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Functional and structural basis of Omicron BA.3.2.1 spike.

Created on 10 Aug 2026

Authors

Yan Wang, Yanping Hu, Zhenhang Chen, Jing Zou, Ke Zhang, Ping Ren, Pei-Yong Shi, Bo Liang, Xuping Xie

Published in

Cell reports. Volume 45. Issue 8. Pages 117812. Aug 08, 2026. Epub Aug 08, 2026.

Abstract

SARS-CoV-2 BA.3.2 sublineages, derived from BA.3 and carrying substantial spike divergence, raised concerns about altered fitness and antigenicity. Using BA.3.2.1 as a representative strain, we engineered live-attenuated SARS-CoV-2 encoding BA.3.2.1, LP.8.1, or XEC spikes and benchmarked them against BA.3 and KP.3. BA.3.2.1 outcompetes BA.3 in primary human airway epithelium but replicates less efficiently than JN.1 descendants and shows the greatest resistance to neutralization by KP.2/KP.3 convalescent sera. Although BA.3.2.1 RBD binds hACE2 with high affinity, its trimeric spike engages hACE2 less efficiently than LP.8.1. Cryoelectron microscopy structures reveal that BA.3.2.1 spike predominantly adopts a compact, asymmetric closed conformation stabilized by protomer rearrangements, N-linked glycosylation, and a distinct fusion-peptide-proximal region. This architecture increases spike stability, limits receptor engagement, reduces fusogenicity, and masks antibody-sensitive epitopes. Thus, BA.3.2.1 enhances immune evasion at the cost of replication fitness, providing a structural-functional explanation for BA.3.2's limited prevalence and underscoring the need for continued variant surveillance.

PMID:
42571698
Bibliographic data and abstract were imported from PubMed on 10 Aug 2026.

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