Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019

ABSTRACT

Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.

KEYWORDS:

• Influenza virus
• Africa
• phylogeny
• antigenic cartography
• one health

Acknowledgments

We acknowledge the originating and submitting laboratories of the sequences from GISAID’s EpiFlu Database, on which this research is based, Kim Friedman and Rebecca Badra for data management, and Nisha Badders for scientific editing. This study was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health (CEIRS HHSN266200700005C and HHSN272201400006C). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. M.F.B. is supported by a PhD scholarship of the French Ministry of Research and Higher Education. Samples collection and virus isolation of Ugandan isolates received support to DKB from the Department of Defense Armed Forces Health Surveillance Branch Global Emerging Infections Surveillance Section [grant number: P0136_19_KY_08]. Material has been reviewed by the Walter Reed Army Institute of Research. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by Department of Defense: [grant number P0136_19_KY_08]; National Institute of Allergy and Infectious Diseases: [grant number CEIRS HHSN266200700005C, CEIRS HHSN272201400006C].