Highly pathogenic avian influenza H5N1 virus outbreak among common terns (Sterna hirundo) in Namibia, 2025-2026.

Abstract

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b continue to spread globally, causing major outbreaks in wild birds and poultry. In Africa, however, genomic data remain limited, restricting understanding of viral introduction routes and circulation patterns. Here, we report the whole-genome characterisation of an HPAI A(H5N1) virus detected in a common tern (Sterna hirundo) found dead on the Namibian coast during the most recent avian influenza outbreak recorded in the country. Viral RNA was subjected to whole-genome sequencing using the Illumina Viral Surveillance Panel v2 on a NextSeq 1000 platform. Complete or near-complete sequences were obtained for all eight genome segments and deposited in GenBank. Phylogenetic analyses, performed using African clade 2.3.4.4b H5Nx sequences and the closest related sequences identified through database searches, showed that the Namibian virus belonged to clade 2.3.4.4b and clustered within the EA-2024-DI.2 subgenotype. Across all segments, the virus grouped with contemporary European EA-2024-DI.2 viruses circulating during the 2024-2025 epidemic wave, supporting a likely Eurasian origin. For six of the eight segments, it also clustered closely with an EA-2024-DI.2 virus detected in a gull-billed tern in Uganda in December 2024. Molecular analysis identified a polybasic haemagglutinin cleavage site consistent with high pathogenicity and a mutational profile broadly similar to contemporary EA-2024-DI.2 viruses. The HA substitution, associated in previous studies with increased binding to mammalian-type α2-6 receptors, may warrant further investigation. These findings highlight the role of migratory seabirds in H5N1 dissemination and reinforce the need for strengthened genomic surveillance in African wild birds and poultry.