Avian influenza in the United States: H5N1 activity rises again as autumn migration begins

Highly pathogenic avian influenza A(H5N1) is becoming more visible again in U.S. poultry as the autumn migration season develops. During the past ten days, Iowa confirmed a new H5N1 outbreak in a backyard flock, while USDA surveillance continues to show the broader return of poultry infections that began in September, particularly in the northern United States.

The latest confirmed event was reported in Boone County, Iowa, on 22 September, where H5N1 was detected in a mixed-species backyard flock. The flock contained 138 birds, according to state authorities. It was Iowa’s seventh H5N1 detection of 2026, but importantly, none of the state’s outbreaks this year has involved a commercial poultry operation. Iowa had not reported H5N1 in domestic birds since March, making the September detection another sign that the epidemiological situation is changing as migratory birds move south.

USDA APHIS explicitly notes that poultry detections tend to increase during autumn and spring migration, when infected wild birds can introduce virus into new areas and contaminate environments around poultry premises.

Commercial poultry infections returned in September

The Iowa backyard outbreak follows a broader resurgence that started earlier in the month. After several relatively quiet summer months, H5N1 returned to commercial turkey production in Minnesota, North Dakota, South Dakota and Idaho. By mid-September, seven commercial poultry detections had already been reported since the beginning of the month, with roughly 360,000 birds affected across commercial and backyard flocks during the preceding 30 days.

Among the largest outbreaks were commercial turkey operations involving approximately 61,300 birds in McPherson County, South Dakota; 43,800 in Turner County, South Dakota; 41,600 birds in LaMoure County, North Dakota; and 29,800 turkeys in Wright County, Minnesota.

Minnesota’s Wright County outbreak, confirmed on 1 September, was the state’s first poultry HPAI detection since 20 May. Veterinary authorities had already warned that the combination of autumn migration and unusually wet conditions could increase contact between wild waterfowl and poultry farms.

Wild birds remain the main epidemiological signal

The renewed poultry activity coincides with continuing H5 detections in wild birds. USDA’s wild-bird surveillance system recorded multiple Eurasian-lineage H5 detections in Minnesota during September, including Canada geese, mallards, great horned owls and bald eagles. Samples collected in late August and early September were confirmed positive on 16 September.

APHIS describes wild-bird surveillance as an early-warning system because infected migratory birds can introduce virus into areas where commercial and backyard poultry are susceptible. This link does not mean every poultry outbreak results directly from contact with an infected wild bird. Virus can also reach farms indirectly through contaminated water, equipment, clothing, vehicles or other environmental pathways. But the seasonal return of wild-bird detections increases the pressure on poultry biosecurity.

More than 208 million U.S. poultry affected since 2022

The current autumn activity remains far below the largest waves of the U.S. H5N1 epizootic, but it adds to an already substantial cumulative burden.

Since the current outbreak began in February 2022, more than 208 million domestic birds have been affected nationally, according to USDA figures cited by Iowa authorities. Iowa alone has accounted for more than 30 million birds over that period.

APHIS recommends reducing contact between poultry and wild birds, protecting feed and water sources, controlling movement between poultry houses and strengthening cleaning and disinfection procedures.

Autumn 2026 is beginning with a familiar pattern

The most recent ten-day period does not yet indicate a return to the massive poultry losses seen during earlier epidemic waves. Instead, it shows the reappearance of H5N1 in domestic birds as autumn migration intensifies, following commercial turkey outbreaks in the northern states earlier in September and the new backyard detection in Iowa.

The next several weeks will be particularly informative. USDA’s own surveillance strategy focuses on the most recent 30 days because HPAI activity can change rapidly with wild-bird movements.

For U.S. poultry producers, the September pattern therefore marks the beginning of another high-risk seasonal period rather than a new epidemiological phase: H5N1 remains established in wild birds and continues to spill back into both commercial and backyard poultry whenever ecological and biosecurity conditions allow.