Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Genome characterization and mutation analysis of human influenza A virus in Thailand

  • Rattanaburi, Somruthai (Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University) ;
  • Sawaswong, Vorthon (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Nimsamer, Pattaraporn (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Mayuramart, Oraphan (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Sivapornnukul, Pavaret (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Khamwut, Ariya (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Chanchaem, Prangwalai (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Kongnomnan, Kritsada (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Suntronwong, Nungruthai (Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University) ;
  • Poovorawan, Yong (Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University) ;
  • Payungporn, Sunchai (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University)
  • Received : 2022.12.01
  • Accepted : 2022.04.05
  • Published : 2022.06.30
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Abstract

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

Keywords

Acknowledgement

This work was partly supported by a grant from the National Science and Technology Development Agency (NSTDA) (P-17-51377), the Royal Golden Jubilee (RGJ) Ph.D. Programme scholarship (PHD/0150/2558), National Research Council of Thailand (NRCT)[2564NRCT321520] and Thailand Research Fund (TRF), the Chulalongkorn University Center of Excellence in Systems Biology and Chulalongkorn Academic Advancement into its 2nd Century Project. We would like to express gratitude to all the members of the Center of Excellence in Clinical Virology (Miss Preeyaporn Vichaiwattana and Mr. Sumeth Korkong), Faculty of Medicine, Chulalongkorn University for facilitating the sample collection. Moreover, we would like to thank the Department of Virology, Faculty of Veterinary Medicine Chulalongkorn University for support in influenza virus isolation (Assistant Prof. Aunyaratana Thontiravong, D.V.M., Ph.D.).

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