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Historical origins and zoonotic potential of avian influenza virus H9N2 in Tunisia revealed by Bayesian analysis and molecular characterization

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Abstract

During 2009–2012, several outbreaks of avian influenza virus H9N2 were reported in Tunisian poultry. The circulating strains carried in their hemagglutinins the human-like marker 226L, which is known to be important for avian-to-human viral transmission. To investigate the origins and zoonotic potential of the Tunisian H9N2 viruses, five new isolates were identified during 2012–2016 and their whole genomes were sequenced. Bayesian-based phylogeny showed that the HA, NA, M and NP segments belong to the G1-like lineage. The PB1, PB2, PA and NS segments appeared to have undergone multiple intersubtype reassortments and to be only distantly related to all of the Eurasian lineages (G1-like, Y280-like and Korean-like). The spatiotemporal dynamic of virus spread revealed that the H9N2 virus was transferred to Tunisia from the UAE through Asian and European pathways. As indicated by Bayesian analysis of host traits, ducks and terrestrial birds played an important role in virus transmission to Tunisia. The subtype phylodynamics showed that the history of the PB1 and PB2 segments was marked by intersubtype reassortments with H4N6, H10N4 and H2N2 subtypes. Most of these transitions between locations, hosts and subtypes were statistically supported (BF > 3) and not influenced by sampling bias. Evidence of genetic evolution was observed in the predicted amino acid sequences of the viral proteins of recent Tunisian H9N2 viruses, which were characterized by the acquisition of new mutations involved in virus adaptation to avian and mammalian hosts and amantadine resistance. This study is the first comprehensive analysis of the evolutionary history of Tunisian H9N2 viruses and highlights the zoonotic risk associated with their circulation in poultry, indicating the need for continuous surveillance of their molecular evolution.

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Acknowledgements

This work was supported by resources from the Tunisian Ministry for Research and Technology, Grant No. LR19IPT06 (LEMV project). We thank Mr. James Mann, an American teacher at AMIDEAST Tunisia, for editing the publication.

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Authors and Affiliations

  1. Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University Tunis El Manar, 13, Place Pasteur, BP74, 1002, Tunis, Belvedere, Tunisia

    Marwa Arbi, Imen Larbi, Abdeljelil Ghram & Mehdi Houimel

  2. Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia

    Oussema Souiai

  3. Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay

    Natalia Rego & Hugo Naya

  4. Departmento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Av. Gral. Eugenio Garzón 780, 12900, Montevideo, Uruguay

    Hugo Naya

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  1. Marwa Arbi
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Arbi, M., Souiai, O., Rego, N. et al. Historical origins and zoonotic potential of avian influenza virus H9N2 in Tunisia revealed by Bayesian analysis and molecular characterization. Arch Virol 165, 1527–1540 (2020). https://doi.org/10.1007/s00705-020-04624-4

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