H3N2 influenza virus characteristics in China (2019–2022): Genetic, antigenic, and infection dynamics during the COVID-19 pandemic
Jiaming Li,
Yu Huan,
Qianfeng Xia,
Yan Li,
Rahat Ullah Khan,
Qingzhi Liu,
Chuanran Dou,
Marina Gulyaeva,
Alexander Shestopalov,
Ning Zhang,
Xuefeng Duan,
Jing Yang,
Hongchun Zhang,
Yuhai Bi
Affiliations
Jiaming Li
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
Yu Huan
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
Qianfeng Xia
Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Hainan, China
Yan Li
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
Rahat Ullah Khan
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
Qingzhi Liu
Department of Biostatistics, University of Michigan-Ann Arbor, Michigan, USA
Chuanran Dou
Lafayette College, Pennsylvania, USA
Marina Gulyaeva
Federal Research Center of Fundamental and Translational Medicine, Federal State Budget Scientific Institution, Siberian Branch of Russian Academy of Sciences, Novosibirsk State University, Novosibirskaya Oblast, Russia
Alexander Shestopalov
Federal Research Center of Fundamental and Translational Medicine, Federal State Budget Scientific Institution, Siberian Branch of Russian Academy of Sciences, Novosibirsk State University, Novosibirskaya Oblast, Russia
Ning Zhang
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
Xuefeng Duan
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
Jing Yang
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
Hongchun Zhang
Center of Respiratory Medicine, China-Japan Friendship Hospital, National Center for Respiratory Medicine, Beijing, China; Correspondence:
Yuhai Bi
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Correspondence:
Seasonal influenza activity significantly decreased in China during the coronavirus disease 2019 (COVID-19) pandemic, yet the H3N2 virus led to three epidemic waves. Understanding the characteristics of H3N2 epidemic viruses is essential for recognizing influenza during COVID-19 and for updating vaccines. In this study, we analyzed 579 respiratory samples from patients exhibiting influenza-like symptoms, collected in 2019–2022, leading to the successful sequencing of 36 complete H3N2 genomes. Genomic analysis indicated that the epidemic strains from these periods belonged to different hemagglutinin (HA) clades and exhibited phylogenetic divergence from the concurrently used vaccine strains. Significant antigenic differences were identified through cross-hemagglutination inhibition (HI) and cross-microneutralization (MN) assays. Furthermore, pathogenicity studies showed that representative strains replicated in Madin-Darby canine kidney (MDCK) cells, with varying abilities, and all replicated more effectively at 37 °C compared to 33 °C. These strains also replicated well in the respiratory tracts of mice and guinea pigs. The findings indicate a mismatch between circulating H3N2 viruses and recommended vaccine strains, highlighting the need for improved international cooperation and epidemiological surveillance of influenza viruses post-COVID-19. Optimizing effective vaccine strain update strategy and developing a universal influenza vaccine are crucial for future preparedness.
