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TitlePathogenicity, virological features, and immune evasion of SARS-CoV-2 JN.1-derived variants including JN.1.7, KP.2, KP.3, and KP.3.1.1.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 11002, Year 2025
Publish dateDec 11, 2025
AuthorsJialu Shi / Xiaoyu Zhao / Xiaohui Jin / Jiayan Li / Yuanchen Liu / Huan Liu / Ye-Fan Hu / Zhe Chen / Yuxin Xiao / Lei Wang / Yajie Wang / Yixin He / Yue Chai / Bingjie Hu / Huiping Shuai / Yang Wang / Xiangnan Li / Shujun Jiang / Yanliang Zhang / Xiaojuan Zhang / Wan-Mui Chan / Lin-Lei Chen / Jian-Piao Cai / Baokun Sui / Honglei Zhang / Dong Yang / Longchao Zhu / Shuofeng Yuan / Jie Zhou / Jian-Dong Huang / Kwok-Yung Yuen / Kelvin Kai-Wang To / Jasper Fuk-Woo Chan / Bao-Zhong Zhang / Qiao Wang / Maozhou He / Lei Sun / Pengfei Wang / Hin Chu /
PubMed AbstractKP.3.1.1 became a dominant successor to JN.1 by the second half of 2024 but the intrinsic pathogenicity and virological feature of KP.3.1.1 remain incompletely understood. Here, we comprehensively ...KP.3.1.1 became a dominant successor to JN.1 by the second half of 2024 but the intrinsic pathogenicity and virological feature of KP.3.1.1 remain incompletely understood. Here, we comprehensively evaluated the pathogenesis and characteristics of KP.3.1.1 in comparison to JN.1 and other JN.1-derived variants including JN.1.7, KP.2, and KP.3. The unique S31del mutation on KP.3.1.1 spike confers further evasion to the clinically authorized mAb Pemivibart and reduces convalescent serum neutralization efficiency. Structural analysis indicates that S31del induces novel glycosylation sites that facilitates evasion of neutralizing antibodies. We further reveal that S31del significantly enhances pseudovirus entry efficiency in all evaluated cell types including the human primary nasal epithelial cells. Nevertheless, the intrinsic pathogenicity of KP.3.1.1 is similar to JN.1 and KP.3, and higher than that of JN.1.7 and KP.2 in a male hamster model. Interestingly, the increased virus infectivity conferred by S31del in KP.3.1.1 spike is counterbalanced by the NSP10 S33C mutation. Overall, our study indicates that a single spike mutation can confer both enhanced immune escape and increased viral infectivity. The opposing effects of spike and non-spike mutations highlight the complex interplay of viral genomic elements in shaping their overall fitness, and reveal the high plasticity of coronavirus evolution.
External linksNat Commun / PubMed:41381428 / PubMed Central
MethodsEM (single particle)
Resolution2.27 - 2.9 Å
Structure data

64077

9ue6

EMDB-64077, PDB-9ue6:
Cryo-EM structure of SARS-CoV-2 KP.2 spike RBD in complex with ACE2
Method: EM (single particle) / Resolution: 2.9 Å

64078

9ue7

EMDB-64078, PDB-9ue7:
Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2
Method: EM (single particle) / Resolution: 2.27 Å

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/HYDROLASE / Spike and ACE2 complex / VIRAL PROTEIN-HYDROLASE complex

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