Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand

Pirom Noisumdaeng; Juthamas Phadungsombat; Sasrinakarn Weerated; Witthawat Wiriyarat; Pilaipan Puthavathana

doi:10.7717/peerj.14419

Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand

PeerJ. 2022 Nov 30:10:e14419. doi: 10.7717/peerj.14419. eCollection 2022.

Authors

Pirom Noisumdaeng^{1

2}, Juthamas Phadungsombat^{3

4}, Sasrinakarn Weerated¹, Witthawat Wiriyarat⁵, Pilaipan Puthavathana⁶

Affiliations

¹ Faculty of Public Health, Thammasat University, Khlong Luang, Pathum Thani, Thailand.
² Thammasat University Research Unit in Modern Microbiology and Public Health Genomics, Thammasat University, Khlong Luang, Pathum Thani, Thailand.
³ Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
⁴ Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
⁵ Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
⁶ Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand.

Abstract

Background: Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses.

Methods: Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4.

Results: ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4.

Conclusion: H5N1 viruses existed, and were presumably introduced and circulated in avian species in Thailand, before they were officially reported in 2004. HA and NA genes continuously evolved during circulation between 2004 and 2010. This study provides a better understanding of genetic evolution with respect to molecular epidemiology. Monitoring and surveillance of emerging variants/reassortants should be continued.

Keywords: Genetic evolution; H5N1 highly pathogenic avian influenza (HPAI) virus; Hemagglutinin; Neuraminidase; Reassortant H5Nx viruses.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bayes Theorem
Birds
Evolution, Molecular
Hemagglutinins
Influenza A Virus, H5N1 Subtype* / genetics
Influenza A virus*
Influenza in Birds* / epidemiology
Neuraminidase / genetics
Phylogeny
Thailand / epidemiology

Substances

Hemagglutinins
Neuraminidase

Grants and funding

This work was supported by the National Research Council of Thailand (NRCT). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.