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

Abstract

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.

The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022

“…The ML trees concur with the findings of previous phylogenetic studies [ 11 , 12 , 13 ] that the clade 2.3.4.4B H5N1 strains in West Africa in late 2020 and early 2021, but especially Senegal, were the progenitors of the southern African viruses. The molecular clock analysis of the HA gene ( Figure 4 ) dated the time to the most recent common ancestor (tMRCA) of the general South Africa/Lesotho/Namibia sub-clade to December 2020 (95% HPD October 2020–February 2021), consistent with the timing of the Senegalese outbreaks first detected on 23 December 2020 [ 9 ].…”

“…After removing duplicates, the top 100 matches in each were used for the initial analysis, but ultimately this was downsampled to the closest relatives only. Full or partial sequences were available for the H5N1 outbreaks in Lesotho ( n = 2; [ 11 ]), Botswana ( n = 6; [ 12 ]) and Namibia ( n = 1; [ 13 ]). MEGA-X (v10.2.5) [ 19 ] was used to concatenate the complete genome sequences and subsequently generate a distance matrix.…”

“…Backyard chickens, African mourning doves ( Streptopelia decipiens ) and an African fish eagle ( Haliaeetus vocifer ) were affected in the Bokaa, Kgatleng District, and/or around the Okavango Delta, Northwest District [ 12 ]. Later that year in December, Namibian veterinary authorities reported an H5N1 HPAI outbreak that caused the deaths of >6500 Cape cormorants ( Phalacrocorax capensis ) in the breeding colony at Bird Island, Walvis Bay [ 13 ]. With the limited number of sequences available at the time from Lesotho, Botswana and Namibia but none from South Africa, tentative phylogenetic links between the southern African outbreaks were made, with origins in West Africa and Europe from early 2021 [ 11 , 12 , 13 ].…”

“…Later that year in December, Namibian veterinary authorities reported an H5N1 HPAI outbreak that caused the deaths of >6500 Cape cormorants ( Phalacrocorax capensis ) in the breeding colony at Bird Island, Walvis Bay [ 13 ]. With the limited number of sequences available at the time from Lesotho, Botswana and Namibia but none from South Africa, tentative phylogenetic links between the southern African outbreaks were made, with origins in West Africa and Europe from early 2021 [ 11 , 12 , 13 ]. In the present study, we describe the epidemiology of the South African H5N1 HPAI outbreaks from April 2021 to December 2022.…”

Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses

“…The impact of highly pathogenic avian influenza (HPAI) clade 2.3.4.4b H5N1 viruses and their derived reassortants (H5Nx) on both wild and domestic birds in recent years has been unprecedented (Careen et al, 2024; Lane et al, 2023; Ramey et al, 2022). This virus has also been responsible for disease and mortality events in an unprecedented number of wild bird species worldwide (Avery-Gomm et al, 2024; Leguia et al, 2023; Molini et al, 2023; Rijks et al, 2022). Another concerning development with this virus has been the positive detection in a wide variety of marine mammals and terrestrial mesopredators (Alkie et al, 2023; Plaza et al, 2024).…”