Importance: Wild aquatic birds are reservoirs of avian influenza viruses (AIVs). South Korea has conducted national wild-bird surveillance since 2008 to enable early detection of highly pathogenic AIVs (HPAIVs) and rapid response in poultry.

Objective: We investigated the distribution of AI viruses in fecal samples from wild bird habitats (and nearby poultry-farm areas) surveyed between September and March from 2019 to 2025 and identified associated epidemiological risk factors.

Methods: Samples were screened for influenza A (M, H5, H7) genes using real-time reverse transcription polymerase chain reaction (PCR), subjected to virus isolation in embryonated chicken eggs, and subtyped by PCR and sequencing. Host species were identified through DNA barcoding. Relative risks (RRs) with 95% confidence intervals were estimated for province, month, and waterfowl density.

Results: Overall prevalence of HPAI and low pathogenic AI (LPAI) virus was 0.10% and 3.21%, respectively. HPAI virus was continuously isolated since 2020-2021, except 2019-2020, while LPAI prevalence steadily increased (3.01%-4.35%). Twelve hemagglutinin (H1-H12) subtypes were identified in 1,722 isolates, and H3 (16.5%) was the most prevalent, followed by H5 (11.1%) and H7 (5.2%). LPAI H5N3 (55.7%) and H7N7 (75.5%) were the predominant H5 and H7 subtypes, respectively. Detection was higher in western coastal provinces, and higher mallard/spot-billed duck density and sampling in September-December were associated with increased risk.

Conclusions and relevance: Continued surveillance of migratory-bird habitats can provide early warning of HPAIV incursions and support targeted biosecurity measures in high-risk regions and seasons.