Genetic analysis of the complete genome of influenza A (H1N1) pdm09 during the first wave of the pandemic season in Indonesia

Hana Apsari Pawestri; Ni K. Susilarini; Kartika D. Puspa; Hartanti D. Ikawati; Kindi Adam; Arie A. Nugraha; Vivi Setiawaty

doi:10.15562/bmj.v6i3.576

Genetic analysis of the complete genome of influenza A (H1N1) pdm09 during the first wave of the pandemic season in Indonesia

Hana Apsari Pawestri ,

Ni K. Susilarini ,

Kartika D. Puspa ,

Hartanti D. Ikawati ,

Kindi Adam ,

Arie A. Nugraha ,

Vivi Setiawaty ,

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DOI: https://doi.org/10.15562/bmj.v6i3.576 |
Published: 2017-07-22

Abstract

Background: During 2009, Indonesia reported human cases of pandemic influenza A(H1N1) virus. Although the fatality rate was not as high as for H5N1 virus infection, genetic information has not yet been published. We generated whole-genome sequences from 28 influenza A(H1N1)pdm09 isolates during the first wave of the 2009 pandemic in Indonesia to determine the genetic characteristics related to clades, receptor-binding sites, antiviral resistance, virulence, pathogenicity, and polymerase activity.

Method: We detected, amplified, and sequenced the influenza A(H1N1)pdm09 viruses using real-time PCR, egg culture, reverse transcriptase PCR (RT-PCR), and Sanger sequencing. In addition, we analyzed the genetic characteristics using BioEdit and MEGA6 software.

Results: The phylogenetic analysis of the hemagglutinin (HA) gene showed similar clusters to one of the first 2009 pandemic viruses, A/California/07/2009. Resistance to amantadine in the matrix (M) gene was suggested by a fixed mutation, S31N. No mutations were found in the polymerase acid (PA) gene (T515A) or polymerase basic 2 (PB2) (E627, D701). An analysis of the neuraminidase (NA) gene did not indicate the presence of a deletion mutation, and the NS genes of the viruses did not contain the ESEV motif of the PDZ-binding domain.

Conclusion: This study produced comprehensive information through the genetic analysis of influenza A(H1N1) pdm09 viruses isolated during the 2009 pandemic outbreak. The findings of this study have increased the level of awareness of the importance of surveillance for monitoring the evolution of influenza viruses in Indonesia.Â

References

Fischer WA, 2nd, Gong M, Bhagwanjee S, et al. Global burden of influenza as a cause of cardiopulmonary morbidity and mortality. Glob Heart. 2014;9(3):325-336.
Taubenberger JK, Morens DM. Influenza: the once and future pandemic. Public Health Rep. 2010;125 Suppl 3:16-26.
Morens DM, Taubenberger JK, Harvey HA, et al. The 1918 influenza pandemic: lessons for 2009 and the future. Crit Care Med. 2010;38(4 Suppl):e10-20.
Anton A, Pozo F, Niubo J, et al. Influenza A(H1N1)pdm09 virus: viral characteristics and genetic evolution. Enferm Infecc Microbiol Clin. 2012;30 Suppl 4:10-17.
LaRussa P. Pandemic novel 2009 H1N1 influenza: what have we learned? Semin Respir Crit Care Med. 2011;32(4):393-399.
Adisasmito W, Suwandono A, Aisyah DN. Measuring Indonesia H1N1 Pandemic Preparedness through Stakeholder Analysis. Health Care Current Reviews. 2014;2(1):119.
CDC. CDC protocol of real-time RTPCR for swine influenza A(H1N1) (2009) 2009. Accessed 15 December 2011, 2009.
Pedersen JC. Hemagglutination-inhibition assay for influenza virus subtype identification and the detection and quantitation of serum antibodies to influenza virus. Methods Mol Biol. 2014;1161:11-25.
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Paper presented at: Nucleic Acids Symposium Series.
Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24(8):1596-1599.
Shu Y, Li CK, Li Z, et al. Avian influenza A(H5N1) viruses can directly infect and replicate in human gut tissues. J Infect Dis. 2010;201(8):1173-1177.
Blumenkrantz D, Roberts KL, Shelton H, et al. The short stalk length of highly pathogenic avian influenza H5N1 virus neuraminidase limits transmission of pandemic H1N1 virus in ferrets. J Virol. 2013;87(19):10539-10551.
Schaduangrat N, Phanich J, Rungrotmongkol T, et al. The significance of naturally occurring neuraminidase quasispecies of H5N1 avian influenza virus on resistance to oseltamivir: a point of concern. J Gen Virol. 2016;97(6):1311-1323.
Bouvier NM, Rahmat S, Pica N. Enhanced mammalian transmissibility of seasonal influenza A/H1N1 viruses encoding an oseltamivir-resistant neuraminidase. J Virol. 2012;86(13):7268-7279.
Okomo-Adhiambo M, Sleeman K, Lysen C, et al. Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Influenza Other Respir Viruses. 2013;7(5):645-658.
Goka EA, Vallely PJ, Mutton KJ, et al. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol. 2014;159(12):3167-3183.
Caglioti C, Selleri M, Rozera G, et al. In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. PLoS One. 2016;11(5):e0155661.
Furuse Y, Suzuki A, Kamigaki T, et al. Evolution of the M gene of the influenza A virus in different host species: large-scale sequence analysis. Virol J. 2009;6:67.
Pielak RM, Chou JJ. Influenza M2 proton channels. Biochim Biophys Acta. 2011;1808(2):522-529.
Li W, Chen H, Sutton T, et al. Interactions between the influenza A virus RNA polymerase components and retinoic acid-inducible gene I. J Virol. 2014;88(18):10432-10447.
Zhang H, Li X, Guo J, et al. The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. J Gen Virol. 2014;95(Pt 4):779-786.
Steel J, Staeheli P, Mubareka S, et al. Transmission of pandemic H1N1 influenza virus and impact of prior exposure to seasonal strains or interferon treatment. J Virol. 2010;84(1):21-26.
Suzuki Y, Uchida Y, Tanikawa T, et al. Amino acid substitutions in PB1 of avian influenza viruses influence pathogenicity and transmissibility in chickens. J Virol. 2014;88(19):11130-11139.
Mehle A, Dugan VG, Taubenberger JK, et al. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012;86(3):1750-1757.
Turrell L, Lyall JW, Tiley LS, et al. The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes. Nat Commun. 2013;4:1591.

[1] Fischer WA, 2nd, Gong M, Bhagwanjee S, et al. Global burden of influenza as a cause of cardiopulmonary morbidity and mortality. Glob Heart. 2014;9(3):325-336.

[2] Taubenberger JK, Morens DM. Influenza: the once and future pandemic. Public Health Rep. 2010;125 Suppl 3:16-26.

[3] Morens DM, Taubenberger JK, Harvey HA, et al. The 1918 influenza pandemic: lessons for 2009 and the future. Crit Care Med. 2010;38(4 Suppl):e10-20.

[4] Anton A, Pozo F, Niubo J, et al. Influenza A(H1N1)pdm09 virus: viral characteristics and genetic evolution. Enferm Infecc Microbiol Clin. 2012;30 Suppl 4:10-17.

[5] LaRussa P. Pandemic novel 2009 H1N1 influenza: what have we learned? Semin Respir Crit Care Med. 2011;32(4):393-399.

[6] Adisasmito W, Suwandono A, Aisyah DN. Measuring Indonesia H1N1 Pandemic Preparedness through Stakeholder Analysis. Health Care Current Reviews. 2014;2(1):119.

[7] CDC. CDC protocol of real-time RTPCR for swine influenza A(H1N1) (2009) 2009. Accessed 15 December 2011, 2009.

[8] Pedersen JC. Hemagglutination-inhibition assay for influenza virus subtype identification and the detection and quantitation of serum antibodies to influenza virus. Methods Mol Biol. 2014;1161:11-25.

[9] Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Paper presented at: Nucleic Acids Symposium Series.

[10] Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24(8):1596-1599.

[11] Shu Y, Li CK, Li Z, et al. Avian influenza A(H5N1) viruses can directly infect and replicate in human gut tissues. J Infect Dis. 2010;201(8):1173-1177.

[12] Blumenkrantz D, Roberts KL, Shelton H, et al. The short stalk length of highly pathogenic avian influenza H5N1 virus neuraminidase limits transmission of pandemic H1N1 virus in ferrets. J Virol. 2013;87(19):10539-10551.

[13] Schaduangrat N, Phanich J, Rungrotmongkol T, et al. The significance of naturally occurring neuraminidase quasispecies of H5N1 avian influenza virus on resistance to oseltamivir: a point of concern. J Gen Virol. 2016;97(6):1311-1323.

[14] Bouvier NM, Rahmat S, Pica N. Enhanced mammalian transmissibility of seasonal influenza A/H1N1 viruses encoding an oseltamivir-resistant neuraminidase. J Virol. 2012;86(13):7268-7279.

[15] Okomo-Adhiambo M, Sleeman K, Lysen C, et al. Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Influenza Other Respir Viruses. 2013;7(5):645-658.

[16] Goka EA, Vallely PJ, Mutton KJ, et al. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol. 2014;159(12):3167-3183.

[17] Caglioti C, Selleri M, Rozera G, et al. In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. PLoS One. 2016;11(5):e0155661.

[18] Furuse Y, Suzuki A, Kamigaki T, et al. Evolution of the M gene of the influenza A virus in different host species: large-scale sequence analysis. Virol J. 2009;6:67.

[19] Pielak RM, Chou JJ. Influenza M2 proton channels. Biochim Biophys Acta. 2011;1808(2):522-529.

[20] Li W, Chen H, Sutton T, et al. Interactions between the influenza A virus RNA polymerase components and retinoic acid-inducible gene I. J Virol. 2014;88(18):10432-10447.

[21] Zhang H, Li X, Guo J, et al. The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. J Gen Virol. 2014;95(Pt 4):779-786.

[22] Steel J, Staeheli P, Mubareka S, et al. Transmission of pandemic H1N1 influenza virus and impact of prior exposure to seasonal strains or interferon treatment. J Virol. 2010;84(1):21-26.

[23] Suzuki Y, Uchida Y, Tanikawa T, et al. Amino acid substitutions in PB1 of avian influenza viruses influence pathogenicity and transmissibility in chickens. J Virol. 2014;88(19):11130-11139.

[24] Mehle A, Dugan VG, Taubenberger JK, et al. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012;86(3):1750-1757.

[25] Turrell L, Lyall JW, Tiley LS, et al. The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes. Nat Commun. 2013;4:1591.

Genetic analysis of the complete genome of influenza A (H1N1) pdm09 during the first wave of the pandemic season in Indonesia

Abstract

References

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