Pandemic (H1N1) 2009 virus revisited: An evolutionary retrospective

Infection, Genetics and Evolution

Volumn 11, Issue 5, 2011, Pages 803-811

  Christman, Mary C ^a   Kedwaii, Ambreen ^a   Xu, Jianpeng ^a   Donis, Ruben O ^b   Lu, Guoqing ^a  

^a UNIVERSITY OF NEBRASKA AT OMAHA   (United States)

^b CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

Evolution; Genetic mutation; Genome reassortment; Influenza; Pandemic H1N1; Phylodynamics

Indexed keywords

AMANTADINE; INFLUENZA VACCINE; INFLUENZA VIRUS HEMAGGLUTININ; OSELTAMIVIR; SIALIDASE INHIBITOR; VIRUS NUCLEOPROTEIN; VIRUS SIALIDASE;

2009 H1N1 INFLUENZA; ANTIVIRAL RESISTANCE; ANTIVIRAL SUSCEPTIBILITY; BIOINFORMATICS; DISEASE SEVERITY; DISEASE SURVEILLANCE; EARLY DIAGNOSIS; EARLY INTERVENTION; GENE CLUSTER; GENE MUTATION; GENETIC REASSORTMENT; GENETIC SELECTION; HA GENE; HOST RANGE; HUMAN; INFECTION PREVENTION; INFLUENZA VACCINATION; INFLUENZA VIRUS A H1N1; MEDICAL LITERATURE; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; NA GENE; NONHUMAN; NP GENE; PANDEMIC INFLUENZA; PORK; PRIORITY JOURNAL; REVIEW; SPECIES DIFFERENCE; SWINE; VIRAL GENETICS; VIRUS GENE; VIRUS TRANSMISSION; VIRUS VIRULENCE;

ANIMALS; BIOLOGICAL EVOLUTION; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA, HUMAN; ORTHOMYXOVIRIDAE INFECTIONS; PANDEMICS; POPULATION SURVEILLANCE;

SUIDAE;

EID: 79956298771     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.02.021     Document Type: Review

References (78)

1. Bao Y., Bolotov P., Dernovoy D., Kiryutin B., Zaslavsky L., Tatusova T., Ostell J., Lipman D. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 2008, 82(2):596-601.
2. Booy, R., Khandaker, G., Heron, L., Yin, J., Doyle, B., Tudo, K., Hueston, L., Gilbert, G.L., MacIntyre, C.R., Dwyer, D.E., 2010. Cross-reacting antibodies against pandemic influenza A (H1N1) 2009 virus in elderly Australians. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 228.
3. Brockwell-Staats C., Webster R.G., Webby R.J. Diversity of Influenza Viruses in Swine and the Emergence of a Novel Human Pandemic Influenza A (H1N1). Influenza Other Respir. Viruses 2009, 3(5):207-213.
4. Burnett F. Mucins and mucoids in relation to influenza virus action. III. Inhibition of virus haemagglutination by glandular mucins. Aust. J. Exp. Biol. Med. Sci. 1948, 26:403-411.
5. CDC Swine Influenza A (H1N1) Infection in Two Children - Southern California, March-April 2009 2009, http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5815a5.htm.
6. CDC Swine influenza A (H1N1) infection in two children - Southern California, March-April 2009. Morbidity and Mortality Weekly Report 2009, The Centers for Disease Control and Prevention, Atlanta, Georgia.
7. CDC Key Facts about Influenza (Flu) & Flu Vaccine 2010, The Centers for Disease Control and Prevention.
8. Chen H., Wen X., To K.K., Wang P., Tse H., Chan J.F., Tsoi H.W., Fung K.S., Tse C.W., Lee R.A., Chan K.H., Yuen K.Y. Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A (H1N1) 2009 virus from patients with severe disease in Hong Kong. China J. Infect. Dis. 2010, 201(10):1517-1521.
9. Chen L.M., Davis C.T., Zhou H., Cox N.J., Donis R.O. Genetic compatibility and virulence of reassortants derived from contemporary avian H5N1 and human H3N2 influenza A viruses. PLoS Pathog. 2008, 4(5):e1000072.
10. Dawood F.S., Jain S., Finelli L., Shaw M.W., Lindstrom S., Garten R.J., Gubareva L.V., Xu X., Bridges C.B., Uyeki T.M. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N. Engl. J. Med. 2009, 360(25):2605-2615.
11. Deng, Y.-M., Iannello, P., Smith, I., Watson, J., Daniels, P., Komadina, N., Barr, I., Harrower, B., Wong, F., 2010. No reassortment in pandemic (H1N1) 2009 viruses isolated from swine in Australia. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 117.
12. Desselberger U., Nakajima K., Alfino P., Pedersen F.S., Haseltine W.A., Hannoun C., Palese P. Biochemical evidence that " new" influenza virus strains in nature may arise by recombination (reassortment). Proc. Natl. Acad. Sci. U.S.A. 1978, 75(7):3341-3345.
13. Deyde V.M., Sheu T.G., Trujillo A.A., Okomo-Adhiambo M., Garten R., Klimov A.I., Gubareva L.V. Detection of molecular markers of drug resistance in 2009 pandemic influenza A (H1N1) viruses by pyrosequencing. Antimicrob. Agents Chemother. 2010, 54(3):1102-1110.
14. Doudnaa J.A., Mehle A. Adaptive strategies of the influenza virus polymerase for replication in humans. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(50):21312-21316.
15. Drake J.W. Rates of spontaneous mutation among RNA viruses. Proc. Natl. Acad. Sci. U.S.A. 1993, 90(9):4171-4175.
16. Drake J.W., Holland J.J. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. U.S.A. 1999, 96(24):13910-13913.
17. Fereidouni S.R., Beer M., Vahlenkamp T., Starick E. Differentiation of two distinct clusters among currently circulating influenza A (H1N1)v viruses, March-September2009. Euro. Surveill. 2009, 14(46).
18. Fitch W.M., Leiter J.M., Li X.Q., Palese P. Positive Darwinian evolution in human influenza A viruses. Proc. Natl. Acad. Sci. U.S.A. 1991, 88(10):4270-4274.
19. Fouchier R.A.M., Munster V.J., Keawcharoen J., Osterhaus A.D.M.E., Kuiken T. Virology of avian influenza in relations to wild birds. J. Wildl. Dis. 2007, 43(Suppl. 3):7-14.
20. Frosner G., Gerth H.J., Flehmig B., Vallbracht A. Functional significance of neuraminidase in the replication cycle of influenza viruses. Zentralbl. Bakteriol. [Orig A] 1975, 232:178-188.
21. Garten R.J., Davis C.T., Russell C.A., Shu B., Lindstrom S., Balish A., Sessions W.M., Xu X., Skepner E., Deyde V., Okomo-Adhiambo M., Gubareva L., Barnes J., Smith C.B., Emery S.L., Hillman M.J., Rivailler P., Smagala J., de Graaf M., Burke D.F., Fouchier R.A., Pappas C., Alpuche-Aranda C.M., López-Gatell H., Olivera H., López I., Myers C.A., Faix D., Blair P.J., Yu C., Keene K.M., Dotson P.D., Boxrud D., Sambol A.R., Abid S.H., St George K., Bannerman T., Moore A.L., Stringer D.J., Blevins P., Demmler-Harrison G.J., Ginsberg M., Kriner P., Waterman S., Smole S., Guevara H.F., Belongia E.A., Clark P.A., Beatrice S.T., Donis R., Katz J., Finelli L., Bridges C.B., Shaw M., Jernigan D.B., Uyeki T.M., Smith D.J., Klimov A.I., Cox N.J. Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 2009, 325(5937):197-201.
22. Ghedin E., Wentworth D.E., Halpin R.A., Lin X., Bera J., DePasse J., Fitch A., Griesemer S., Hine E., Katzel D.A., Overton L., Proudfoot K., Sitz J., Szczypinski B., StGeorge K., Spiro D.J., Holmes E.C. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. J. Virol. 2010, 84(11):5715-5718.
23. Gibbs A.J., Armstrong J.S., Downie J.C. From where did the 2009 'swine-origin' influenza A virus (H1N1) emerge?. Virol. J. 2009, 6 (November 24):207.
24. Gramer M.R. Reassortant human/swine H1N1 and H1N2 influenza virus infections in US swine. J. Swine Health Prod. 2009, 463-464.
25. Gray G.C., McCarthy T., Capuano A.W., Setterquist S.F., Olsen C.W., Alavanja M.C. Swine workers and swine influenza virus infections. Emerg. Infect. Dis. 2007, 13(12):1871-1878.
26. Guan Y., Poon L.L., Cheung C.Y., Ellis T.M., Lim W., Lipatov A.S., Chan K.H., Sturm-Ramirez K.M., Cheung C.L., Leung Y.H., Yuen K.Y., Webster R.G., Peiris J.S. H5N1 influenza: a protean pandemic threat. Proc. Natl. Acad. Sci. U.S.A. 2004, 101(21):8156-8161.
27. Hancock K., Veguilla V., Lu X., Zhong W., Butler E.N., Sun H., Liu F., Dong L., DeVos J.R., Gargiullo P.M., Brammer T.L., Cox N.J., Tumpey T.M., Katz J.M. Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus. N. Engl. J. Med. 2009, 361:1945-1952.
28. Helferty, M., Vachon, J., Tarasuk., J., Rodin, R., Spika, J., Pelletier, L., 2010. Epidemiology of hospitalized pandemic H1N1 2009 cases in Canada: a comparison of the first and second pandemic waves. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 207.
29. Holmes E.C., Ghedin E., Miller N., Taylor J., Bao Y., St George K., Grenfell B.T., Salzberg S.L., Fraser C.M., Lipman D.J., Taubenberger J.K. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005, 3(9):e300.
30. Huang R.T., Rott R., Klenk H.D. On the receptor of influenza viruses. 1. Artificial receptor for influenza virus. Z. Naturforsch. [C] 1973, 28:342-345.
31. Ikematsu, H., Kawai, N., Iwaki, N., Hirotsu, N., 2010. Clinical symptoms and the effectiveness of neuraminidase inhibitor for patients with pandemic influenza H1N1 2009 in Japan: comparison with seasonal H1N1 influenza in the 2007-2008 and 2008-2009 seasons. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 141.
32. Jacobs, J., Archer, B., Baker, M., Cowling, B., Heffernan, R., Mercer, G., Uez, O., Tchetgen, E., Lipsitch, M., 2010. Epidemiologic evidence on age-related immunity to 2009 H1N1 influenza. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 258.
33. Jagger B.W., Memoli M.J., Sheng Z.-M., Qi L., Hrabal R.J., Allen G.L., Dugan V.G. The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. MBio 2010, 1-10.
34. Katagiri S., Ohizumi A., Homma M. An outbreak of type C influenza in a children's home. J. Infect. Dis. 1983, 148(1):51-56.
35. Klumpp K., Ruigrok R.W., Baudin F. Roles of the influenza virus polymerase and nucleoprotein in forming a functional RNP structure. EMBO J. 1997, 16:1248-1257.
36. Lamb R.A., Choppin P.W. The gene structure and replication of influenza virus. Annu. Rev. Biochem. 1983, 52:467-506.
37. Leon, A., Lei, Y., Wang, P., Huang, J., Lin, J., Farooqui, A., Guan, Y., Kelvin, D., 2010. Isolation and characterization of three 2009-H1N1 influenza strains from Nanchang, China. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 130.
38. Lessler, J., Reich, N.G., Cummings, D.A.; New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team, Nair, H.P., Jordan, H.T., Thompson, N., 2009. Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. N. Engl. J. Med. 361(27):2628-2636.
39. Lu G., Rowley T., Garten R., Donis R. FluGenome: a web tool for genotyping influenza A virus. Nucleic Acids Res. 2007, 35:W275-W279.
40. Manzoor R., Sakoda Y., Nomura N., Tsuda Y., Ozaki H., Okamatsu M., Kida H. PB2 protein of a highly pathogenic avian influenza virus strain A/chicken/Yamaguchi/7/2004 (H5N1) determines its replication potential in pigs. J. Virol. 2009, 83(4):1572-1578.
41. Matsuzaki Y., Katsushima N., Nagai Y., Shoji M., Itagaki T., Sakamoto M., Kitaoka S., Mizuta K., Nishimura H. Clinical features of influenza C virus infection in children. J. Infect. Dis. 2006, 193(9):1229-1235.
42. Maurer-Stroh S., Ma J., Lee R.T., Sirota F.L., Eisenhaber F. Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biol. Direct. 2009, 4:18.
43. Mercola, J, 2003. More evidence that stress is major factor for infections. Last accessed: 13.01.11. http://articles.mercola.com/sites/articles/archive/2003/07/16/stress-infections.aspx.
44. Monto A.S., McKimm-Breschkin J.L., Macken C., Hampson A.W., Hay A., Klimov A., Tashiro M., Webster R.G., Aymard M., Hayden F.G., Zambon M. Detection of influenza viruses resistant to neuraminidase inhibitors in global surveillance during the first 3 years of their use. Antimicrob. Agents Chemother. 2006, 50(7):2395-2402.
45. Moore J.R. Swine Production: A Global Perspective 2004, Alltech Inc., Nicholasville, Kentucky, USA.
46. Morens D.M., Taubenberger J.K., Fauci A.S. The 2009 H1N1 pandemic influenza virus: what next?. MBio 2010, 1(4.):e00211-e310.
47. Morgan O.W., Bramley A., Fowlkes A., Freedman D.S., Taylor T.H., Gargiullo P., Belay B., Jain S., Cox C., Kamimoto L., Fiore A., Finelli L., Olsen S.J., Fry A.M. Morbid obesity as a risk factor for hospitalization and death due to 2009 pandemic influenza A (H1N1) disease. PLoS One 2009, 5(3):e9694.
48. Nagarajan K., Saikumar G., Arya R.S., Gupta A., Somvanshi R., Pattnaik B. Influenza A H1N1 virus in Indian pigs & its genetic relatedness with pandemic human influenza A 2009 H1N1. Indian J. Med. Res. 2010, 132:160-167.
49. Noble S., McGregor M.S., Wentworth D.E., Hinshaw V.S. Antigenic and genetic conservation of the haemagglutinin in H1N1 swine influenza viruses. J. Gen. Virol. 1993, 74(Pt 6):1197-1200.
50. O'Brien, K.B., Govorkova, E.A., Webby, R.J., McCullers, J.A., Schultz-Cherry, S., 2010. Obesity is a risk factor for developing severe influenza infection. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 334.
51. Olsen, S.J., Baggett, H., Chittaganpitch, M., Thamthitiwat, S., Prapasiri, P., Naorat, S., Ditsungnoen, D., Simmerman, J.M., Chantra, S., Sawanpanyalert, P., Maloney, S.A., Akarasewi, P., 2010. Clinical characteristics of hospitalized influenza patients by subtype in Thailand, 2009. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 198.
52. 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(3):e9549.
53. Pappaioanou M. Highly pathogenic H5N1 avian influenza virus: cause of the next pandemic?. ILAR J. 2009, 51(3):268-280.
54. Poon L.L., Mak P.W., Li O.T., Chan K.H., Cheung C.L., Ma E.S., Yen H.L., Vijaykrishna D., Guan Y., Peiris J.S. Rapid detection of reassortment of pandemic H1N1/2009 influenza virus. Clin. Chem. 2010, 56(8):1340-1344.
55. Potdar V.A., Chadha M.S., Jadhav S.M., Mullick J., Cherian S.S., Mishra A.C. Genetic characterization of the influenza A pandemic (H1N1) 2009 virus isolates from India. PLoS One 2010, 5(3):e9693.
56. Shih, S-R., Hsieh, E-F., Lin, S-J., Mok, C-K., Huang, C-H., Chao, C-C., Chen, G-W., in press. Alteration of viral replication rate and pathogenicity for a mild influenza virus by single reassortment of PA gene derived from the pandemic (H1N1) 2009 influenza virus. In: Options for the Control of Influenza VII. Hong Kong SAR, China.
57. Shiino T., Okabe N., Yasui Y., Sunagawa T., Ujike M., Obuchi M., Kishida N., Xu H., Takashita E., Anraku A., Ito R., Doi T., Ejima M., Sugawara H., Horikawa H., Yamazaki S., Kato Y., Oguchi A., Fujita N., Odagiri T., Tashiro M., Watanabe H. Molecular evolutionary analysis of the influenza A (H1N1)pdm, May-September, 2009: temporal and spatial spreading profile of the viruses in Japan. PLoS One 2010, 5(6):e11057.
58. Smith G.J., Vijaykrishna D., Bahl J., Lycett S.J., Worobey M., Pybus O.G., Ma S.K., Cheung C.L., Raghwani J., Bhatt S., Peiris J.S., Guan Y., Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009, 459(7250):1122-1125.
59. Smith G.J., Bahl J., Vijaykrishna D., Zhang J., Poon L.L., Chen H., Webster R.G., Peris J.S., Guan Y. Dating the emergence of pandemic influenza viruses. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(28):11709-11712.
60. Smith W., Andrewes C.H., Laidlaw P.P., Timbury M.C. A virus obtained from influenza patients. Lancet 1933, (225):66-68.
61. Solovyov A., Greenbaum B., Palacios G., Lipkin W.I., Rabadan R. Host dependent evolutionary patterns and the origin of 2009 H1N1 pandemic influenza. PLoS Curr. 2010, 2. RRN1147.
62. Song, M., Lee, J., Pascua, P., Baek, Y., Kwon, H., Park, K., Choi, H., Shin, Y., Song, J., Kim, C., Choi, Y., 2010. Occurrence of human-to-swine transmission of the pandemic (H1N1) 2009 influenza virus in South Korea. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 104.
63. Steel J., Lowen A.C., Mubareka S., Palese P. Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. PLoS Pathog. 2009, 5(1):e1000252.
64. Steinhauer D.A., Skehel J.J. Genetics of influenza viruses. Annu. Rev. Genet. 2002, 36:305-332.
65. Subbarao E.K., London W., Murphy B.R. A single amino acid in the PB2 gene of influenza A virus is determinant of host range. J. Virol. 1993, 67(4):1761-1764.
66. Trifonov V., Khiabanian H., Rabadan R. Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus. N. Engl. J. Med. 2009, 361(2):115-119.
67. Vijaykrishna D., Poon L.L., Zhu H.C., Ma S.K., Li O.T., Cheung C.L., Smith G.J., Peiris J.S., Guan Y. Reassortment of pandemic H1N1/2009 influenza A virus in swine. Science 2010, 328(5985):1529.
68. Vogel, G.E., Back, T., Blasini, R., Doerr, H.W., Hofler, H., Komm, C., Manych, M., Moeller, R., Schaefer, B., Schoettler, M., Tsokos, M., Wutzler, P., 2010. Influenza, MRSA, cytokines: diagnosis, treatment, prevention - a possible strategy for outpatient care. In: Options for the Control of Influenza VII Abstract Book. Hong Kong SAR, China, 164.
69. Webster R.G. Evolution and ecology of influenza viruses: interspecies transmission. Textbook of Influenza 1998, Blackwell Science, Oxford, pp. 109-119.
70. Webster R.G. The importance of animal influenza for human disease. Vaccine 2002, 20(Suppl. 2):S16-S20.
71. Webster R.G., Bean W.J. Genetics of Influenza Virus. Annu. Rev. Genet. 1978, 12(1):415-431.
72. Webster R.G., Bean W.J., Gorman O.T., Chambers T.M., Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol. Rev. 1992, 56(1):152-179.
73. Webster R.G., Isachenko V.A., Carter M. A new avian influenza virus from feral birds in the USSR: recombination in nature?. Bull. World Health Organ. 1974, 51(4):325-332.
74. Wilson I.A., Skehel J.J., Wiley D.C. Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3Å resolution. Nature 1981, 289:366-373.
75. Xu R., Ekiert D.C., Krause J.C., Hai R., Crowe J.E., Wilson I.A. Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Science 2010, 328(5976):357-360.
76. Yang E.V., Glaser R. Stress-induced immunomodulation and the implications for health review article. Int. Immunopharmacol. 2002, 2(2-3):315-324.
77. Zahniser, S., 2006 U.S.-Mexico agricultural trade during the NAFTA Era. In: Doha, NAFTA, and California Agriculture. U.S.D.A., ed. Sacramento, CA.
78. Zhou N.N., Senne D.A., Landgraf J.S., Swenson S.L., Erickson G., Rossow K., Liu L., Yoon K., Krauss S., Webster R.G. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J. Virol. 1999, 73(10):8851-8856.