Characteristics and evolution of hemagglutinin and neuraminidase genes of Influenza A(H3N2) viruses in Thailand during 2015 to 2018

Sasiprapa Anoma; Parvapan Bhattarakosol; Ekasit Kowitdamrong

doi:10.7717/peerj.17523

Characteristics and evolution of hemagglutinin and neuraminidase genes of Influenza A(H3N2) viruses in Thailand during 2015 to 2018

PeerJ. 2024 Jun 3:12:e17523. doi: 10.7717/peerj.17523. eCollection 2024.

Authors

Sasiprapa Anoma^{1

2}, Parvapan Bhattarakosol^{2

3}, Ekasit Kowitdamrong^{2

3}

Affiliations

¹ Interdisciplinary Program in Medical Microbiology, Graduated School, Chulalongkorn University, Bangkok, Thailand.
² Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
³ Division of Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.

Abstract

Background: Influenza A(H3N2) virus evolves continuously. Its hemagglutinin (HA) and neuraminidase (NA) genes have high genetic variation due to the antigenic drift. This study aimed to investigate the characteristics and evolution of HA and NA genes of the influenza A(H3N2) virus in Thailand.

Methods: Influenza A positive respiratory samples from 2015 to 2018 were subtyped by multiplex real-time RT-PCR. Full-length HA and NA genes from the positive samples of influenza A(H3N2) were amplified and sequenced. Phylogenetic analysis with the maximum likelihood method was used to investigate the evolution of the virus compared with the WHO-recommended influenza vaccine strain. Homology modeling and N-glycosylation site prediction were also performed.

Results: Out of 443 samples, 147 (33.18%) were A(H1N1)pdm09 and 296 (66.82%) were A(H3N2). The A(H3N2) viruses circulating in 2015 were clade 3C.2a whereas sub-clade 3C.2a1 and 3C.2a2 dominated in 2016-2017 and 2018, respectively. Amino acid substitutions were found in all antigenic sites A, B, C, D, and E of HA but the majority of the substitutions were located at antigenic sites A and B. The S245N and N329S substitutions in the NA gene affect the N-glycosylation. None of the mutations associated with resistance to NA inhibitors were observed. Mean evolutionary rates of the HA and NA genes were 3.47 × 10 ^-3 and 2.98 × 10^-3 substitutions per site per year.

Conclusion: The influenza A(H3N2) virus is very genetically diverse and is always evolving to evade host defenses. The HA and NA gene features including the evolutionary rate of the influenza A(H3N2) viruses that were circulating in Thailand between 2015 and 2018 are described. This information is useful for monitoring the genetic characteristics and evolution in HA and NA genes of influenza A(H3N2) virus in Thailand which is crucial for predicting the influenza vaccine strains resulting in high vaccine effectiveness.

Keywords: Evolutionary rate; Genetic variation; Hemagglutinin; Influenza A(H3N2); Neuraminidase; Phylogenetic; Thailand; Vaccine effectiveness.

MeSH terms

Amino Acid Substitution
Evolution, Molecular*
Hemagglutinin Glycoproteins, Influenza Virus* / genetics
Humans
Influenza A Virus, H3N2 Subtype* / genetics
Influenza, Human* / epidemiology
Influenza, Human* / virology
Neuraminidase* / genetics
Phylogeny*
Thailand / epidemiology

Substances

Neuraminidase
Hemagglutinin Glycoproteins, Influenza Virus

Grants and funding

This research was funded by the 100th Anniversary Chulalongkorn University for Doctoral Scholarship, CU Graduated School Thesis Grant from Chulalongkorn University and Ratchadaphiseksomphot Matching Fund (grant number RA-MF-15/65 by Parvapan Bhattarakosol), Faculty of Medicine, Chulalongkorn University. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.