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TitleFunctional and structural basis of Omicron BA.3.2.1 spike.
Journal, issue, pagesCell Rep, Vol. 45, Issue 8, Page 117812, Year 2026
Publish dateAug 8, 2026
AuthorsYan Wang / Yanping Hu / Zhenhang Chen / Jing Zou / Ke Zhang / Ping Ren / Pei-Yong Shi / Bo Liang / Xuping Xie /
PubMed AbstractSARS-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 ...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.
External linksCell Rep / PubMed:42571698
MethodsEM (single particle)
Resolution2.35 - 2.82 Å
Structure data

76501

12jz

EMDB-76501, PDB-12jz:
Cryo-EM structure of SARS-CoV-2 BA.3.2.1 Spike with K852A mutation, closed conformation
Method: EM (single particle) / Resolution: 2.35 Å

EMDB-76694: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutation, flexible conformation
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-76706: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with N529Q mutation, flexible conformation
Method: EM (single particle) / Resolution: 2.82 Å

76713

12rp

EMDB-76713, PDB-12rp:
Local refinement of RBDA, RBDC, and NTDB of SARS-CoV-2 BA.3.2.1 spike with K852A mutation, closed conformation
Method: EM (single particle) / Resolution: 2.78 Å

EMDB-76849: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutation, open conformation
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-76850: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with N529Q mutation, open conformation
Method: EM (single particle) / Resolution: 2.73 Å

76936

13bd

EMDB-76936, PDB-13bd:
Local refinement of the RBD and NTD in the closed BA.3.2.1 spike with N529Q mutant
Method: EM (single particle) / Resolution: 2.65 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-CoV-2

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