Reverse mutational scanning of spike BA.2.86 identifies the epitopes contributing to immune escape from polyclonal sera

Abstract

SUMMARYThe recently detected Omicron BA.2.86 lineage contains more than 30 amino acid mutations relative to BA.2. Here, we identify the epitopes driving immune escape of BA.2.86 and its derivative JN.1 (BA.2.86 + S455L) lineage. We investigated the cross-reactive humoral immunity within a cohort of health care workers against Omicron BA.2.86 and JN.1 by employing pseudo-viral mutants. We demonstrate that BA.2.86 and especially JN.1 evaded neutralization by serum antibodies of fully vaccinated individuals. To discern the contribution of individual epitope mutations to immune escape, we constructed a library of 33 BA.2.86 mutants, each of which harbored a single revertant mutation going back to BA.2. This library was used in a reverse mutational scanning approach to define serum neutralization titers against each epitope separately. The mutations within the receptor binding domain (RBD) at position K356T and to a lesser extent the mutations N460K, V483Δ, A484K, and F486P enhanced the immune escape. More surprisingly, the mutation 16insMPLF within the spike N-terminal domain (NTD) and the mutation P621S in S1/S2 significantly contributed to antibody escape of BA.2.86. Upon XBB.1.5 booster vaccination, neutralization titers against JN.1 and BA.2.86 improved relative to all ancestral strains, and the residual immune escape was driven by mutations at positions 16insMPLF, Δ144Y, E544K, P621S, and A484K.