition. IC₅₀ values are also presented. Data are shown as mean ± SEM for three technical replicates. (C) Structural analysis of S31Δ and F59S in the complex of C1717 and NTD (PDB: 7UAR). (D) Structural analysis of T22N, S31Δ, and F59S in the SARS-CoV-2 spike (PDB: 7KRR), shown in complex with VYD222 (cyan; PDB: 7U2D) and 25F9 (green; PDB: 8GB5).