Genomic signature and protein sequence analysis of a novel influenza A(H7N9) virus that causes an outbreak in humans in China

Microbes and Infection

Volumn 15, Issue 6-7, 2013, Pages 432-439

  Liu, Qi ^a,c   Lu, Lu ^a   Sun, Zhiwu ^a   Chen, Guang Wu ^d   Wen, Yumei ^a   Jiang, Shibo ^a,b  

^a FUDAN UNIVERSITY   (China)

^b NEW YORK BLOOD CENTER   (United States)

^c DALI UNIVERSITY   (China)

^d CHANG GUNG UNIVERSITY   (Taiwan)

Author keywords

A(H7N9); A(H9N2); Avian flu; Influenza; Influenza A virus

Indexed keywords

AMANTADINE; AMINO ACID; LYSINE; PROTEIN M2; RIMANTADINE; VIRUS PROTEIN;

ADULT; AGED; ARTICLE; CHILD; CHINA; CLINICAL ARTICLE; EPIDEMIC; FEMALE; HUMAN; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; INFLUENZA VIRUS A H7N9; MALE; NONHUMAN; PANDEMIC; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS STRAIN;

CHINA; DISEASE OUTBREAKS; GENOME, VIRAL; HUMANS; INFLUENZA A VIRUS, H7N9 SUBTYPE; INFLUENZA, HUMAN; MUTATION, MISSENSE; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; VIRAL PROTEINS; VIRULENCE;

AVES; INFLUENZA A VIRUS; MAMMALIA;

EID: 84879167494     PISSN: 12864579     EISSN: 1769714X     Source Type: Journal    
DOI: 10.1016/j.micinf.2013.04.004     Document Type: Article

References (54)

1. Pica N., Palese P. Toward a universal influenza virus vaccine: prospects and challenges. Annu. Rev. Med. 2013, 64:189-202.
2. Yen H.L., Webster R.G. Pandemic influenza as a current threat. Curr. Top. Microbiol. Immunol. 2009, 333:3-24.
3. Yuen K.Y., Chan P.K., Peiris M., Tsang D.N., Que T.L., Shortridge K.F., Cheung P.T., To W.K., Ho E.T., Sung R., Cheng A.F. Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus. Lancet 1998, 351:467-471.
4. Subbarao K., Klimov A., Katz J., Regnery H., Lim W., Hall H., Perdue M., Swayne D., Bender C., Huang J., Hemphill M., Rowe T., Shaw M., Xu X., Fukuda K., Cox N. Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. Science 1998, 279:393-396.
5. Claas E.C., Osterhaus A.D., van B.R., De Jong J.C., Rimmelzwaan G.F., Senne D.A., Krauss S., Shortridge K.F., Webster R.G. Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus. Lancet 1998, 351:472-477.
6. http://www.who.int/influenza/human_animal_interface/H5N1_cumulative_%20table_archives/en/.
7. Campbell C.H., Webster R.G., Breese S.S. Fowl plague virus from man. J. Infect. Dis. 1970, 122:513-516.
8. Taylor H.R., Turner A.J. A case report of fowl plague keratoconjunctivitis. Br. J. Ophthalmol. 1977, 61:86-88.
9. Webster R.G., Hinshaw V.S., Bean W.J., Van Wyke K.L., Geraci J.R., St Aubin D.J., Petursson G. Characterization of an influenza A virus from seals. Virology 1981, 113:712-724.
10. Kurtz J., Manvell R.J., Banks J. Avian influenza virus isolated from a woman with conjunctivitis. Lancet 1996, 348:901-902.
11. Belser J.A., Bridges C.B., Katz J.M., Tumpey T.M. Past, present, and possible future human infection with influenza virus A subtype H7. Emerg. Infect. Dis. 2009, 15:859-865.
12. Wen Y.M., Klenk H.D. H7N9 avian influenza virus - search and re-search. Emerg. Microb. Infect. 2013, 2:e18.
13. 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 G.F., Wu G., Wang Y., Yuan Z., Shu Y. Human infection with a novel avian-origin influenza A (H7N9) virus. N. Engl. J. Med. 2013, 10.1056/NEJMoa1304459.
14. Uyeki T.M., Cox N.J. Global concerns regarding novel influenza A (H7N9) virus infections. N. Engl. J. Med. 2013, 10.1056/NEJMp1304661.
15. Chen G.W., Chang S.C., Mok C.K., Lo Y.L., Kung Y.N., Huang J.H., Shih Y.H., Wang J.Y., Chiang C., Chen C.J., Shih S.R. Genomic signatures of human versus avian influenza A viruses. Emerg. Infect. Dis. 2006, 12:1353-1360.
16. Chen G.W., Shih S.R. Genomic signatures of influenza A pandemic (H1N1) 2009 virus. Emerg. Infect. Dis. 2009, 15:1897-1903.
17. Pan C., Cheung B., Tan S., Li C., Li L., Liu S., Jiang S. Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus. PLoS One 2010, 5:e9549.
18. Clewley J.P., Arnold C. MEGALIGN. The multiple alignment module of LASERGENE. Methods Mol. Biol. 1997, 70:119-129.
19. Pan C., Wang G., Liao M., Zhang G.H., Jiang S. High genetic and antigenic similarity between a swine H3N2 influenza A virus and a prior human influenza vaccine virus: a possible immune pressure-driven cross-species transmission. Biochem. Biophys. Res. Commun. 2009, 385:402-407.
20. Belser J.A., Davis C.T., Balish A., Edwards L.E., Zeng H., Maines T.R., Gustin K.M., Martinez I.L., Fasce R., Cox N.J., Katz J.M., Tumpey T.M. Pathogenesis, transmissibility, and ocular tropism of a highly pathogenic avian influenza A (H7N3) virus associated with human conjunctivitis. J. Virol. 2013, 10.1128/JVI.00154-13.
21. Hai-bo W., Ru-feng L., En-kang W., Jin-biao Y., Yi-ting W., Qiao-gang W., Li-hua X., Nan-ping W., Chao-tan G. Sequence and phylogenetic analysis of H7N3 avian influenza viruses isolated from poultry in China in 2011. Arch. Virol. 2012, 157:2017-2021.
22. Cady S.D., Schmidt-Rohr K., Wang J., Soto C.S., DeGrado W.F., Hong M. Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature 2010, 463:689-692.
23. Delano W.L. The PyMOL Molecular Graphics System 2005, DeLano Scientific LLC, 400, Oyster Point Blvd., Suite 213, South San Francisco, CA 94080-1918, USA. http://www.pymol.org.
24. Cutler J., Schleihauf E., Hatchette T.F., Billard B., Watson-Creed G., Davidson R., Li Y., Bastien N., Sarwal S. Investigation of the first cases of human-to-human infection with the new swine-origin influenza A (H1N1) virus in Canada. CMAJ 2009, 181:159-163.
25. Chen H., Wang Y., Liu W., Zhang J., Dong B., Fan X., de J., Farrar J., Riley S., Smith G.J., Guan Y. Serologic survey of pandemic (H1N1) 2009 virus, Guangxi Province, China. Emerg. Infect. Dis. 2009, 15:1849-1850.
26. http://news.xinhuanet.com/health/2013-04/13/c_115377187.htm.
27. WHO Risk Assessment: Human Infections with Influenza A(H7N9) Virus 13 April 2013, http://www.who.int/influenza/human_animal_interface/influenza_h7n9/en/%20index.html.
28. http://epidemic.bio.ed.ac.uk/influenza_H7N9_background.
29. http://platform.gisaid.org/.
30. Shinya K., Ebina M., Yamada S., Ono M., Kasai N., Kawaoka Y. Avian flu: influenza virus receptors in the human airway. Nature 2006, 440:435-436.
31. Puzelli S., Di T.L., Fabiani C., Campitelli L., De Marco M.A., Capua I., Aguilera J.F., Zambon M., Donatelli I. Serological analysis of serum samples from humans exposed to avian H7 influenza viruses in Italy between 1999 and 2003. J. Infect. Dis. 2005, 192:1318-1322.
32. Bogs J., Kalthoff D., Veits J., Pavlova S., Schwemmle M., Manz B., Mettenleiter T.C., Stech J. Reversion of PB2-627E to -627K during replication of an H5N1 Clade 2.2 virus in mammalian hosts depends on the origin of the nucleoprotein. J. Virol. 2011, 85:10691-10698.
33. Naffakh N., Tomoiu A., Rameix-Welti M.A., Werf S.v.d. Host restriction of avian influenza viruses at the level of the ribonucleoproteins. Annu. Rev. Microbiol. 2008, 62:403-424.
34. Talon J., Horvath C.M., Polley R., Basler C.F., Muster T., Palese P., Garcia-Sastre A. Activation of interferon regulatory factor 3 is inhibited by the influenza A virus NS1 protein. J. Virol. 2000, 74:7989-7996.
35. Wang X., Li M., Zheng H., Muster T., Palese P., Beg A.A., Garcia-Sastre A. Influenza a virus NS1 protein prevents activation of NF-kappa B and induction of alpha/beta interferon. J. Virol. 2000, 74:11566-11573.
36. Seo S.H., Hoffmann E., Webster R.G. Lethal H5N1 influenza viruses escape host anti-viral cytokine responses. Nat. Med. 2002, 8:950-954.
37. Stouffer A.L., Acharya R., Salom D., Levine A.S., Di Costanzo L., Soto C.S., Tereshko V., Nanda V., Stayrook S., DeGrado W.F. Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008, 451:596-599.
38. Hu J., Fu R., Cross T.A. The chemical and dynamical influence of the anti-viral drug amantadine on the M2 proton channel transmembrane domain. Biophys. J. 2007, 93:276-283.
39. Bright R.A., Medina M.J., Xu X., Perez-Oronoz G., Wallis T.R., Davis X.M., Povinelli L., Cox N.J., Klimov A.I. Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern. Lancet 2005, 366:1175-1181.
40. Stevens J., Blixt O., Tumpey T.M., Taubenberger J.K., Paulson J.C., Wilson I.A. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science 2006, 312:404-410.
41. Rogers G.N., Paulson J.C., Daniels R.S., Skehel J.J., Wilson I.A., Wiley D.C. Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity. Nature 1983, 304:76-78.
42. Matrosovich M.N., Matrosovich T.Y., Gray T., Roberts N.A., Klenk H.D. Human and avian influenza viruses target different cell types in cultures of human airway epithelium. Proc. Natl. Acad. Sci. U. S. A 2004, 101:4620-4624.
43. Wan H., Perez D.R. Amino acid 226 in the hemagglutinin of H9N2 influenza viruses determines cell tropism and replication in human airway epithelial cells. J. Virol. 2007, 81:5181-5191.
44. Wan H., Sorrell E.M., Song H., Hossain M.J., Ramirez-Nieto G., Monne I., Stevens J., Cattoli G., Capua I., Chen L.M., Donis R.O., Busch J., Paulson J.C., Brockwell C., Webby R., Blanco J., Al-Natour M.Q., Perez D.R. Replication and transmission of H9N2 influenza viruses in ferrets: evaluation of pandemic potential. PLoS ONE 2008, 3:e2923.
45. Imai M., Watanabe T., Hatta M., Das S.C., Ozawa M., Shinya K., Zhong G., Hanson A., Katsura H., Watanabe S., Li C., Kawakami E., Yamada S., Kiso M., Suzuki Y., Maher E.A., Neumann G., Kawaoka Y. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 2012, 486:420-428.
46. Herfst S., Osterhaus A.D., Fouchier R.A. The future of research and publication on altered H5N1 viruses. J. Infect. Dis. 2012, 205:1628-1631.
47. Steinhauer D.A. Role of hemagglutinin cleavage for the pathogenicity of influenza virus. Virology 1999, 258:1-20.
48. Matsuoka Y., Swayne D.E., Thomas C., Rameix-Welti M.A., Naffakh N., Warnes C., Altholtz M., Donis R., Subbarao K. Neuraminidase stalk length and additional glycosylation of the hemagglutinin influence the virulence of influenza H5N1 viruses for mice. J. Virol. 2009, 83:4704-4708.
49. Kimm-Breschkin J., Trivedi T., Hampson A., Hay A., Klimov A., Tashiro M., Hayden F., Zambon M. Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir. Antimicrob. Agents Chemother. 2003, 47:2264-2272.
50. http://www.who.int/csr/don/2013_04_07/en/index.html.
51. Centers for Disease Control and Prevention (CDC) Notes from the field: highly pathogenic avian influenza A (H7N3) virus infection in two poultry workers-Jalisco, Mexico, July 2012. MMWR Morb. Mortal. Wkly Rep. 2012, 61:726-727.
52. Peiris M., Yam W.C., Chan K.H., Ghose P., Shortridge K.F. Influenza A H9N2: aspects of laboratory diagnosis. J. Clin. Microbiol. 1999, 37:3426-3427.
53. Butt K.M., Smith G.J., Chen H., Zhang L.J., Leung Y.H., Xu K.M., Lim W., Webster R.G., Yuen K.Y., Peiris J.S., Guan Y. Human infection with an avian H9N2 influenza A virus in Hong Kong in 2003. J. Clin. Microbiol. 2005, 43:5760-5767.
54. http://www.chp.gov.hk/.