Functional and Structural Basis of Omicron BA.3.2.1 Spike

SARS-CoV-2 Omicron descendant BA.3.2, derived from BA.3 and carrying 39 additional spike substitutions, prompts concerns about altered fitness and antigenicity. Using BA.3.2.1 as a representative sublineage, we have engineered live-attenuated mNeonGreen SARS-CoV-2 encoding spikes from BA.3.2.1 and the JN.1-derived LP.8.1 and XEC, and benchmarked them against BA.3 and KP.3 in Calu-3 cells and primary human airway epithelium. BA.3.2.1 outcompetes BA.3 yet replicates more slowly than JN.1-descendants. Despite increased RBD-hACE2 affinity, BA.3.2.1 spike binds hACE2 less efficiently than LP.8.1, and shows the greatest resistance to neutralization by sera from KP.2/KP.3 infections. Cryo-EM reveals a predominantly…