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

被引：3

作者：

Ding, Xiao ^{[1
,2
]}

Liu, Jingze ^{[1
,2
]}

Jiang, Taijiao ^{[1
,3
,4
]}

Wu, Aiping ^{[1
,2
]}

机构：

[1] Chinese Acad Med Sci & Peking Union Med Coll, Suzhou Inst Syst Med, State Key Lab Common Mech Res Major Dis, Suzhou 215123, Peoples R China

[2] Peking Union Med Coll, Key Lab Pathogen Infect Prevent & Control, Minist Educ, Beijing 100730, Peoples R China

[3] Guangzhou Natl Lab, Guangzhou 510006, Peoples R China

[4] Guangzhou Med Univ, Key Lab Adv Interdisciplinary Studies Ctr, State Key Lab Resp Dis, Affiliated Hosp 1, Guangzhou 510030, Peoples R China

来源：

VIROLOGICA SINICA | 2024年 / 39卷 / 04期

基金：

中国国家自然科学基金;

关键词：

Influenza A virus; Genetic diversity; Transmission; Genetic pattern; Genotype;

D O I：

10.1016/j.virs.2024.02.005

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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.

引用

页码：525 / 536

页数：12

共 47 条

[1] Influenza Virus: Tracking, Predicting, and Forecasting [J].

Ali, Sheikh Taslim ;

Cowling, Benjamin J. .

ANNUAL REVIEW OF PUBLIC HEALTH, VOL 42, 2021, 2021, 42 :43-57

[2] Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses [J].

Barrat-Charlaix, Pierre ;

Huddleston, John ;

Bedford, Trevor ;

Neher, Richard A. .

MOLECULAR BIOLOGY AND EVOLUTION, 2021, 38 (07) :2767-2777

[3]

Benson DA, 2017, NUCLEIC ACIDS RES, V45, pD37, DOI [10.1093/nar/gkl986, 10.1093/nar/gkw1070, 10.1093/nar/gks1195, 10.1093/nar/gkp1024, 10.1093/nar/gkq1079, 10.1093/nar/gkg057, 10.1093/nar/gkx1094, 10.1093/nar/gkn723, 10.1093/nar/gkr1202]

[4] Influenza virus genotype to phenotype predictions through machine learning: a systematic review Computational Prediction of Influenza Phenotype [J].

Borkenhagen, Laura K. ;

Allen, Martin W. ;

Runstadler, Jonathan A. .

EMERGING MICROBES & INFECTIONS, 2021, 10 (01) :1896-1907

[5] Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses [J].

Brown, Ian H. ;

Capua, Ilaria ;

Cattoli, Giovanni ;

Chen, Hualan ;

Cox, Nancy ;

Davis, C. Todd ;

Donis, Ruben O. ;

Fouchier, Ron A. M. ;

Garten, Rebecca ;

Guan, Yi ;

Hay, Alan ;

Kawaoka, Yoshihiro ;

Mackenzie, John ;

McCauley, John ;

Mumford, Elizabeth ;

Olsen, Christopher ;

Perdue, Michael L. ;

Russell, Colin A. ;

Smith, Catherine ;

Smith, Derek ;

Smith, Gavin J. D. ;

Shu, Yuelong ;

Tashiro, Masato ;

Vijaykrishna, Dhanasekaran ;

Webster, Robert .

INFLUENZA AND OTHER RESPIRATORY VIRUSES, 2009, 3 (02) :59-62

[6] Design and Characterization of a Computationally Optimized Broadly Reactive Hemagglutinin Vaccine for H1N1 Influenza Viruses [J].

Carter, Donald M. ;

Darby, Christopher A. ;

Lefoley, Bradford C. ;

Crevar, Corey J. ;

Alefantis, Timothy ;

Oomen, Raymond ;

Anderson, Stephen F. ;

Strugnell, Tod ;

Cortes-Garcia, Guadalupe ;

Vogel, Thorsten U. ;

Parrington, Mark ;

Kleanthous, Harold ;

Ross, Ted M. .

JOURNAL OF VIROLOGY, 2016, 90 (09) :4720-4734

[7] Influenza A Viruses: Understanding Human Host Determinants [J].

Ciminski, Kevin ;

Chase, Geoffrey P. ;

Beer, Martin ;

Schwemmle, Martin .

TRENDS IN MOLECULAR MEDICINE, 2021, 27 (02) :104-112

[8] Progress and Challenge in Computational Identification of Influenza Virus Reassortment [J].

Ding, Xiao ;

Qin, Luyao ;

Meng, Jing ;

Peng, Yousong ;

Wu, Aiping ;

Jiang, Taijiao .

VIROLOGICA SINICA, 2021, 36 (06) :1273-1283

[9] FluReassort: a database for the study of genomic reassortments among influenza viruses [J].

Ding, Xiao ;

Yuan, Xuye ;

Mao, Longfei ;

Wu, Aiping ;

Jiang, Taijiao .

BRIEFINGS IN BIOINFORMATICS, 2020, 21 (06) :2126-2132

[10] Advances in research of HIV transmission networks [J].

Dong, Zhi-Long ;

Gao, George Fu ;

Lyu, Fan .

CHINESE MEDICAL JOURNAL, 2020, 133 (23) :2850-2858

← 1 2 3 4 5 →