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Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India

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Abstract

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.

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Acknowledgments

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.

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The authors have declared that no conflict of interests exists.

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Authors and Affiliations

  1. Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme XM, Beliaghata, Kolkata, 700010, West Bengal, India

    Mehuli Sarkar, Anurodh S. Agrawal, Rakhi Sharma Dey, Shiladitya Chattopadhyay, Ranajoy Mullick, Papiya De, Sekhar Chakrabarti & Mamta Chawla-Sarkar

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  1. Mehuli Sarkar
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Correspondence to Mamta Chawla-Sarkar.

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Sarkar, M., Agrawal, A.S., Sharma Dey, R. et al. Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India. Arch Virol 156, 207–217 (2011). https://doi.org/10.1007/s00705-010-0842-6

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