Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus

Xiao Ding; Jingze Liu; Taijiao Jiang; Aiping Wu

doi:10.1016/j.virs.2024.02.005

August 2024

Citation: Xiao Ding, Jingze Liu, Taijiao Jiang, Aiping Wu. Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus .VIROLOGICA SINICA, 2024, 39(4) : 525-536. http://dx.doi.org/10.1016/j.virs.2024.02.005

Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus

Xiao Ding ^a,b ,
Jingze Liu ^a,b ,
Taijiao Jiang ^{a,c,d
,,} ,
Aiping Wu ^{a,b
,,}

a. State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, China;
b. Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, 100730, China;
c. Guangzhou National Laboratory, Guangzhou, 510006, China;
d. State Key Laboratory of Respiratory Disease, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510030, China

Corresponding author: Taijiao Jiang, taijiao@ibms.pumc.edu.cn
Aiping Wu, wap@ism.cams.cn
Received Date: 04 December 2023
Accepted Date: 22 February 2024
Available online: 27 February 2024

Abstract

Influenza A virus (IAV) shows an extensive host range and rapid genomic variations, leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species transmission. This causes global pandemics and seasonal flu outbreaks, posing sustained threats worldwide. Thus, studying all IAVs' evolutionary patterns and underlying mechanisms is crucial for effective prevention and control. We developed FluTyping to identify IAV genotypes, to explore overall genetic diversity patterns and their restriction factors. FluTyping groups isolates based on genetic distance and phylogenetic relationships using whole genomes, enabling identification of each isolate's genotype. Three distinct genetic diversity patterns were observed: one genotype domination pattern comprising only H1N1 and H3N2 seasonal influenza subtypes, multi-genotypes co-circulation pattern including majority avian influenza subtypes and swine influenza H1N2, and hybrid-circulation pattern involving H7N9 and three H5 subtypes of influenza viruses. Furthermore, the IAVs in multi-genotypes co-circulation pattern showed region-specific dominant genotypes, implying the restriction of virus transmission is a key factor contributing to distinct genetic diversity patterns, and the genomic evolution underlying different patterns was more influenced by host-specific factors. In summary, a comprehensive picture of the evolutionary patterns of overall IAVs is provided by the FluTyping's identified genotypes, offering important theoretical foundations for future prevention and control of these viruses.
- Influenza A virus
- , Genetic diversity
- , Transmission
- , Genetic pattern
- , Genotype

Electronic Supplementary Material

10.1016j.virs.2024.02.005-ESM.docx
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