Molecular evolution and emergence of H5N6 avian influenza virus in central China

Journal of Virology

Volumn 91, Issue 12, 2017, Pages

  Du, Yingying ^a   Chen, Mingyue ^a   Yang, Jiayun ^a   Jia, Yane ^a   Han, Shufang ^a   Holmes, Edward C ^b   Cui, Jie ^a  

^a WUHAN INSTITUTE OF VIROLOGY   (China)

^b University of Sydney   (Australia)

Author keywords

Avian influenza virus; Evolution; H5N6; Molecular epidemiology; Reassortment

Indexed keywords

ARTICLE; BIRD; CHINA; CLADISTICS; EVOLUTION; GENETIC ANALYSIS; GENETIC REASSORTMENT; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC ORIGIN; HA GENE; INFLUENZA A VIRUS; INFLUENZA A VIRUS (H5N6); INFLUENZA A VIRUS (H7N3); MIGRANT BIRD; MOLECULAR EVOLUTION; NONHUMAN; NP GENE; PHYLOGENY; POULTRY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; VIRUS GENE; VIRUS GENOME; ANIMAL; EPIDEMIOLOGICAL MONITORING; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLUENZA; INFLUENZA IN BIRDS; VIROLOGY;

INFLUENZA VIRUS HEMAGGLUTININ; VIRUS RNA;

ANIMALS; BIRDS; CHINA; EPIDEMIOLOGICAL MONITORING; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; GENOTYPE; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFLUENZA A VIRUS; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; PHYLOGENY; POULTRY; REASSORTANT VIRUSES; RNA, VIRAL;

EID: 85019667087     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00143-17     Document Type: Article

References (24)

1. Li KS, Guan Y, Wang J, Smith GJ, Xu KM, Duan L, Rahardjo AP, Puthavathana P, Buranathai C, Nguyen TD, Estoepangestie AT, Chaisingh A, Auewarakul P, Long HT, Hanh NT, Webby RJ, Poon LL, Chen H, Shortridge KF, Yuen KY, Webster RG, Peiris JS. 2004. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430:209-213. https://doi.org/10.1038/nature02746
2. Yuen KY, Chan PK, Peiris M, Tsang DN, Que TL, Shortridge KF, Cheung PT, To WK, Ho ET, Sung R, Cheng AF. 1998. Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus. Lancet 351:467-471. https://doi.org/10.1016/S0140-6736(98) 01182-9
3. Liu J, Xiao H, Lei F, Zhu Q, Qin K, Zhang XW, Zhang XL, Zhao D, Wang G, Feng Y, Ma J, Liu W, Wang J, Gao GF. 2005. Highly pathogenic H5N1 influenza virus infection in migratory birds. Science 309:1206. https://doi.org/10.1126/science.1115273
4. Li Y, Shi J, Zhong G, Deng G, Tian G, Ge J, Zeng X, Song J, Zhao D, Liu L, Jiang Y, Guan Y, Bu Z, Chen H. 2010. Continued evolution of H5N1 influenza viruses in wild birds, domestic poultry, and humans in China from 2004 to 2009. J Virol 84:8389-8397. https://doi.org/10.1128/JVI.00413-10
5. Wong FY, Phommachanh P, Kalpravidh W, Chanthavisouk C, Gilbert J, Bingham J, Davies KR, Cooke J, Eagles D, Phiphakhavong S, Shan S, Stevens V, Williams DT, Bounma P, Khambounheuang B, Morrissy C, Douangngeun B, Morzaria S. 2015. Reassortant highly pathogenic influenza A(H5N6) virus in Laos. Emerg Infect Dis 21:511-516. https://doi.org/10.3201/eid2103.141488
6. Wu H, Lu R, Peng X, Xu L, Cheng L, Lu X, Jin C, Xie T, Yao H, Wu N. 2015. Novel reassortant highly pathogenic H5N6 avian influenza viruses in poultry in China. Infect Genet Evol 31:64-67. https://doi.org/10.1016/j.meegid.2015.01.019
7. Li X, Fu Y, Yang J, Guo J, He J, Guo J, Weng S, Jia Y, Liu B, Li X, Zhu Q, Chen H. 2015. Genetic and biological characterization of two novel reassortant H5N6 swine influenza viruses in mice and chickens. Infect Genet Evol 36:462-466. https://doi.org/10.1016/j.meegid.2015.08.017
8. Yang ZF, Mok CK, Peiris JS, Zhong NS. 2015. Human infection with a novel avian influenza A(H5N6) virus. N Engl J Med 373:487-489. https://doi.org/10.1056/NEJMc1502983
9. Yuan R, Wang Z, Kang Y, Wu J, Zou L, Liang L, Song Y, Zhang X, Ni H, Lin J, Ke C. 2016. Continuing reassortant of H5N6 subtype highly pathogenic avian influenza virus in Guangdong. Front Microbiol 7:520. https://doi.org/10.3389/fmicb.2016.00520
10. Bi Y, Liu H, Xiong C, Liu D, Shi W, Li M, Liu S, Chen J, Chen G, Li Y, Yang G, Lei Y, Xiong Y, Lei F, Wang H, Chen Q, Chen J, Gao GF. 2016. Novel avian influenza A (H5N6) viruses isolated in migratory waterfowl before the first human case reported in China, 2014. Sci Rep 6:29888. https://doi.org/10.1038/srep29888
11. Xu W, Li X, Bai T, Zhao X, Zhao X, Zhang Y, Guo J, Li Z, Yang L, Wang D, Shu Y. 2016. A fatal case of infection with a further reassortant, highly pathogenic avian influenza (HPAI) H5N6 virus in Yunnan, China. Infect Genet Evol 40:63-66. https://doi.org/10.1016/j.meegid.2016.02.020
12. Shen YY, Ke CW, Li Q, Yuan RY, Xiang D, Jia WX, Yu YD, Liu L, Huang C, Qi WB, Sikkema R, Wu J, Koopmans M, Liao M. 2016. Novel reassortant avian influenza A(H5N6) viruses in humans, Guangdong, China, 2015. Emerg Infect Dis 22:1507-1509. https://doi.org/10.3201/eid2208.160146
13. Zhang Z, Li R, Jiang L, Xiong C, Chen Y, Zhao G, Jiang Q. 2016. The complexity of human infected AIV H5N6 isolated from China. BMC Infect Dis 16:600. https://doi.org/10.1186/s12879-016-1932-1
14. Bi Y, Chen Q, Wang Q, Chen J, Jin T, Wong G, Quan C, Liu J, Wu J, Yin R, Zhao L, Li M, Ding Z, Zou R, Xu W, Li H, Wang H, Tian K, Fu G, Huang Y, Shestopalov A, Li S, Xu B, Yu H, Luo T, Lu L, Xu X, Luo Y, Liu Y, Shi W, Liu D, Gao GF. 2016. Genesis, evolution and prevalence of H5N6 avian influenza viruses in China. Cell Host Microbe 20:810-821. https://doi.org/10.1016/j.chom.2016.10.022
15. Duchêne S, Holmes EC, Ho SY. 2014. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc Biol Sci 281:20140732. https://doi.org/10.1098/rspb.2014.0732
16. Holmes EC. 2016. Complexities of estimating evolutionary rates in viruses. J Virol 90:2155. https://doi.org/10.1128/JVI.02570-15
17. Li X, Yang J, Liu B, Jia Y, Guo J, Gao X, Weng S, Yang M, Wang L, Wang LF, Cui J, Chen H, Zhu Q. 2016. Co-circulation of H5N6, H3N2, H3N8, and emergence of novel reassortant H3N6 in a local community in Hunan province in China. Sci Rep 6:25549. https://doi.org/10.1038/srep25549
18. Yang L, Zhu W, Li X, Bo H, Zhang Y, Zou S, Gao R, Dong J, Zhao X, Chen W, Dong L, Zou X, Xing Y, Wang D, Shu Y. 2017. Genesis and dissemination of highly pathogenic H5N6 avian influenza viruses. J Virol 91: e02199-16. https://doi.org/10.1128/JVI.02199-16
19. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. https://doi.org/10.1093/nar/gkh340
20. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321. https://doi.org/10.1093/sysbio/syq010
21. Guindon S, Delsuc F, Dufayard JF, Gascuel O. 2009. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537:113-137. https://doi.org/10.1007/978-1-59745-251-9_6
22. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. 2016. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol 2:vew007. https://doi.org/10.1093/ve/vew007
23. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969-1973. https://doi.org/10.1093/molbev/mss075
24. Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23:7-9