Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (Phalacrocorax capensis) in Namibia, 2022

In January 2022, significant mortality was observed among Cape cormorants (Phalacrocorax capensis) on the west coast of Namibia. Samples collected were shown to be positive for H5N1 avian influenza by multiplex RT-qPCR. Full genome analysis and phylogenetic analysis identified the viruses as belonging to clade 2.3.4.4b and that it clustered with similar viruses identified in Lesotho and Botswana in 2021. This is the first genomic characterization of H5N1 viruses in Namibia and has important implications for poultry disease management and wildlife conservation in the region.

Automated summary

In January 2022, a significant number of Cape cormorants in Namibia's west coast were found dead, and subsequent testing confirmed the presence of H5N1 avian influenza. Genomic and phylogenetic analysis revealed that the viruses belonged to clade 2.3.4.4b and were closely related to viruses identified in Lesotho and Botswana in 2021. This study provides the first genomic characterization of H5N1 viruses in Namibia and highlights the significance for poultry disease management and wildlife conservation in the region.