, Volume 29, Issue 1, pp 54–60 | Cite as

Molecular analysis of hemagglutinin, neuraminidase, matrix genes provide insight into the genetic diversity of seasonal H3N2 human influenza a viruses in Bangladesh during July–August, 2012

  • Mukesh Jain
  • Sohidul Islam
  • A. S. M. Zisanur Rahman
  • Sharmin Akhtar
  • Kazi Nadim Hasan
  • Gias Uddin Ahsan
  • Abdul Khaleque
  • Maqsud Hossain
Original Article


Influenza A virus subtype H3 is a threat to public health and it is important to understand the evolution of the viruses for the surveillance and the selection of vaccine strains. Comparative analysis of four Bangladeshi isolates with isolates circulating other parts of the world based on three candidate genes hemagglutinin (HA), neuraminidase (NA), matrix protein (MA) showed no evidence of significant distinct subclade of viruses circulating in the country over the period of study. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. All H3N2 Influenza subtypes in the study had amino acid substitution at position 31 on the M2 protein (Aspartic acid to Asparagine) which is known to be responsible for amantadine drug resistance.


H3N2 Hemagglutinin Neuraminidase Matrix genes 



We acknowledge Dhaka Medical College Hospital for providing the samples and the financial support of North South University.

Supplementary material

13337_2018_431_MOESM1_ESM.jpg (92 kb)
Supplementary Figure 1 Neighbor-joining phylogenetic tree based on partial gene sequences of HA (Hemagglutinine) of A/H3N2 strains from Bangladesh and sequences (n = 37) from other countries available in GenBank and GSAID. Five major groups have been found and the representative Bangladeshi isolate cluster with the Vaccine strain A/Victoria/361/HA/2011. (JPEG 91 kb)
13337_2018_431_MOESM2_ESM.jpg (86 kb)
Supplementary Figure 2 Neighbor-joining phylogenetic tree based on representative complete gene sequences of NA (Neuraminidase) of A/H3N2 strains from Bangladesh and sequences (n = 37) from other countries available in GenBank and GSAID. The representative Bangladeshi isolate cluster with the Vaccine strain A/Victoria/361/HA/2011. (JPEG 85 kb)
13337_2018_431_MOESM3_ESM.jpg (91 kb)
Supplementary Figure 3 Neighbor-joining phylogenetic tree based on the representative partial gene sequences of MP (Matrix Protein) of A/H3N2 strains from Bangladesh and sequences (n = 37) from other countries available in GenBank and GSAID. The representative Bangladeshi isolate cluster with the Vaccine strain A/Victoria/361/HA/2011. (JPEG 91 kb)
13337_2018_431_MOESM4_ESM.xls (66 kb)
Supplementary material 4 (XLS 65 kb)
13337_2018_431_MOESM5_ESM.xlsx (24 kb)
Supplementary material 5 (XLSX 23 kb)
13337_2018_431_MOESM6_ESM.xlsx (23 kb)
Supplementary material 6 (XLSX 23 kb)


  1. 1.
    Alymova IV, Taylor G, Mishin VP, Watanabe M, Murti KG, Boyd K, et al. Loss of the N-linked glycan at residue 173 of human parainfluenza virus type 1 hemagglutinin-neuraminidase exposes a second receptor-binding site. J Virol. 2008;82:8400–10.CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Blick TJ, Sahasrabudhe A, McDonald M, Owens IJ, Morley PJ, Fenton RJ, McKimm-Breschkin JL. The interaction of neuraminidase and hemagglutinin mutations in influenza virus in resistance to 4-guanidino-Neu5Ac2en. Virology. 1998;246:95–103.CrossRefPubMedGoogle Scholar
  3. 3.
    Chutinimitkul S, Chieochansin T, Payungporn S, Samransamruajkit R, Hiranras T, Theamboonlers A, et al. Molecular characterization and phylogenetic analysis of H1N1 and H3N2 human influenza A viruses among infants and children in Thailand. Virus Res. 2008;132:122–31.CrossRefPubMedGoogle Scholar
  4. 4.
    Clarke LM, Alexander H, Baker MB, Bankowski MJ, Kirk C, et al. Viral culture; approved guideline. CLSI document M41-A. In: Wilhelm DM, editor. Viral culture; approved guideline CLSI document M41-A. Wayne: Clinical And Laboratory Standards Institute; 2003.Google Scholar
  5. 5.
    Colman PM, Hoyne PA, Lawrence MC. Sequence and structure alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase. J Virol. 1993;67:2972–80.PubMedPubMedCentralGoogle Scholar
  6. 6.
    Daum LT, Shaw MW, Klimov AI, Canas LC, Macias EA, Niemeyer D, et al. Influenza A (H3N2) outbreak, Nepal. Emerg Infect Dis. 2005;11:1186–91.CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Gulati U, Hwang C-C, Venkatramani L, Gulati S, Stray SJ, Lee JT, Laver WG, Bochkarev A, Zlotnick A, Air GM. Antibody epitopes on the neuraminidase of a recent H3N2 influenza virus (A/Memphis/31/98). J Virol. 2002;76:12274–80.CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Hungnes O. Early detection of A/California/7/2004-like A (H3N2) strains in Norway during the 2004–2005 season, and emergence of a novel H3N2 genetic sub-variant toward the end. Vaccine. 2006;24(44):6694–6.CrossRefPubMedGoogle Scholar
  9. 9.
    Ison MG, Hayden FG. Viral infections in immunocompromised patients: what’s new with respiratory viruses? Curr Opin Infect Dis. 2002;15:355–67.CrossRefPubMedGoogle Scholar
  10. 10.
    Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–20.CrossRefPubMedGoogle Scholar
  11. 11.
    Kiso M, Mitamura K, Sakai-Tagawa Y, Shiraishi K, Kawakami C, Kimura K, Hayden FG, Sugaya N, Kawaoka Y. Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet. 2004;364:759–65.CrossRefPubMedGoogle Scholar
  12. 12.
    Long J, Bushnell RV, Tobin JK, Pan K, Deem MW, Nara PL, et al. Evolution of H3N2 influenza virus in a Guinea pig model. PLoS ONE. 2011;6:e22844.CrossRefGoogle Scholar
  13. 13.
    Mishin VP, Novikov D, Hayden FG, Gubareva LV. Effect of hemagglutinin glycosylation on influenza virus susceptibility to neuraminidase inhibitors. J Virol. 2005;79:12416–24.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Palese P, Shaw ML. Orthomyxoviridae Viruses Their Replication. In: Knipe DM, Howley PM, editors. Fields Virology. Philadelphia, PA: Lippincott Williams Wilkins, Alphen aan den Rijn: Wolters Kluwer Bus; 2007. 1647–89.Google Scholar
  15. 15.
    Pechirra P, Gonçalves P, Arraiolos A, Coelho A, Rebelo-de-Andrade H. Characterization of influenza A/Fujian/411/2002 (H3N2)-like viruses isolated in Portugal between 2003 and 2005. J Med Virol. 2008;80(9):1624–30.CrossRefPubMedGoogle Scholar
  16. 16.
    Reid AH, Taubenberger JK, The Fanning TG. Spanish influenza: integrating history and biology. Microbes Infect. 1918;2001:81–7.Google Scholar
  17. 17.
    Saito R, Sakai T, Sato I, Sano Y, Oshitani H, Sato M, Suzuki H. Frequency of amantadine-resistant influenza A viruses during two seasons featuring cocirculation of H1N1 and H3N2. J Clin Microbiol. 2003;41:2164–5.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
  19. 19.
    Sun S, Wang Q, Zhao F, Chen W, Li Z. Glycosylation site alteration in the evolution of influenza a (H1N1) viruses. PLoS ONE. 2011;6:e22844.CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Tomar AK, Sooch BS, Yadav S. Computational analysis of Concanavalin A binding glycoproteins of human seminal plasma. Bioinformation. 2011;7:69–75.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Tong S, Zhu X, Li Y, Shi M, Zhang J, Bourgeois M, Bourgeois M, Yang H, Chen X, Recuenco S, Gomez J, Chen LM, Johnson A, Tao Y, Dreyfus C, Yu W, McBride R, Carney PJ, Gilbert AT, Chang J, Guo Z, Davis CT, Paulson JC, Stevens J, Rupprecht CE, Holmes EC, Wilson IA, Donis RO. New world bats harbor diverse influenza a viruses. PLoS Pathog. 2013;9:e1003657.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Underwood PA. Mapping of antigenic changes in the haemagglutinin of Hong Kong influenza (H3N2) strains using a large panel of monoclonal antibodies. J Gen Virol. 1982;62:153–69.CrossRefPubMedGoogle Scholar
  24. 24.
    Vigerust DJ, Ulett KB, Boyd KL, Madsen J, Hawgood S, Mccullers JA. N-linked glycosylation attenuates H3N2 influenza viruses. J Virol. 2007;81:8593–600.CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000;25:300–2.CrossRefPubMedGoogle Scholar
  26. 26.
    Whitley RJ, Hayden FG, Reisinger KS, Young N, Dutkowski R, Ipe D, Mills RG, Ward P. Oral oseltamivir treatment of influenza in children. Pediatr Infect Dis J. 2001;20:127–33.CrossRefPubMedGoogle Scholar
  27. 27.
    Wiley DC, Wilson IA, Skehel JJ. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature. 1981;289:373–8.CrossRefPubMedGoogle Scholar

Copyright information

© Indian Virological Society 2018

Authors and Affiliations

  • Mukesh Jain
    • 1
  • Sohidul Islam
    • 1
  • A. S. M. Zisanur Rahman
    • 1
  • Sharmin Akhtar
    • 1
  • Kazi Nadim Hasan
    • 1
  • Gias Uddin Ahsan
    • 2
    • 3
  • Abdul Khaleque
    • 1
  • Maqsud Hossain
    • 1
    • 3
  1. 1.Department of Biochemistry and MicrobiologyNorth South UniversityDhakaBangladesh
  2. 2.Department of Public HealthNorth South UniversityDhakaBangladesh
  3. 3.NSU Genome Research Institute (NGRI)North South UniversityDhakaBangladesh

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