H5N1 in Africa: two decades of data reveal persistent poultry hotspots and uneven zoonotic risk

A continent-wide analysis of avian influenza in Africa shows that H5N1 has dominated reported animal outbreaks since 2004 and remains concentrated in a limited number of major poultry hotspots, particularly Egypt. The study also identifies marked weaknesses in surveillance timeliness and large geographical differences in spillover risk, reinforcing the need for more targeted One Health monitoring rather than uniform continent-wide measures.

The study analysed 8,037 animal outbreak events and 369 laboratory-confirmed human cases recorded between 2004 and 2025 using data from FAO EMPRES-i+, WHO and WOAH. The authors combined spatial modelling, notification delays and estimates of human transmissibility to identify where animal circulation and zoonotic risk overlap.

H5N1 accounted for nearly 88% of animal events

Highly pathogenic H5N1 represented 87.8% of reported animal outbreak events. Most detections occurred in domestic poultry, which accounted for 95.5% of records, while wild birds represented 4.2%. Chickens were the most frequently reported host, with 2,790 events, followed by ducks with 1,286.

The geographical concentration was striking. North Africa accounted for 69.5% of all outbreak events, and Egypt alone for 5,308 events, 66% of the continental total. Nigeria followed with 999 events and South Africa with 951.

The model estimated that H5N1 was associated with a substantially higher animal infection risk than the other influenza subtypes included in the analysis, with an incidence rate ratio of 8.37.

Human cases were overwhelmingly concentrated in Egypt

The same geographical pattern was even more pronounced in humans. Among the 369 laboratory-confirmed human infections, 364 were attributed to H5N1. Egypt accounted for 365 cases, or 98.9% of the continental total. The study recorded 119 deaths, again overwhelmingly concentrated in Egypt.

Most human infections were associated with direct exposure to infected poultry. Familial clusters were reported, but the authors found no evidence that these represented sustained human-to-human transmission; shared exposure to contaminated poultry environments remained the more likely explanation.

The model identified areas where high poultry risk and human infection overlapped, creating what the authors describe as dual animal–human hotspots. H5N1 was associated with a roughly 67-fold higher incidence of reported human infection than other avian influenza subtypes in the dataset.

Surveillance delays remain substantial

The study also examined how rapidly outbreaks moved from detection to official notification. Around 71% of animal outbreaks were reported within five days, but 12% experienced delays of at least 15 days. These delays varied considerably between regions.

For a rapidly spreading poultry disease, such delays can be epidemiologically important. Late reporting allows infected birds, products and equipment to move before control measures are implemented, particularly in informal poultry systems with frequent market and farm-to-farm movements.

Africa is not one epidemiological unit

One of the most important conclusions is the degree of heterogeneity across the continent. The apparent dominance of Egypt partly reflects genuinely intense H5N1 circulation, but also far stronger surveillance than in many other countries. The authors acknowledge that this reporting imbalance may obscure transmission in under-sampled regions, particularly outside North Africa.

They also note that the historical human burden in Egypt was heavily influenced by the 2.2.1 H5N1 lineage before 2016, whereas the more recent clade 2.3.4.4b panzootic has a different epidemiological profile. The study therefore combines several distinct phases of H5N1 evolution over two decades.

The practical implication is that surveillance and control priorities should be geographically targeted. Poultry-dense areas with repeated animal outbreaks, frequent human–bird contact and slower reporting require stronger biosecurity and faster diagnostic response than regions with little documented circulation.

For animal health, the study shows that the African H5N1 problem remains above all a poultry disease burden with sharply uneven surveillance, while zoonotic infections remain concentrated in a small number of historical hotspots.