Molecular characterization and phylogenetic analysis of highly pathogenic avian influenza A(H5N8) viruses isolated from chicken flocks during the 2016 outbreak in Iran

Roohani, Kiarash; Vatandour, Safieh; Shoushtari, Abdolhamid; Charkhkar, Saeid; Fallah Mehrabadi, Mohammad Hossein

doi:10.66224/ari.2026.373696.4259

Molecular characterization and phylogenetic analysis of highly pathogenic avian influenza A(H5N8) viruses isolated from chicken flocks during the 2016 outbreak in Iran

Articles in Press

Document Type : Original Articles

Authors

¹ Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Science and Research Branch, Tehran, Iran.

² Department of Animal Science, QaS.C., Islamic Azad University, Qaemshahr, Iran

³ Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

10.66224/ari.2026.373696.4259

Abstract

Introduction: The objective of this study was to investigate the genetic diversity, evolutionary relationships, and molecular characteristics of highly pathogenic avian influenza A(H5N8) viruses isolated from Iranian poultry during the 2016 outbreak through sequencing and phylogenetic analysis of the hemagglutinin (HA), neuraminidase (NA), and matrix (M) gene segments.
Materials & Methods: Four H5-positive isolates were characterized using RT-PCR, Sanger sequencing, comparative sequence analysis, and maximum-likelihood phylogenetic reconstruction, followed by evaluation of molecular markers associated with pathogenicity, host adaptation, antiviral susceptibility, and viral fitness.
Results: Phylogenetic analyses placed all four isolates within HPAI clade 2.3.4.4b and demonstrated close genetic relationships with contemporary strains from Egypt, Nigeria, and Cameroon, while molecular characterization identified a conserved polybasic HA cleavage site, mutations linked to enhanced binding to human-type receptors, the NA I314V substitution associated with reduced oseltamivir susceptibility, and the absence of major M2 antiviral resistance markers.
Conclusion: These findings provide an important molecular baseline for H5N8 viruses circulating in Iran, emphasize the value of continuous genomic surveillance for early detection of viral evolution and transboundary spread, and support strengthened veterinary biosecurity and integrated One Health surveillance to reduce risks to poultry production, animal health, and potential zoonotic transmission.

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