In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019
-
Arshi Siddiqui
,
Rashmi Chowdhary
,
Harjeet Singh Maan
,
Sudhir Kumar Goel
,
Nidhi Tripathi
,
Anil Prakash
Abstract
Background and Objectives: Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/H1N1pdm09 surveillance is essential for uncovering emerging variants of epidemiologic and vaccine efficacy. The present study attempts in silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India during 2009-2019.
Materials and Methods: We have investigated the antigenic drift analysis of 96 isolates’ hemagglutinin (HA) gene sequences (59 central Indian and 37 local Indian and 28 global reference HA gene sequences) of Influenza A/H1N1pdm09 viruses from 2009 to 2019. The study includes mutational (Multiple sequence Alignment), phylogenetic (Maximum Likelihood Method), and statistical analysis (Covariance and correlation) of HA sequences submitted in NCBI, IRD and GISAID from central India.
Results: Phylogenetic analysis indicated maximum clustering of central Indian HA gene sequences in genogroup 6B. Analysis of amino acid sequence alignment revealed changes in receptor binding site (RBS). The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. The Karl Pearson correlation coefficient (r) and covariance between the number of mutations and the death toll was found +0.246 and +100.3 respectively.
Conclusion: The study identifies the continuous genetic variations in the HA gene sequences of circulating Influenza A/H1N1pdm09 in central India from the year 2009 to 2019. Further suggesting importance of monitoring the gradual evolution of the virus with regards to an increase in virulence, pathogenicity and vaccine efficacy timely.
1. World Health Organization. WHO | Influenza. Available at: https://www.who.int/biologicals/vaccines/influenza/en/. Accessed on 15th June 2020.
2. Rafeek RAM, Divarathna MVM, Noordeen F. History and current trends in influenza virus infections with special reference to Sri Lanka. Virusdisease 2017;28:225-232.
3. World Health Organization. WHO | Influenza (Seasonal) Available at: https://www.who.int/news-room/fact-sheets/detail/influenza-(seasonal). Accessed on 12th June 2020.
4. Hsieh YC, Tsao KC, Huang CT, Chang KY, Huang YC, Gong YN. Clinical characteristics of patients with laboratory-confirmed influenza A(H1N1)pdm09 during the 2013/2014 and 2015/2016 clade 6B/6B.1/6B.2-predominant outbreaks. Sci Rep 2018;8:15636.
5. Mostafa A, Abdelwhab EM, Mettenleiter TC, Pleschka S. Zoonotic Potential of Influenza A Viruses: A comprehensive overview. Viruses 2018;10:497.
6. Gabriele Neumann, Takeshi Noda, Yoshihiro Kawaoka. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009;459:931-939.
7. Dou D, Revol R, Östbye H, Wang H, Daniels R. Influenza A virus cell entry, replication, virion assembly and movement. Front Immunol 2018; 9:1581.
8. Kim H, Webster RG, Webby RJ. Influenza virus: Dealing with a drifting and shifting pathogen. Viral Immunol 2018;31:174-183.
9. Jang J, Bae SE. Comparative co-evolution analysis between the HA and NA genes of Influenza A virus. Virology (Auckl) 2018;9: 1178122X18788328.
10. Korsun N, Angelova S, Gregory V, Daniels R, Georgieva I, McCauley J. Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Infect Genet Evol 2017;49:241-250.
11. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009;325:197-201.
12. Kulkarni PS, Raut SK, Dhere RM. A post-marketing surveillance study of a human live-virus pandemic influenza A (H1N1) vaccine (Nasovac (®)) in India. Hum Vaccin Immunother 2013;9:122-124.
13. Choudhry A, Singh S, Khare S, Rai A, Rawat DS, Aggarwal RK, et al. Emergence of pandemic 2009 influenza A H1N1, India. Indian J Med Res 2012;135:534-537.
14. Mishra B. Resurgence of Influenza A (H1N1) 09: smoldering pandemic in India?. J Glob Infect Dis 2015;7:56-59.
15. Ministry of Health and Family Welfare, Government of India. Press Releases. Update on Influenza a (H1N1) as on 27th October 2019 Available on https://ncdc.gov.in/showfile.php?lid=280. Accessed on 1st November 2019.
16. Mukherjee A, Nayak MK, Dutta S, Panda S, Satpathi BR, Chawla-Sarkar M. Genetic Characterization of circulating 2015 A(H1N1)pdm09 Influenza viruses from Eastern India. PLoS One 2016; 11(12): e0168464.
17. Shao W, Li X, Goraya MU, Wang S, Chen JL. Evolution of Influenza A virus by mutation and re-assortment. Int J Mol Sci 2017;18:1650.
18. World Health Organization. WHO | Global Influenza Strategy 2019-2030 Available at: https://apps.who.int/iris/bitstream/handle/10665/311184/9789241515320-eng.pdf?ua=1
19. Chen X, Liu S, Goraya MU, Maarouf M, Huang S, Chen JL. Host immune response to influenza A virus infection. Front Immunol 2018;9:320.
20. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2019- 2020 northern hemisphere influenza season. Available at: https://www.who.int/influenza/vaccines/virus/recommendations/201902_recommendation.pdf?ua=1
21. Zhang Y, Xu C, Zhang H, Liu GD, Xue C, Cao Y. Targeting Hemagglutinin: approaches for broad protection against the influenza A virus. Viruses 2019;11:405.
22. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2011-2012 northern hemisphere influenza season. Available at: https://www.who.int/influenza/vaccines/2011_02_recommendation.pdf
23. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2018 southern hemisphere influenza season 2017. Available at: https://www.who.int/influenza/vaccines/virus/recommendations/201709_recommendation.pdf?ua=1
24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547-1549.
25. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512-526.
26. Bhat S, Nagarajan S, Kumar M, Murugkar HV, Kalaiyarasu S, Venkatesh G, et al. Antigenic characterization of H5N1 highly pathogenic avian influenza viruses isolated from poultry in India, 2006-2015. Arch Virol 2017;162:487-494.
27. Sarmah K, Borkakoty B, Sarma K, Hazarika R, Das PK, Jakharia A, et al. Genetic variations of the hemagglutinin gene of pandemic Influenza A (H1N1) viruses in Assam, India during 2016. 3 Biotech 2018;8:408.
28. EDUCBA. Available at: https://www.educba.com/covariance-formula/
29. Karl Pearson coefficient of correlation. Available at https://businessjargons.com/karl-pearsons-coefficient-of-correlation.html
30. Zolotarova O, Budzanivska I, Leibenko L, Radchenko L, Mironenko A. Antigenic site variation in the hemagglutinin of pandemic Influenza A(H1N1)pdm09 viruses between 2009-2017 in Ukraine. Pathogens 2019;8:194.
31. Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, et al. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2018;90:447-455.
32. Pandey S, Sahu M, Potdar V, Barde P. Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017. Virusdisease 2018;29:380-384.
33. Al Khatib HA, Al Thani AA, Gallouzi I, Yassine HM. Epidemiological and genetic characterization of pH1N1 and H3N2 influenza viruses circulated in MENA region during 2009-2017. BMC Infect Dis 2019;19:314.
34. Sullivan SJ, Jacobson RM, Dowdle WR, Poland GA. 2009 H1N1 influenza. Mayo Clin Proc 2010;85:64-76.
35. Opanda S, Bulimo W, Gachara G, Ekuttan C, Amukoye E. Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene. PLoS One 2020;15(2):e0228029.
36. Monamele CG, Munshili Njifon HL, Vernet MA, Njankouo MR, Kenmoe S, Yahaya AA, et al. Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. PLoS One 2019;14(1): e0210119.
37. Bakri M, Samuh M, Azzeh M. Molecular epidemiology survey and characterization of human influenza A viruses circulating among Palestinians in East Jerusalem and the West Bank in 2015. PLoS One 2019;14(3):e0213290.
38. Jones S, Nelson-Sathi S, Wang Y, Prasad R, Rayen S, Nandel V, et al. Evolutionary, genetic, structural characterization and its functional implications for the influenza A (H1N1) infection outbreak in India from 2009 to 2017. Sci Rep 2019; 9:14690.
39. Prasad R, Mohanakumari VV, Sasi RV, Nair R, Jones S, Pillai MR. Complete genome analysis of Influenza A(H1N1) viruses isolated in Kerala, India. Microbiol Resour Announc 2020;9(12): e00062-20.
40. Pandey S, Sahu M, Potdar V, Barde P. Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017. Virusdisease 2018;29:380-384.
41. Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, et al. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2018;90:447-455.
42. Maines TR, Jayaraman A, Belser JA, Wadford DA, Pappas C, Zeng H, et al. Transmission and pathogenesis of swine-origin 2009 a(H1N1) influenza viruses in ferrets and mice. Science 2009;325:484-487.
43. de Vries RP, de Vries E, Martínez-Romero C, McBride R, Kuppeveld FJ, Rottier PJM, et al. Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions. J Virol 2013; 87: 13868-13877.
44. Biswas D, Dutta M, Sarmah K, Yadav K, Buragohain M, Sarma K, et al. Genetic characterisation of influenza A(H1N1)pdm09 viruses circulating in Assam, Northeast India during 2009–2015. Indian J Med Microbiol 2019;37:42-49.
45. Science. The wire. https://science.thewire.in/health/influenza-niv-h1n1-h3n2-reassortant/
46. Wu A, Peng Y, Du X, Shu Y, Jiang T. Correlation of influenza virus excess mortality with antigenic variation: application to rapid estimation of influenza mortality burden. PLoS Comput Biol 2010;6(8):e1000882.
47. Adam DC, Scotch M, MacIntyre CR. Phylodynamics of Influenza A/H1N1pdm09 in India reveals circulation patterns and increased selection for clade 6b residues and other high mortality mutants. Viruses 2019;11:791.
48. Parida M, Dash P, Kumar J, Joshi G, Tandel K, Sharma S, et al. Emergence of influenza A(H1N1) pdm09 genogroup 6B and drug resistant virus, India, January to May 2015. Euro Surveill 2016;21:6-11.
49. Gao F, Loring C, Laviolette M, Bolton D, Daly ER, Bean C. Detection of 2009 pandemic influenza A(H1N1) virus Infection in different age groups by using rapid influenza diagnostic tests. Influenza Other Respir Viruses 2012;6(3): e30-e34.
2. Rafeek RAM, Divarathna MVM, Noordeen F. History and current trends in influenza virus infections with special reference to Sri Lanka. Virusdisease 2017;28:225-232.
3. World Health Organization. WHO | Influenza (Seasonal) Available at: https://www.who.int/news-room/fact-sheets/detail/influenza-(seasonal). Accessed on 12th June 2020.
4. Hsieh YC, Tsao KC, Huang CT, Chang KY, Huang YC, Gong YN. Clinical characteristics of patients with laboratory-confirmed influenza A(H1N1)pdm09 during the 2013/2014 and 2015/2016 clade 6B/6B.1/6B.2-predominant outbreaks. Sci Rep 2018;8:15636.
5. Mostafa A, Abdelwhab EM, Mettenleiter TC, Pleschka S. Zoonotic Potential of Influenza A Viruses: A comprehensive overview. Viruses 2018;10:497.
6. Gabriele Neumann, Takeshi Noda, Yoshihiro Kawaoka. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009;459:931-939.
7. Dou D, Revol R, Östbye H, Wang H, Daniels R. Influenza A virus cell entry, replication, virion assembly and movement. Front Immunol 2018; 9:1581.
8. Kim H, Webster RG, Webby RJ. Influenza virus: Dealing with a drifting and shifting pathogen. Viral Immunol 2018;31:174-183.
9. Jang J, Bae SE. Comparative co-evolution analysis between the HA and NA genes of Influenza A virus. Virology (Auckl) 2018;9: 1178122X18788328.
10. Korsun N, Angelova S, Gregory V, Daniels R, Georgieva I, McCauley J. Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Infect Genet Evol 2017;49:241-250.
11. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009;325:197-201.
12. Kulkarni PS, Raut SK, Dhere RM. A post-marketing surveillance study of a human live-virus pandemic influenza A (H1N1) vaccine (Nasovac (®)) in India. Hum Vaccin Immunother 2013;9:122-124.
13. Choudhry A, Singh S, Khare S, Rai A, Rawat DS, Aggarwal RK, et al. Emergence of pandemic 2009 influenza A H1N1, India. Indian J Med Res 2012;135:534-537.
14. Mishra B. Resurgence of Influenza A (H1N1) 09: smoldering pandemic in India?. J Glob Infect Dis 2015;7:56-59.
15. Ministry of Health and Family Welfare, Government of India. Press Releases. Update on Influenza a (H1N1) as on 27th October 2019 Available on https://ncdc.gov.in/showfile.php?lid=280. Accessed on 1st November 2019.
16. Mukherjee A, Nayak MK, Dutta S, Panda S, Satpathi BR, Chawla-Sarkar M. Genetic Characterization of circulating 2015 A(H1N1)pdm09 Influenza viruses from Eastern India. PLoS One 2016; 11(12): e0168464.
17. Shao W, Li X, Goraya MU, Wang S, Chen JL. Evolution of Influenza A virus by mutation and re-assortment. Int J Mol Sci 2017;18:1650.
18. World Health Organization. WHO | Global Influenza Strategy 2019-2030 Available at: https://apps.who.int/iris/bitstream/handle/10665/311184/9789241515320-eng.pdf?ua=1
19. Chen X, Liu S, Goraya MU, Maarouf M, Huang S, Chen JL. Host immune response to influenza A virus infection. Front Immunol 2018;9:320.
20. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2019- 2020 northern hemisphere influenza season. Available at: https://www.who.int/influenza/vaccines/virus/recommendations/201902_recommendation.pdf?ua=1
21. Zhang Y, Xu C, Zhang H, Liu GD, Xue C, Cao Y. Targeting Hemagglutinin: approaches for broad protection against the influenza A virus. Viruses 2019;11:405.
22. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2011-2012 northern hemisphere influenza season. Available at: https://www.who.int/influenza/vaccines/2011_02_recommendation.pdf
23. World Health Organization. WHO | Recommended composition of influenza virus vaccines for use in the 2018 southern hemisphere influenza season 2017. Available at: https://www.who.int/influenza/vaccines/virus/recommendations/201709_recommendation.pdf?ua=1
24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547-1549.
25. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512-526.
26. Bhat S, Nagarajan S, Kumar M, Murugkar HV, Kalaiyarasu S, Venkatesh G, et al. Antigenic characterization of H5N1 highly pathogenic avian influenza viruses isolated from poultry in India, 2006-2015. Arch Virol 2017;162:487-494.
27. Sarmah K, Borkakoty B, Sarma K, Hazarika R, Das PK, Jakharia A, et al. Genetic variations of the hemagglutinin gene of pandemic Influenza A (H1N1) viruses in Assam, India during 2016. 3 Biotech 2018;8:408.
28. EDUCBA. Available at: https://www.educba.com/covariance-formula/
29. Karl Pearson coefficient of correlation. Available at https://businessjargons.com/karl-pearsons-coefficient-of-correlation.html
30. Zolotarova O, Budzanivska I, Leibenko L, Radchenko L, Mironenko A. Antigenic site variation in the hemagglutinin of pandemic Influenza A(H1N1)pdm09 viruses between 2009-2017 in Ukraine. Pathogens 2019;8:194.
31. Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, et al. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2018;90:447-455.
32. Pandey S, Sahu M, Potdar V, Barde P. Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017. Virusdisease 2018;29:380-384.
33. Al Khatib HA, Al Thani AA, Gallouzi I, Yassine HM. Epidemiological and genetic characterization of pH1N1 and H3N2 influenza viruses circulated in MENA region during 2009-2017. BMC Infect Dis 2019;19:314.
34. Sullivan SJ, Jacobson RM, Dowdle WR, Poland GA. 2009 H1N1 influenza. Mayo Clin Proc 2010;85:64-76.
35. Opanda S, Bulimo W, Gachara G, Ekuttan C, Amukoye E. Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene. PLoS One 2020;15(2):e0228029.
36. Monamele CG, Munshili Njifon HL, Vernet MA, Njankouo MR, Kenmoe S, Yahaya AA, et al. Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. PLoS One 2019;14(1): e0210119.
37. Bakri M, Samuh M, Azzeh M. Molecular epidemiology survey and characterization of human influenza A viruses circulating among Palestinians in East Jerusalem and the West Bank in 2015. PLoS One 2019;14(3):e0213290.
38. Jones S, Nelson-Sathi S, Wang Y, Prasad R, Rayen S, Nandel V, et al. Evolutionary, genetic, structural characterization and its functional implications for the influenza A (H1N1) infection outbreak in India from 2009 to 2017. Sci Rep 2019; 9:14690.
39. Prasad R, Mohanakumari VV, Sasi RV, Nair R, Jones S, Pillai MR. Complete genome analysis of Influenza A(H1N1) viruses isolated in Kerala, India. Microbiol Resour Announc 2020;9(12): e00062-20.
40. Pandey S, Sahu M, Potdar V, Barde P. Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017. Virusdisease 2018;29:380-384.
41. Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, et al. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2018;90:447-455.
42. Maines TR, Jayaraman A, Belser JA, Wadford DA, Pappas C, Zeng H, et al. Transmission and pathogenesis of swine-origin 2009 a(H1N1) influenza viruses in ferrets and mice. Science 2009;325:484-487.
43. de Vries RP, de Vries E, Martínez-Romero C, McBride R, Kuppeveld FJ, Rottier PJM, et al. Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions. J Virol 2013; 87: 13868-13877.
44. Biswas D, Dutta M, Sarmah K, Yadav K, Buragohain M, Sarma K, et al. Genetic characterisation of influenza A(H1N1)pdm09 viruses circulating in Assam, Northeast India during 2009–2015. Indian J Med Microbiol 2019;37:42-49.
45. Science. The wire. https://science.thewire.in/health/influenza-niv-h1n1-h3n2-reassortant/
46. Wu A, Peng Y, Du X, Shu Y, Jiang T. Correlation of influenza virus excess mortality with antigenic variation: application to rapid estimation of influenza mortality burden. PLoS Comput Biol 2010;6(8):e1000882.
47. Adam DC, Scotch M, MacIntyre CR. Phylodynamics of Influenza A/H1N1pdm09 in India reveals circulation patterns and increased selection for clade 6b residues and other high mortality mutants. Viruses 2019;11:791.
48. Parida M, Dash P, Kumar J, Joshi G, Tandel K, Sharma S, et al. Emergence of influenza A(H1N1) pdm09 genogroup 6B and drug resistant virus, India, January to May 2015. Euro Surveill 2016;21:6-11.
49. Gao F, Loring C, Laviolette M, Bolton D, Daly ER, Bean C. Detection of 2009 pandemic influenza A(H1N1) virus Infection in different age groups by using rapid influenza diagnostic tests. Influenza Other Respir Viruses 2012;6(3): e30-e34.
| Files | ||
| Issue | Vol 12 No 5 (2020) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v12i5.4611 | |
| Keywords | ||
| Influenza A virus H1N1 subtype; Haemagglutinin; Central India | ||
| Rights and permissions | |
|
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Siddiqui A, Chowdhary R, Singh Maan H, Goel S, Tripathi N, Prakash A. In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. Iran J Microbiol. 2020;12(5):483-494.
