Influenza H7N9 and H9N2 viruses: Coexistence in poultry linked to human H7N9 infection and genome characteristics

Journal of Virology

Volumn 88, Issue 6, 2014, Pages 3423-3431

  Yu, Xinfen ^a   Jin, Tao ^b   Cui, Yujun ^b,c   Pu, Xiaoying ^a   Li, Jun ^a   Xu, Jin ^b   Liu, Guang ^d   Jia, Huijue ^b   Liu, Dan ^e   Song, Shili ^e   Yu, Yang ^f   Xie, Li ^a   Huang, Renjie ^a   Ding, Hua ^a   Kou, Yu ^a   Zhou, Yinyan ^a   Wang, Yayu ^b   Xu, Xun ^b   Yin, Ye ^b   Wang, Jian ^b   Guo, Chenyi ^c,g   Yang, Xianwei ^b,c   Hu, Liangping ^g   Wu, Xiaopeng ^f   Wang, Hailong ^f   Liu, Jun ^h,i   Zhao, Guoqiu ^a   Zhou, Jiyong ^f   Pan, Jingcao ^a   Gao, George F ^h,i   Yang, Ruifu ^b,c   Wang, Jun ^b,j,k   more..

^a HANGZHOU CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^b BGI SHENZHEN   (China)

^c BEIJING INSTITUTE OF MICROBIOLOGY AND EPIDEMIOLOGY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e Yuhang District Center for Disease Control and Prevention   (China)

^f ZHEJIANG UNIVERSITY   (China)

^g Beijing Consulting Centre of Biomedical Statistics   (China)

^h INSTITUTE OF MICROBIOLOGY   (China)

ⁱ CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^j UNIVERSITY OF COPENHAGEN   (Denmark)

^k KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ANIMAL EXPERIMENT; ARTICLE; AVIAN INFLUENZA; CHICKEN; CHINA; CONTROLLED STUDY; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; INFLUENZA VIRUS A H7N9; INFLUENZA VIRUS A H9N2; METAGENOMICS; MOLECULAR PHYLOGENY; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; POULTRY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SOCIAL MARKETING; UNINDEXED SEQUENCE; VIRUS GENOME; VIRUS IDENTIFICATION;

AMINO ACID SEQUENCE; ANIMALS; CHICKENS; CHINA; COINFECTION; DUCKS; GENOME, VIRAL; HUMANS; INFLUENZA A VIRUS, H7N9 SUBTYPE; INFLUENZA A VIRUS, H9N2 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84894575872     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02059-13     Document Type: Article

References (24)

1. Gao R, Cao B, Hu Y, Feng Z, Wang D, Hu W, Chen J, Jie Z, Qiu H, Xu K, Xu X, Lu H, Zhu W, Gao Z, Xiang N, Shen Y, He Z, Gu Y, Zhang Z, Yang Y, Zhao X, Zhou L, Li X, Zou S, Zhang Y, Li X, Yang L, Guo J, Dong J, Li Q, Dong L, Zhu Y, Bai T, Wang S, Hao P, Yang W, Zhang Y, Han J, Yu H, Li D, Gao GF, Wu G, Wang Y, Yuan Z, Shu Y. 2013. Human infection with a novel avian-origin influenzaA(H7N9) virus. N. Engl. J. Med. 368:1888-1897. http://dx.doi.org/10.1056/NEJMoa1304459.
2. Liu D, Shi W, Shi Y, Wang D, Xiao H, Li W, Bi Y, Wu Y, Li X, Yan J, Liu W, Zhao G, Yang W, Wang Y, Ma J, Shu Y, Lei F, Gao GF. 2013. Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet 381:1926-1932. http://dx.doi.org/10.1016/S0140-6736(13)60938-1.
3. Li J, Yu X, Pu X, Xie L, Sun Y, Xiao H, Wang F, Din H, Wu Y, Liu D, Zhao G, Liu J, Pan J. 2013. Environmental connections of novel avianorigin H7N9 influenza virus infection and virus adaptation to the human. Sci. China Life Sci. 56:485-492. http://dx.doi.org/10.1007/s11427-013-4491-3.
4. Li Q, Zhou L, Zhou M, Chen Z, Li F, Wu H, Xiang N, Chen E, Tang F, Wang D, Meng L, Hong Z, Tu W, Cao Y, Li L, Ding F, Liu B, Wang M, Xie R, Gao R, Li X, Bai T, Zou S, He J, Hu J, Xu Y, Chai C, Wang S, Gao Y, Jin L, Zhang Y, Luo H, Yu H, Gao L, Pang X, Liu G, Shu Y, Yang W, Uyeki TM, Wang Y, Wu F, Feng Z. 24 April 2013. Preliminary report: epidemiology of the avian influenzaA(H7N9) outbreak in China. N. Engl. J. Med. http://dx.doi.org/10.1056/NEJMoa1304617.
5. Shi J, Deng G, Liu P, Zhou J, Guan L, Li W, Li X, Guo J, Wang G, Fan J, Wang J, Li Y, Jiang Y, Liu L, Tian G, Li C, Chen H. 2013. Isolation and characterization of H7N9 viruses from live poultry markets-implication of the source of current H7N9 infection in humans. Chin Sci. Bull. 58: 1857-1863. http://dx.doi.org/10.1007/s11434-013-5873-4.
6. Liu M, He S, Walker D, Zhou N, Perez DR, Mo B, Li F, Huang X, Webster RG, Webby RJ, et al. 2003. The influenza virus gene pool in a poultry market in south central china. Virology 305:267-275. http://dx.doi.org/10.1006/viro.2002.1762.
7. Chen Y, Liang W, Yang S, Wu N, Gao H, Sheng J, Yao H, Wo J, Fang Q, Cui D, Li Y, Yao X, Zhang Y, Wu H, Zheng S, Diao H, Xia S, Zhang Y, Chan KH, Tsoi HW, Teng JL, Song W, Wang P, Lau SY, Zheng M, Chan JF, To KK, Chen H, Li L, Yuen KY. 2013. Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet 381:1916-1925. http://dx.doi.org/10.1016/S0140-6736(13)60903-4.
8. Zhou B, Donnelly ME, Scholes DT, St George K, Hatta M, Kawaoka Y, Wentworth DE. 2009. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J. Virol. 83:10309-10313. http://dx.doi.org/10.1128/JVI.01109-09.
9. Hoffmann E, Stech J, Guan Y, Webster RG, Perez DR. 2001. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146:2275-2289. http://dx.doi.org/10.1007/s007050170002.
10. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966-1967. http://dx.doi.org/10.1093/bioinformatics/btp336.
11. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265-272. http://dx.doi.org/10.1101/gr.097261.109.
12. Hernandez D, Francois P, Farinelli L, Osterås M, Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18:802-809. http://dx.doi.org/10.1101/gr.072033.107.
13. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. 2008. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82:596-601.
14. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. http://dx.doi.org/10.1093/bioinformatics/btp324.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
16. Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. 2012. De novo assembly of highly diverse viral populations. BMC Genomics 13:475. http://dx.doi.org/10.1186/1471-2164-13-475.
17. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739. http://dx.doi.org/10.1093/molbev/msr121.
18. Guo Y, Rumschlag-Booms E, Wang J, Xiao H, Yu J, Wang J, Guo L, Gao GF, Cao Y, Caffrey M, Rong L. 2009. Analysis of hemagglutininmediated entry tropism of H5N1 avian influenza. Virol. J. 6:39. http://dx.doi.org/10.1186/1743-422X-6-39.
19. Srinivasan K, Raman R, Jayaraman A, Viswanathan K, Sasisekharan R. 2013. Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. PLoS One 8:e49597. http://dx.doi.org/10.1371/journal.pone.0049597.
20. Li J, Zu Dohna H, Cardona CJ, Miller J, Carpenter TE. 2011. Emergence and genetic variation of neuraminidase stalk deletions in avian influenza viruses. PLoS One 6:e14722. http://dx.doi.org/10.1371/journal.pone.0014 722.
21. Sun Y, Tan Y, Wei K, Sun H, Shi Y, Pu J, Yang H, Gao GF, Yin Y, Feng W, Perez DR, Liu J. 2013. Amino acid 316 of hemagglutinin and the neuraminidase stalk length influence virulence of H9N2 influenza virus in chickens and mice. J. Virol. 87:2963-2968. http://dx.doi.org/10.1128/JVI.02688-12.
22. Chen RA, Lai HZ, Li L, Liu YP, Pan WL, Zhang WY, Xu JH, He DS, Tang ZX. 2013. Genetic variation and phylogenetic analysis of hemagglutinin genes of H9 avian influenza viruses isolated in China during 2010-2012. Vet. Microbiol. 165:312-318. http://dx.doi.org/10.1016/j.vetmic.2013.04.005.
23. Sun Y, Pu J, Jiang Z, Guan T, Xia Y, Xu Q, Liu L, Ma B, Tian F, Brown EG, Liu J. 2010. Genotypic evolution and antigenic drift of H9N2 influenza viruses in China from 1994 to 2008. Vet. Microbiol. 146:215-225. http://dx.doi.org/10.1016/j.vetmic.2010.05.010.
24. Bi Y, Lu L, Li J, Yin Y, Zhang Y, Gao H, Qin Z, Zeshan B, Liu J, Sun L, Liu W. 2011. Novel genetic reassortants in H9N2 influenza A viruses and their diverse pathogenicity to mice. Virol. J. 8:505. http://dx.doi.org/10.1186/1743-422X-8-505.