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Phylogenetic analysis of the hemagglutinin gene of influenza A(H1N1)pdm09 and A(H3N2) virus isolates from Haryana, India

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Abstract

Influenza A viruses are highly adaptable and are the main pathogen behind winter time morbidity. The present study reports the molecular and phylogenetic characterization of A(H1N1)pdm09 and H3N2 isolates from Haryana, India during 2015 influenza outbreak. A total of 144 nasopharyngeal samples were collected from Post Graduate Institute of Medical Sciences, Rohtak, Haryana, India form September 2014 to February 2016. The samples were screened for influenza A subtypes; A(H1N1)pdm09 and H3N2 by using real-time RT-PCR. Virus isolation and hemagglutinin gene sequencing studies were performed for selected positive samples. Out of 24 (16.6%) Influenza A positive samples, 13 (54.2%) and 11 (45.8%) were subtyped into A(H1N1)pdm09 and H3N2, respectively by real-time RT-PCR. Genetic analysis of A(H1N1)pdm09 isolates revealed the presence of key mutations (P100S, S202T and S220T) in HA gene as compare to reference strain A/California/07/2009 and these isolates were grouped in clade 6B.1 and 6B.2. All A(H3N2) isolates were clustered in clade 3C.2a and revealed specific amino acid substitutions of N161S and P214S in their HA genes in comparison to the reference strain A/Texas/50/2012. The HA gene sequences of all isolates showed 97–98% of nucleotide sequence similarity with their respective reference strains. Influenza A(H1N1)pdm09 and H3N2 isolates were drifted significantly from their respective vaccines strains of 2015–2016 and were more closely related to recommended vaccine strains for flu season 2017–2018. The study supports the need of routine influenza surveillance and continuous monitoring of the genetic changes in the major antigenic sites of these viruses.

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Acknowledgements

Authors are thankful to Council of Scientific & Industrial Research, New Delhi, India for providing financial support in Fellowship to Vikrant Sharma and to Post Graduate Institute of Medical Sciences (PGIMS), Rohtak, Haryana, India for providing clinical samples for the study.

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Authors and Affiliations

  1. Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India

    Vikrant Sharma, Divya Dhull & Samander Kaushik

  2. Department of Biotechnology, Shoolini Institute of Life Sciences and Business Management, Solan, 173212, India

    Manisha Sharma

  3. Department of Genetics, Maharshi Dayanand University, Rohtak, 124001, India

    Sulochana Kaushik

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  1. Vikrant Sharma
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Correspondence to Samander Kaushik.

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All procedures performed in studies involving human samples were in accordance with the ethical standards of the Human Ethical Committee (HEC) of Maharshi Dayanand University, Rohtak, Haryana, India (Letter No. PHY/13/362).

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Sharma, V., Sharma, M., Dhull, D. et al. Phylogenetic analysis of the hemagglutinin gene of influenza A(H1N1)pdm09 and A(H3N2) virus isolates from Haryana, India. VirusDis. 30, 336–343 (2019). https://doi.org/10.1007/s13337-019-00532-7

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