Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India
During the peak outbreak (July–September 2009), a total 1886 patients were screened in eastern India, of which 139 (7.37%) and 52 (2.76%) were positive for pH1N1 and seasonal H1N1, respectively. Full-length HA1, NA, NS1 and PB1-F2 genes of representative strains were sequenced. Phylogenetic analysis of deduced amino acid sequences of pH1N1 strains revealed HA1 and NS1 to be of North American swine lineage, and the NA gene of Eurasian swine lineage. Consistent with previous reports, the PB1-F2 gene of pH1N1 strains was unique due to a mutation resulting in a truncated protein of 11 aa. The HA, NA and NS1 genes of H1N1/2009 strains clustered with H1N1 strains of 2000–2009, whereas a subset of strains contained a pH1N1-like truncated PB1-F2. The truncated PB1-F2 may confer the advantage of lower pathogenicity but higher replication and infectivity to the human H1N1 strains. This is the first report of seasonal H1N1/2009 strains with a pH1N1/2009-like gene segment.
This study was supported by financial assistance from the Indian Council of Medical Research (ICMR), Department of Health Research, New Delhi. M. Sarkar is supported by Women Scientist Scheme-A, Department of Science and Technology, Govt of India. Dr. R. Sharma Dey and A. S. Agrawal are supported by SRA- Pool Scheme, CSIR and Senior Research Fellowship from ICMR, respectively. The authors acknowledge technical support by Swati Ghosh, Malay Dey-Sarkar, Shyam Jaiswara and Shyamal Mandal. The authors are thankful for the support provided by the Administration, Store/Purchase and Accounts departments during the pandemic period.
Conflict of interest
The authors have declared that no conflict of interests exists.
- 1.Wright PF, Neumann G, Kawaoka Y (2007) Fields Virology, 5th edn. Williams and Wilkins, Philadelphia, Lippincott, pp. 1692Google Scholar
- 4.Tumpey TM, García-Sastre A, Taubenberger JK, Palese P, Swayne DE, Basler CF (2004) Pathogenicity and immunogenicity of influenza viruses with genes from the 1918 pandemic virus. Proc Natl Acad Sci USA 101:3166–3171Google Scholar
- 5.Karasin AI, Schutten MM, Cooper LA, Smith CB, Subbarao K, Anderson GA, Carman S, Olsen CW (2000) Genetic characterization of H3N2 influenza viruses isolated from pigs in North America, 1977–1999: evidence for wholly human and reassortant virus genotypes. Virus Res 68:71–85CrossRefPubMedGoogle Scholar
- 8.Shinde V, Bridges CB, Uyeki TM, Shu B, Balish A, Xu X, Lindstrom S, Gubareva LV, Deyde V, Garten RJ, Harris M, Gerber S, Vagasky S, Smith F, Pascoe N, Martin K, Dufficy D, Ritger K, Conover C, Quinlisk P, Klimov A, Bresee JS, Finelli L (2009) Triple reassortant swine influenza A (H1) in humans in the United States, 2005–2009. N Engl J Med 360:2616–2625CrossRefPubMedGoogle Scholar
- 10.MacKenzie D (2009) Deadly New Flu Virus in US and Mexico May Go Pandemic. New Scientist http://www.webcitation.org/5gNd9HTT9
- 11.Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, Lopez-Gatell H, Olivera H, Lopez I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ (2009) Antigenic and genetic variation of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 325:197–201CrossRefPubMedGoogle Scholar
- 14.Agrawal AS, Sarkar M, Chakrabarti S, Rajendran K, Kaur H, Mishra AC, Chatterjee MK, Naik TN, Chadha MS, Chawla-Sarkar M (2009) Comparative evaluation of real-time PCR and conventional RT-PCR during a 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection. J Med Microbiol 58:1616–1622CrossRefPubMedGoogle Scholar
- 15.Beklemishev AB, Blinov VM, Vasilenko SK, Golovin SY, Gutorov VV, Karginov VA, Mamaev LV, Mikryukov NN, Netesov SV, Petrenko VA, Petrov NA, Sandakhchiev LS (1984) Synthesis of a full-length DNA copy of the hemagglutinin gene of the influenza virus A H1N1 subtype, its cloning and primary structure. Bioorg Khim 10:1535–1543PubMedGoogle Scholar
- 18.WHO (2010) Preliminary review of D222G amino acid substitution in the haemagglutinin of pandemic influenza A (H1N1) 2009 viruses. Weekly Epidemiological Record No. 4Google Scholar
- 20.Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, Viboud C, Holmes E, Henrickson K (2009) The early diversification of influenza A/H1N1 pdm. PLoS Curr 1:RRN1126. doi: 10.1371/currents.RRN1126
- 24.Padlan EA (2009) The pandemic 2009 (H1N1) swine influenza virus is mild compared to the pandemic 1918 (H1N1) virus because of a proline-to-serine substitution in the receptor-binding site of its hemagglutinin—a hypothesis. Med Hypotheses doi: 10.1016/j.mehy.2009.09.034
- 26.Agrawal AS, Sarkar M, Ghosh S, Roy T, Chakrabarti S, Lal R, Mishra AC, Chadha MS, Chawla-Sarkar M (2010) Genetic characterization of circulating seasonal Influenza A viruses (2005–2009) revealed introduction of oseltamivir resistant H1N1 strains during 2009 in eastern India. Infect Genet Evol 10:1188–1198Google Scholar
- 36.Itoh Y, Shinya K, Kiso M, Watanabe T, Sakoda Y, Hatta M, Muramoto Y, Tamura D, Sakai-Tagawa Y, Noda T, Sakabe S, Imai M, Hatta Y, Watanabe S, Li C, Yamada S, Fuji K, Murakami S, Imai H, Kakugawa S, Ito M, Takano R, Iwatsuki-Horimoto K, Shimojima M, Horimoto T, Goto H, Takahasi K, Warshauer D, Shult PA, Saito R, Suzuki H, Furuta Y, Yamashita M, Mitamura K, Nakano K, Nakamura M, Brockman-Schneider R, Mitamura H, Yamazaki M, Sugaya N, Suresh M, Ozawa M, Neumann G, Gern J, Kida H, Ogasawara K, Kawaoka Y (2009) In vtiro and in vivo characterization of new swine-origin H1N1 influenza viruses. Nature 460:1021–1025PubMedGoogle Scholar
- 37.Lange E, Kalthoff D, Blohm U, Teifke JP, Breithaupt A, Maresch C, Starick E, Fereidouni S, Hoffmann B, Mettenleiter TC, Beer M, Vahlenkamp TW (2009) Pathogenesis and transmission of the novel swine-origin influenza virus A/H1N1 after experimental infection of pigs. J Gen Virol 90:2119–2123CrossRefPubMedGoogle Scholar
- 38.Writing committee of the WHO consultation on clinical aspects of pandemic (H1N1) 2009 influenza (2010) Clinical aspects of pandemic 2009 influenza A (H1N1) virus infection. N Engl J Med 362:1708–1719Google Scholar