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

Xiao Ding, Jingze Liu, Taijiao Jiang and Aiping Wu. Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus[J]. Virologica Sinica, 2024, 39(4): 525-536. doi: 10.1016/j.virs.2024.02.005

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

甲型流感病毒的传播限制和基因组进化共同塑造了遗传多样性模式

丁啸 ^a,b ,
刘竞择 ^a,b ,
蒋太交 ^a,c,d,, ,
吴爱平 ^a,b,,

cstr: 32224.14.j.virs.2024.02.005

a. 中国医学科学院，北京协和医学院，苏州系统医学研究所，重大疾病常见机制研究国家重点实验室;
b. 北京协和医学院，病原感染预防与控制教育部重点实验室;
c. 广州国家实验室;
d. 广州医科大学第一附属医院呼吸疾病国家重点实验室，高级交叉学科研究中心重点实验室

通讯作者： 蒋太交, taijiao@ibms.pumc.edu.cn; 吴爱平, wap@ism.cams.cn
收稿日期： 2023-12-04
录用日期： 2024-02-22

摘要

甲型流感病毒（IAV）具有广泛的宿主群体和快速的基因组变异，导致具有显著抗原变异的新病毒不断涌现，并具有跨物种传播的潜力。这导致全球性大流行和季节性流感的暴发，对全球造成持续性的威胁。因此，深入研究IAV整体的进化模式和潜在机制对其有效预防和控制至关重要。在这项研究中，我们开发了FluTyping工具，根据流感病毒完整基因组的遗传距离和系统发育关系对每个基因片段进行分组，进而识别每一株流感病毒的基因型，探索其整体遗传多样性模式及其限制因素。我们观察到三种不同的IAV遗传多样性模式：一是单一基因型优势流行模式，仅包括H1N1和H3N2季节性流感亚型；二是多种基因型共同流行模式，涵盖大多数禽流感亚型和猪流感H1N2；三是包含H7N9和三种H5亚型流感病毒的混合流行模式。此外，在多种基因型共同流行模式中，流感病毒显示出区域特异性的优势基因型，暗示病毒传播的限制是导致不同遗传多样性模式的关键因素，而不同模式下病毒的基因组进化更受宿主特异性影响。总之，基于FluTyping识别的基因型从宏观上展示了甲型流感的进化和遗传多样性模式，为未来该病毒的防控提供了重要的理论基础。
- 甲型流感病毒
- , 遗传多样性
- , 传播
- , 遗传模式
- , 基因型

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

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

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10.1016j.virs.2024.02.005-ESM.docx