Molecular evolution of the hemagglutinin and neuraminidase genes of pandemic (H1N1) 2009 influenza viruses in Sendai, Japan, during 2009-2011

Virus Genes

Volumn 47, Issue 3, 2013, Pages 456-466

  Khandaker, Irona ^a   Suzuki, Akira ^a   Kamigaki, Taro ^a   Tohma, Kentaro ^a   Odagiri, Takashi ^a   Okada, Takashi ^a   Ohno, Ayumu ^a   Otani, Kanako ^a   Sawayama, Rumi ^a   Kawamura, Kazuhisa ^b   Okamoto, Michiko ^a   Oshitani, Hitoshi ^a  

^a TOHOKU UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b Kawamura Pediatric Clinic   (Japan)

Author keywords

A(H1N1)pdm09; Antiviral drug susceptibility; Neuraminidase; Oseltamivir resistant; Positive selection

Indexed keywords

HEMAGGLUTININ; OSELTAMIVIR; SIALIDASE; SIALIDASE INHIBITOR; ZANAMIVIR;

AMINO ACID SUBSTITUTION; ANTIVIRAL RESISTANCE; ARTICLE; BAYES THEOREM; GENE MUTATION; GENETIC SELECTION; GENETIC VARIABILITY; HEMAGGLUTININ GENE; INFLUENZA VIRUS A H1N1; JAPAN; MOLECULAR EVOLUTION; MONTE CARLO METHOD; NEURAMINIDASE GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VIRUS GENE; VIRUS ISOLATION; VIRUS STRAIN;

EID: 84890505824     PISSN: 09208569     EISSN: 1572994X     Source Type: Journal    
DOI: 10.1007/s11262-013-0980-5     Document Type: Article

References (55)

1. World Health Organization: Influenza-like illness in the United States and Mexico. World Health Organization, Geneva, Switzerland; 2009. http://www.who.int/csr/don/2009-04-24/en/index.html. Accessed 20 March 2010
2. World Health Organization: Pandemic (H1N1) 2009 - update 92. World Health Organization, Geneva, Switzerland; 19 March 2010. http://www.whoint/csr/don/ 2010-03-19/en/index.html
3. National Institute of Infectious Diseases and Kobe Institute of Health: interim report on clinical presentation of the novel influenza A (H1N1) cases reported from Kobe City; 19 May 2009. http://idsc.nih.go.jp/disease/swine- influenza-e/idsc-e2009/clinical-epi-kobe.html. Accessed 18 Oct 2012
4. National Institute of Infectious Diseases and Tuberculosis and Infectious Diseases Control Division, Ministry of Health, Labour and Welfare: Pandemic (H1N1) 2009 in Japan, May-September 2009. Infect. Agents Surveillance Rep; 2009
5. P. Palese, M. L. Shaw, in Fields Virology, ed. by D. M. Knipe et al. (Philadelphia, Lippincott Williams & Wilkins, 2007), pp. 1647-1690
6. P. F. Wright, G. Neumann, Y. Kawaoka, in Fields Virology, ed. by D. M. Knipe et al. (Philadelphia, Lippincott Williams & Wilkins, 2007), pp. 1691-1740
7. J.K. Taubenberger, Influenza virus hemagglutinin cleavage into HA1: HA2. Proc. Natl. Acad. Sci. USA 95, 9713-9715 (1998)
8. M.J. Gibbs, P. Wayper, M.L. Fourment, J.T. Wood, K. Ohshima, J.S. Armstrong, A.J. Gibbs, The variable codons of H3 influenza A virus haemagglutinin genes. Arch. Virol. 152, 9713-9715 (2007)
9. L.J. Mitnaul, M.N. Matrosovich, M.R. Castrucci, A.B. Tuzikov, N.V. Bovin, D. Kobasa, Y. Kawaoka, Balanced hemagglutinin and neuraminidase activities are critical for efficient replication of influenza A virus. J. Virol. 74, 6015-6020 (2000)
10. Y.I. Wolf, C. Viboud, E.C. Holmes, E.V. Koonin, D.J. Lipman, Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol. Direct 1, 34 (2006)
11. J. Long, R.V. Bushnell, J.K. Tobin, K. Pan, M.W. Deem, P.L. Nara, G.J. Tobin, Evolution of H3N2 influenza virus in a guinea pig model. PLoS One 6, e20130 (2011)
12. C. Scholtissek, Source for influenza pandemics. Eur. J. Epidemiol. 10, 455-458 (1994)
13. Japan's Infectious Diseases Surveillance Center(IDSC)-weekly report. http://idsc.nih.go.jp/idwr/index-e.html. Accessed 18 Dec 2012
14. J.É. Morlighem, S. Aoki, M. Kishima, M. Hanami, C. Ogawa, A. Jalloh, Y. Takahashi, Y. Kawai, S. Saga, E. Hayashi, T. Ban, S. Izumi, A. Wada, M. Mano, M. Fukunaga, Y. Kijima, M. Shiomi, K. Inoue, T. Hata, Y. Koretsune, K. Kudo, Y. Himeno, A. Hirai, K. Takahashi, Y. Sakai-Tagawa, K. Iwatsuki-Horimoto, Y. Kawaoka, Y. Hayashizaki, T. Ishikawa, Mutation analysis of 2009 pandemic influenza A(H1N1) pandemic influenza A(H1N1) viruses collected in japan during the peak phase of the pandemic. PLoS One 6(2011), e18956 (2009)
15. E. Hoffmann, J. Stech, Y. Guan, R.G. Webster, D.R. Perez, Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146, 2275-2289 (2001)
16. E. Inoue, X. Wang, Y. Osawa, K. Okazaki, Full genomic amplification and subtyping of influenza A virus using a single set of universal primers. Microbiol. Immunol. 54, 129-134 (2010)
17. National Institute of Technology and Evaluation and National Institute of Infectious Diseases of Japan. http://www.bio.nite.go.jp/ngac/flu-sequence- protocol.pdf. Accessed 15 Jan 2010
18. Y. Furuse, K. Shimabukuro, T. Odagiri, R. Sawayama, T. Okada, I. Khandaker, A. Suzuki, H. Oshitani, Comparison of selection pressures on the HA gene of pandemic (2009) and seasonal human and swine influenza A H1 subtype viruses. Virology 405, 314-321 (2010)
19. Y. Bao, P. Bolotov, D. Dernovoy, B. Kiryutin, L. Zaslavsky, T. Tatusova, J. Ostell, D. Lipman, The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82, 596-601 (2008)
20. The Global Initiative on Sharing All Influenza Data database. http://platform.gisaid.org/epi3/frontend#24b06e. Accessed 13 June 2012
21. K. Tamura, J. Dudley, M. Nei, S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599 (2007)
22. A.J. Drummond, A. Rambaut, BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007)
23. A.J. Drummond, G.K. Nicholls, A.G. Rodrigo, W. Solomon, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161, 1307-1320 (2002)
24. A.J. Drummond, A. Rambaut, B. Shapiro, O.G. Pybus, Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22, 1185-1192 (2005)
25. A.J. Drummond, S.Y.W. Ho, M.J. Phillips, A. Rambaut, Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006)
26. S. L. Pond and S. D. Frost, Estimating selection pressures on alignments of coding sequences analyses using HyPhy (2007). http://www.hyphy.org/pubs/ hyphybook2007.pdf. Accessed 18 Feb 2012
27. J. Bahl, D. Vijaykrishna, E.C. Holmes, G.J. Smith, Y. Guan, Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts. Virology 390, 1185-1192 (2009)
28. S.L. Pond, S.D. Frost, Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21, 2531-2533 (2005)
29. S.L. Pond, S.D. Frost, Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22, 1208-1222 (2005)
30. W. Delport, A.F. Poon, S.D. Frost, S.L. Kosakovsky Pond, Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26, 2455-2457 (2010)
31. M. Nelson, D. Spiro, D. Wentworth, E. Beck, J. Fan, E. Ghedin, R. Halpin, J. Bera, E. Hine, K. Proudfoot, T. Stockwell, X. Lin, S. Griesemer, S. Kumar, M. Bose, C. Viboud, E. Holmes, K. Henrickson, The early diversification of influenza A/H1N1pdm. PLoS Curr. 1, RRN1126 (2009)
32. V.N. Minin, E.W. Bloomquist, M.A. Suchard, Smooth skyride through a rough skyline: bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25, 1459-1471 (2008)
33. M. Igarashi, K. Ito, R. Yoshida, D. Tomabechi, H. Kida, A. Takada, Predicting the antigenic structure of the pandemic (H1N1) 2009 influenza virus hemagglutinin. PLoS One 5, e8553 (2010)
34. M.F. Boni, J.R. Gog, V. Anderson, M.W. Feldman, Epidemic dynamics and antigenic evolution in a single season of influenza A. Proc. Biol. Sci. 273, C8-C14 (2006)
35. Y. Abed, A. Pizzorno, X. Bouhy, G. Boivin, Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. PLoS Pathog. 7, e1002431 (2011)
36. L.V. Gubareva, R.G. Webster, F.G. Hayden, Detection of influenza virus resistance to neuraminidase inhibitors by an enzyme inhibition assay. Antiviral Res. 53, 47-61 (2002)
37. A.C. Hurt, J.K. Holien, M. Parker, A. Kelso, I.G. Barr, Zanamivir-resistant influenza viruses with a novel neuraminidase mutation. J. Virol. 83, 10366-10373 (2009)
38. M. Graham, B. Liang, G. Van Domselaar, N. Bastien, C. Beaudoin, S. Tyler, B. Kaplen, E. Landry, Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. PLoS One 6, e16087 (2011)
39. M.I. Nelson, E.C. Holmes, The evolution of epidemic influenza. Nat. Rev. Genet. 8, 196-205 (2007)
40. M.F. Boni, Vaccination and antigenic drift in influenza. Vaccine 26, C8-C14 (2008)
41. M.F. Boni, J.R. Gog, V. Anderson, M.W. Feldman, Epidemic dynamics and antigenic evolution in a single season of influenza A. Proc. Biol. Sci. 273, 1307-1316 (2006)
42. R.A. Childs, A.S. Palma, S. Wharton, T. Matrosovich, Y. Liu, W. Chai, M.A. Campanero-Rhodes, Y. Zhang, M. Eickmann, M. Kiso, A. Hay, M. Matrosovich, T. Feizi, Receptor-binding specificity of pandemic influenza A (H1N1) 2009 virus determined by carbohydrate microarray. Nat. Biotechnol. 27, 797-799 (2009)
43. H. Yang, P. Carney, J. Stevens, Structure and receptor binding properties of a pandemic H1N1 virus hemagglutinin, version 2. PLoS Curr. 2, RRN1152 (2010)
44. M.A. Mir, R.B. Lal, W. Sullender, Y. Singh, R. Garten, A. Krishnan, S. Broor, Genetic diversity of HA1 domain of hemagglutinin gene of pandemic influenza H1N1pdm09 viruses in New Delhi India. J Med Virol. 84, 386-393 (2012)
45. G. Neumann, Y. Kawaoka, The first influenza pandemic of the new millennium. Influenza Other Respir. Viruses 5, 157-166 (2011)
46. M. Ujike, M. Ejima, A. Anraku, K. Shimabukuro, M. Obuchi, N. Noriko Kishida et al., Monitoring and characterization of oseltamivir-resistant pandemic (H1N1) 2009 virus, Japan, 2009-2010. Emerg. Infect. Dis. 17, 470-479 (2011)
47. M.T. Gíria, H. Rebelo de Andrade, L.A. Santos, V.M. Correia, S.V. Pedro, M.A. Santos, Genomic signatures and antiviral drug susceptibility profile of A(H1N1)pdm09. J. Clin. Virol. 53, 140-144 (2012)
48. E.C. Holmes, Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11, 543-546 (2003)
49. D.J. Smith, A.S. Lapedes, J.C. de Jong, T.M. Bestebroer, G.F. Rimmelzwaan, A.D. Osterhaus, R.A. Fouchier, Mapping the antigenic and genetic evolution of influenza virus. Science 305, 371-376 (2004)
50. J. Shen, J. Ma, Q. Wang, Evolutionary trends of A(H1N1) influenza virus hemagglutinin since 1918. PLoS One 4, e7789 (2009)
51. L. Glaser, J. Stevens, D. Zamarin, I.A. Wilson, A. Garcia-Sastre, T.M. Tumpey, C.F. Basler, J.K. Taubenberger, P. Palese, A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity. J. Virol. 79, 11533-11536 (2005)
52. J. Stevens, O. Blixt, L. Glaser, J.K. Taubenberger, P. Palese, J.C. Paulson, I.A. Wilson, Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals divergent receptor specificities. J. Mol. Biol. 355, 1143-1155 (2006)
53. T.M. Tumpey, T.R. Maines, N. Van Hoeven, L. Glaser, A. Solorzano, C. Pappas, N.J. Cox, D.E. Swayne, P. Palese, J.M. Katz, A. Garcia-Sastre, A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission. Science 315, 655-659 (2007)
54. W. Li, W. Shi, H. Qiao, S.Y. Ho, A. Luo, Y. Zhang, C. Zhu, Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virol. J. 8, 183 (2011)
55. A.U. Tamuri, M. dos Reis, A.J. Hay, R.A. Goldstein, Identifying changes in selective constraints: host shifts in influenza. PLoS Comput. Biol. 5, e1000564 (2009)