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

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.