Phylogenetic Analysis of Avian Influenza Viruses in the Iran-Pakistan Region

Khosrowjerdi, Amirhossein; Abtin, Alireza; Naderian, Ali; Yazdanmanesh, Mohammad

doi:10.22092/ari.2026.371831.4002

Phylogenetic Analysis of Avian Influenza Viruses in the Iran-Pakistan Region

Articles in Press

Document Type : Original Articles

Authors

¹ Razi Vaccine and Serum Research Institute, karaj, Iran

² razi institute

³ Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Karaj, Iran.

⁴ Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Karaj, Iran

10.22092/ari.2026.371831.4002

Abstract

Avian influenza viruses (AIVs) are a constant threat to the poultry industry and public health. The H9N2 subtype has been endemic in the Middle East since the 1990s, acting as a genetic segment donor and facilitating the emergence of new viruses through reassortment. In this study, sequences of all six internal genes (PB2, PB1, PA, NP, M, and NS) of avian-origin influenza A viruses from Iran, Pakistan, Iraq, Turkey, and Afghanistan were analyzed. The sequences were obtained from the BV-BRC public database. Phylogenetic reconstruction was performed for each gene segment using the maximum likelihood method in RAxML (version 8.2.12) with the GTR+GAMMA model; topological robustness was assessed with 1000 bootstrap replicates. Examination and analysis of phylogenetic trees revealed distinct viral dynamics. The H9N2 subtype was detected in diverse avian hosts, with sequences from domestic chickens, ducks, and pigeons forming intertwined clusters within the phylogenetic tree, confirming the virus's active circulation and adaptation across multiple avian species. Phylogenetic analysis of H9N2 primarily revealed distinct country-specific clusters for Iranian and Pakistani virus isolates, suggesting independent evolution of local viruses within the poultry populations of each country. However, some regions of the tree exhibited shared phylogenetic branches with closely related sequences from both countries, providing evidence of cross-border transmission. Evidence also suggested a possible reassortment event between a 2009 Iranian H9N2 virus and a 2004 Pakistani H7N3 virus involving the PB1 gene, indicating genetic exchange between this highly pathogenic strain and H9N2.
In conclusion, this study emphasizes the need for continuous surveillance of avian influenza, driven by evidence of the independent evolution of H9N2 viruses in Iran and Pakistan, cross-border transmission, and genetic reassortment events. It also underscores the necessity of establishing a coordinated regional surveillance system based on a One Health approach.

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