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Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa

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  • Idrissa Nonmon Sanogo

    (IHAP - Interactions hôtes-agents pathogènes [Toulouse] - ENVT - Ecole Nationale Vétérinaire de Toulouse - Toulouse INP - Institut National Polytechnique (Toulouse) - UT - Université de Toulouse - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, University of Segou, FAMA-US - Faculté d’Agronomie et de Médecine Animale, Université de Ségou)

  • Claire Guinat

    (IHAP - Interactions hôtes-agents pathogènes [Toulouse] - ENVT - Ecole Nationale Vétérinaire de Toulouse - Toulouse INP - Institut National Polytechnique (Toulouse) - UT - Université de Toulouse - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement)

  • Simon Dellicour

    (ULB - Université libre de Bruxelles, SpELL - Spatial Epidemiology Lab - ULB - Université libre de Bruxelles, Department of Microbiology, Immunology and Transplantation [Leuven] - KU Leuven - Catholic University of Leuven = Katholieke Universiteit Leuven, Rega Institute for Medical Research [Leuven, België] - KU Leuven - Catholic University of Leuven = Katholieke Universiteit Leuven)

  • Mohamed Adama Diakité

    (Laboratoire Central Vétérinaire [Bamako, Mali])

  • Mamadou Niang

    (ECTAD - Food and Agriculture Organization of the United Nations, Global Emergency Centre for Transboundary Animal Diseases - FAO - Food and Agriculture Organization of the United Nations [France] - FAO - Food and Agriculture Organization of the United Nations [Rome, Italie], FAO - FAO Regional Office for Africa [Accra] - FAO - Food and Agriculture Organization of the United Nations [Rome, Italie])

  • Ousmane A Koita

    (USTTB - Université des Sciences, des Techniques et des Technologies de Bamako, LBMA - Laboratoire de Biologie Moléculaire Appliquée E3206 [Bamako, Mali])

  • Christelle Camus

    (IHAP - Interactions hôtes-agents pathogènes [Toulouse] - ENVT - Ecole Nationale Vétérinaire de Toulouse - Toulouse INP - Institut National Polytechnique (Toulouse) - UT - Université de Toulouse - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement)

  • Mariette Ducatez

    (IHAP - Interactions hôtes-agents pathogènes [Toulouse] - ENVT - Ecole Nationale Vétérinaire de Toulouse - Toulouse INP - Institut National Polytechnique (Toulouse) - UT - Université de Toulouse - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement)

Abstract

Avian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of AIVs in the region, lacks more comprehensive data on the genetic characteristics of these viruses, especially the H9N2 subtype. To better understand the genetic characteristics and spatio-temporal dynamics of H9N2 virus within this region, we carried out a comprehensive genetic characterization of H9N2 viruses collected through active surveillance in live bird markets in Mali between 2021 and 2022. We also performed a continuous phylogeographic analysis to unravel the dispersal history of H9N2 lineages between Northern and Western Africa. The identified Malian H9N2 virus belonged to the G1 lineage, similar to viruses circulating in both Western and Northern Africa, and possessed multiple molecular markers associated with an increased potential for zoonotic transmission and virulence. Notably, some Malian strains carried the R-S-N-R motif at their cleavage site, mainly observed in H9N2 strains in Asia. Our continuous phylogeographic analysis revealed a single and significant long-distance lineage dispersal event of the H9N2 virus to Western Africa, likely to have originated from Morocco in 2015, shaping the westward diffusion of the H9N2 virus. Our study highlights the need for long-term surveillance of H9N2 viruses in poultry populations in Western Africa, which is crucial for a better understanding of virus evolution and effective management against potential zoonotic AIV strain emergence.

Suggested Citation

  • Idrissa Nonmon Sanogo & Claire Guinat & Simon Dellicour & Mohamed Adama Diakité & Mamadou Niang & Ousmane A Koita & Christelle Camus & Mariette Ducatez, 2024. "Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa," Post-Print hal-04498485, HAL.
    • Handle: RePEc:hal:journl:hal-04498485
    DOI: 10.1093/ve/veae011
    Note: View the original document on HAL open archive server: https://hal.inrae.fr/hal-04498485v1
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