Unraveling the mechanism behind the probable extinction of the B/Yamagata lineage of influenza B viruses

Wenjie Han, Jinfeng Zeng, Jiayi Shi, Jingru Feng, Yilin Chen, Jialu Zheng, Peiwen Cheng, Ke Zhai, Chi Zhang, Zekai Qiu, Zicheng Cao, Xue Zhang, Jian Chen, Wenping Xie, Xuejie Du, Qing Guo, Yousong Peng, Dayan Wang, Yuelong Shu (), Taijiao Jiang () and Xiangjun Du ()
Additional contact information
Wenjie Han: Sun Yat-sen University, School of Public Health (Shenzhen)
Jinfeng Zeng: Sun Yat-sen University, School of Public Health (Shenzhen)
Jiayi Shi: Sun Yat-sen University, School of Public Health (Shenzhen)
Jingru Feng: Sun Yat-sen University, School of Public Health (Shenzhen)
Yilin Chen: Sun Yat-sen University, School of Public Health (Shenzhen)
Jialu Zheng: Sun Yat-sen University, School of Public Health (Shenzhen)
Peiwen Cheng: Sun Yat-sen University, School of Public Health (Shenzhen)
Ke Zhai: Sun Yat-sen University, School of Public Health (Shenzhen)
Chi Zhang: Sun Yat-sen University, School of Public Health (Shenzhen)
Zekai Qiu: Sun Yat-sen University, School of Public Health (Shenzhen)
Zicheng Cao: Sun Yat-sen University, School of Public Health (Shenzhen)
Xue Zhang: Sun Yat-sen University, School of Public Health (Shenzhen)
Jian Chen: Sun Yat-sen University, School of Public Health (Shenzhen)
Wenping Xie: Huazhong University of Science and Technology, College of Life Science and Technology
Xuejie Du: Chinese Center for Disease Control and Prevention
Qing Guo: Chinese Center for Disease Control and Prevention
Yousong Peng: Hunan University, Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology
Dayan Wang: Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases
Yuelong Shu: Sun Yat-sen University, School of Public Health (Shenzhen)
Taijiao Jiang: Guangzhou National Laboratory
Xiangjun Du: Sun Yat-sen University, School of Public Health (Shenzhen)

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract The COVID-19 pandemic caused an unprecedented disruption to the global circulation of influenza viruses. Among the most notable outcomes was the probable extinction of the B/Yamagata lineage of influenza B viruses, which has been rarely detected since March 2020. However, the underlying mechanism of the probable extinction is unknown. Here, we combine molecular, antigenic, and epidemiological data to explore the drivers of this phenomenon. Our analysis reveals that the probable extinction of B/Yamagata was driven by reduced transmission due to nonpharmaceutical interventions (NPIs) and a depleted susceptible population caused by conserved antigenicity and the 2017/2018 outbreak. Specifically, B/Yamagata exhibited slower antigenic evolution and alternating antigenic dominance compared to the co-circulating B/Victoria lineage, which was consistent with its weaker positive selection pressure. Simulation analysis suggests that B/Yamagata would maintain circulation if it underwent significant antigenic drift around the COVID-19 pandemic or if NPIs were not implemented. These findings provide a mechanistic explanation for the probable extinction of B/Yamagata and offer broader insights for controlling similar respiratory viruses.

Date: 2025
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DOI: 10.1038/s41467-025-65396-6

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