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Nat Commun
. 2025 Dec 11;16(1):11002.
doi: 10.1038/s41467-025-66018-x. Pathogenicity, 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
Jialu Shi # 1 , Xiaoyu Zhao # 2 3 , Xiaohui Jin # 4 , Jiayan Li # 5 , Yuanchen Liu # 1 , Huan Liu # 1 , Ye-Fan Hu # 6 , Zhe Chen 1 , Yuxin Xiao 7 , Lei Wang 1 , Yajie Wang 4 , Yixin He 1 , Yue Chai 1 , Bingjie Hu 1 , Huiping Shuai 1 , Yang Wang 1 , Xiangnan Li 8 , Shujun Jiang 9 , Yanliang Zhang 9 , Xiaojuan Zhang 1 , Wan-Mui Chan 1 , Lin-Lei Chen 1 , Jian-Piao Cai 1 , Baokun Sui 1 , Honglei Zhang 1 , Dong Yang 10 , Longchao Zhu 11 , Shuofeng Yuan 1 12 13 , Jie Zhou 1 12 , Jian-Dong Huang 14 15 , Kwok-Yung Yuen 1 12 13 16 17 18 , Kelvin Kai-Wang To 1 12 13 17 18 , Jasper Fuk-Woo Chan 1 12 13 16 17 18 , Bao-Zhong Zhang 19 , Qiao Wang 20 , Maozhou He 21 , Lei Sun 22 , Pengfei Wang 23 , Hin Chu 24 25 26 27
Affiliations
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.
. 2025 Dec 11;16(1):11002.
doi: 10.1038/s41467-025-66018-x. Pathogenicity, 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
Jialu Shi # 1 , Xiaoyu Zhao # 2 3 , Xiaohui Jin # 4 , Jiayan Li # 5 , Yuanchen Liu # 1 , Huan Liu # 1 , Ye-Fan Hu # 6 , Zhe Chen 1 , Yuxin Xiao 7 , Lei Wang 1 , Yajie Wang 4 , Yixin He 1 , Yue Chai 1 , Bingjie Hu 1 , Huiping Shuai 1 , Yang Wang 1 , Xiangnan Li 8 , Shujun Jiang 9 , Yanliang Zhang 9 , Xiaojuan Zhang 1 , Wan-Mui Chan 1 , Lin-Lei Chen 1 , Jian-Piao Cai 1 , Baokun Sui 1 , Honglei Zhang 1 , Dong Yang 10 , Longchao Zhu 11 , Shuofeng Yuan 1 12 13 , Jie Zhou 1 12 , Jian-Dong Huang 14 15 , Kwok-Yung Yuen 1 12 13 16 17 18 , Kelvin Kai-Wang To 1 12 13 17 18 , Jasper Fuk-Woo Chan 1 12 13 16 17 18 , Bao-Zhong Zhang 19 , Qiao Wang 20 , Maozhou He 21 , Lei Sun 22 , Pengfei Wang 23 , Hin Chu 24 25 26 27
Affiliations
- PMID: 41381428
- PMCID: PMC12699034
- DOI: 10.1038/s41467-025-66018-x
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.