Characteristics of JN.1-derived SARS-CoV-2 subvariants SLip, FLiRT, and KP.2 in neutralization escape, infectivity and membrane fusion

Abstract

SARS-CoV-2 variants derived from the immune evasive JN.1 are on the rise worldwide. Here, we investigated JN.1-derived subvariants SLip, FLiRT, and KP.2 for their ability to be neutralized by antibodies in bivalent-vaccinated human sera, XBB.1.5 monovalent-vaccinated hamster sera, sera from people infected during the BA.2.86/JN.1 wave, and class III monoclonal antibody (Mab) S309. We found that compared to parental JN.1, SLip and KP.2, and especially FLiRT, exhibit increased resistance to COVID-19 bivalent-vaccinated human sera and BA.2.86/JN.1-wave convalescent sera. Interestingly, antibodies in XBB.1.5 monovalent vaccinated hamster sera robustly neutralized FLiRT and KP.2 but had reduced efficiency for SLip. These JN.1 subvariants were resistant to neutralization by Mab S309. In addition, we investigated aspects of spike protein biology including infectivity, cell-cell fusion and processing, and found that these subvariants, especially SLip, had a decreased infectivity and membrane fusion relative to JN.1, correlating with decreased spike processing. Homology modeling revealed that L455S and F456L mutations in SLip reduced local hydrophobicity in the spike and hence its binding to ACE2. In contrast, the additional R346T mutation in FLiRT and KP.2 strengthened conformational support of the receptor-binding motif, thus counteracting the effects of L455S and F456L. These three mutations, alongside D339H, which is present in all JN.1 sublineages, alter the epitopes targeted by therapeutic Mabs, including class I and class III S309, explaining their reduced sensitivity to neutralization by sera and S309. Together, our findings provide insight into neutralization resistance of newly emerged JN.1 subvariants and suggest that future vaccine formulations should consider JN.1 spike as immunogen, although the current XBB.1.5 monovalent vaccine could still offer adequate protection.

Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages

“…The latter scientific rationale is exemplified by the recent XBB.1.5 monovalent vaccine, where selecting a dominant and antigenically distinct spike protein for the vaccine formulation has led to improved serum neutralization of prevalent variants 1 . However, there have only been very limited studies reported on the antibody responses after JN.1 breakthrough infections 14-16 . Moreover, there is a lack of systematic evaluation of antigenicity of key JN.1 sublineages that carry various combinations of the aforementioned recurrent mutations.…”

Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape

“…A series of variants with mutations at L455, F456, and R346 convergent hotspot sites emerged including "SLip" variant which has the JN.1 mutations (L455S) with the additional F456L mutation [36]. More recently, we have seen the emergence of the FLiRT variant, which harbors an additional R346T mutation in the backbone of SLip.…”

“…More recently, we have seen the emergence of the FLiRT variant, which harbors an additional R346T mutation in the backbone of SLip. Recent studies revealed that that F456L (SLip) and R346T (FLiRT) subvariants of JN.1 contribute to further escape of JN.1derived variants from neutralizing antibodies [36,37]. Since January 2024, JN.1 diversified into a number of sublineages, many of which share recurrent mutations R346T ( JN.1.18), F456L ( JN.1.16), T572I ( JN.1.7), or combinations of these mutations (KP.2 variant).…”