3 Biotech

, 8:408 | Cite as

Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016

  • Kimmi Sarmah
  • Biswajyoti BorkakotyEmail author
  • Kishore Sarma
  • Rahul Hazarika
  • Palash Kumar Das
  • Aniruddha Jakharia
  • Mandakini Das
  • Dipankar Biswas
Short Reports


Since its emergence in 2009, Influenza A/H1N1pdm09 virus has evolved continuously. Marked genetic variations have occurred in the HA1 domain of the hemagglutinin gene causing the emergence of new variants. The present study genetically characterized the hemagglutinin (HA) gene of Influenza A/H1N1pdm09 strains from Assam circulating in 2016 that caused a mild outbreak without any reported mortality. Sequence analysis of the HA gene of 20 positive Assam/H1N1pdm09 strains revealed 3 mutations (K180Q, S202T, S220T) at the antigenic sites along with several other reported mutations which are in close proximity to the antigenic sites and therefore might affect the viral antigenicity. Phylogenetically, the Assam/H1N1pdm09 strains clustered into genogroup 6B. These genetic variations highlight the importance of continuous surveillance and characterization of Influenza A/H1N1pdm09 virus activity to track the genetic makeup and diversification that may affect the behavior of the virus.


Influenza A virus Swine flu H1N1 Hemagglutinin Genetic variation Assam 



This work was supported by the Regional Viral Research Diagnostic Laboratory, Dibrugarh, Assam, a scheme under Department of Health Research, Government of India.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13205_2018_1427_MOESM1_ESM.tif (14.1 mb)
Supplementary Fig. 1: (a) Surface representation of HA monomer of the vaccine strain, i.e., A/California/07/2009 (PDB id: 3LZG). (b) Surface representation of the HA monomer from one of the representative Assam/H1N1pdm09 strains. (c) 180°rotation of the representative Assam/H1N1pdm09 HA monomer. HA1 and HA2 polypeptide are colored in wheat and cyan, respectively. Antigenic epitopes are colored in yellow (Sa), green (Sb), blue (Ca1), pink (Ca2) and orange (Cb). Surface-exposed residues that differ between the vaccine strain and Assam/H1N1pdm09 strain are colored in red and labeled accordingly. (TIF 14472 KB)
13205_2018_1427_MOESM2_ESM.tif (1.5 mb)
Supplementary Fig. 2: XY plot shows the sequence relationship of the HA gene within the vaccine and Assam/H1N1pdm09 strains based on synonymous and non-synonymous mutations rates (TIF 1563 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Regional Medical Research CentreICMRDibrugarhIndia

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