Bird Flu in Oregon's Wastewater Came Before Poultry Outbreaks — and Likely from Wild Birds

By Rebecca Falender, Tyler S. Radniecki, Christine Kelly, Paul Cieslak, David Mickle, Harrison Hall, Ryan Scholz and Melissa Sutton — Oregon State University, Oregon Health Authority and Oregon Department of Agriculture

At a glance

• Known: highly pathogenic avian influenza (HPAI) A(H5N1) has broken out in U.S. cattle and poultry. Wastewater testing can detect the A(H5) subtype, but can't tell whether it came from people or animals.
• New: re-testing Oregon wastewater from September 15, 2021–July 11, 2024 found 21 A(H5) detections in 12 communities. They were not linked to poultry outbreaks or to dairies in the sewershed, and were most frequent in two communities with important wild bird habitat.
• So what: wastewater gave early warning of avian flu in Oregon. When A(H5) turns up in wastewater, animals other than cattle — including wild birds — must be considered.

Background

• January 2022: HPAI A(H5N1) clade 2.3.4.4b, from Europe, first found in U.S. wild birds. It has since become enzootic in wild birds across North America, and can infect poultry and some mammals (1).
• February 2022: first U.S. commercial poultry outbreak. By December 5, 2024: more than 112 million domestic birds affected in 49 states (2).
• March 2024: first outbreak in U.S. dairy cattle. By December 5, 2024: 718 herds in 15 states (3).
• Oregon: clade 2.3.4.4b first found in wild birds and poultry in May 2022. By December 5, 2024: 44 poultry outbreaks and none in dairy cattle (2,3).

CDC and state and local health departments use wastewater to track influenza A and the A(H5) subtype (4). It shows what is happening across a whole community, whatever people's symptoms, whether they see a doctor, or whether they can get tested — and it can be turned quickly to new pathogens (4,5). But the PCR test for A(H5) can't distinguish human from animal sources, so reading a detection means knowing what drains into the sewershed: wild birds, farms with poultry or cattle outbreaks, and dairy processing plants (4,6).

What Oregon did

• Samples: Oregon tests wastewater for flu seasonally (September 15, 2021–June 24, 2022, and August 28, 2022–April 30, 2023), and year-round since October 1, 2023. Every flu A–positive sample from 20 communities was re-tested for A(H5).
• Communities were chosen for geographic spread, migratory bird stopovers, past avian flu in wild birds, and licensed Grade A dairy processors and farms in the sewershed.
• Method: 24-hour composite samples of treatment-plant inflow, taken once or twice a week; a duplicate of each is archived at −112°F (−80°C). RNA from the archived flu A–positive samples was tested for A(H5) by digital reverse transcription PCR, in duplicate, with positive and no-template controls.
• Analysis: Fisher's exact test, with p < 0.05 as significant.

What they found

Where

Of 551 flu A–positive samples, 21 (3.8%) held A(H5), in 12 of 20 communities.

• Most detections: Ontario (Malheur County), five of 34 samples.
• Highest share: Newport (Lincoln County), three of 14.
• Poultry: 8 of the 12 communities were in counties with a past poultry outbreak — but that was not a significant link (p = 0.65).
• Dairies: only 4 of the 12 had a licensed Grade A dairy processor or farm in the sewershed (p = 0.65). No A(H5) was found in the two sewersheds with the most dairy processors (Portland, seven) and dairy farms (Tillamook, 13).

Samples tested for A(H5) in each community — detections in black — with communities that had dairy processors or farms in the sewershed, the largest dairy presence, or a county poultry outbreak marked. CDC.

When

A(H5) turned up in several weeks of each of the three flu seasons studied, and in the summer of 2024. It was first detected on March 21, 2022:

• about 6 weeks before HPAI was found in Oregon poultry;
• about 7 weeks before A(H5) was found in Oregon wild birds;
• about 2 years before HPAI A(H5N1) was found in U.S. dairy cattle — which Oregon has never found in its cattle or milk.

A(H5) in Oregon's wastewater (top), in wild birds (middle), and HPAI outbreaks in poultry (bottom). Wastewater was tested only seasonally from June 2022 to August 2023. The wild bird counts may be low after December 2023 because of a USDA testing backlog. CDC.

What it means

Not cattle, not poultry — probably wild birds. Many detections came before the virus spilled into dairy cattle (estimated November 2023–January 2024), and Oregon has had no cattle outbreaks. The results don't point to poultry, dairy farms or processors, but to animals other than cattle, suspected to be wild birds.

• The flyway: Oregon lies on the Pacific Flyway, a north–south route for migratory birds from Alaska to Patagonia, which an estimated 1 billion birds travel each year; the state has many important stopover sites (7).
• The two hot spots hold key habitat: seasonal wetlands at Ontario and major river estuaries at Newport (7,9).
• How bird virus gets in: stormwater in combined (open) sewersheds; leaking pipes in separate (closed) ones; animal products dumped into sewers (6,8); and birds that rest on clarifiers and lagoons, whose droppings a sample from a clarifier may catch. Detections came from both kinds of sewershed.

Limitations

1. Only samples already positive for flu A were tested — and before October 2023, only in flu season — so seasonal patterns are hard to describe.
2. The tests can't tell which animal, or high- from low-pathogenic A(H5) (10).

For public health

• Oregon's first wastewater detections came only after clade 2.3.4.4b reached North America's wild birds, and more than 6 weeks before the state's first poultry outbreak or wild-bird detection.
• They came almost 2 years before the cattle outbreak, ruling out cattle as a source before November 2023.
• Expect occasional detections to continue, even without cattle outbreaks or human cases.
• Wild birds, in which HPAI A(H5) is now enzootic, are an important consideration when interpreting a wastewater result.
• Considering all animal sources, alongside other surveillance, wastewater testing can strengthen avian flu surveillance.

Sources

Based on Rebecca Falender, Tyler S. Radniecki, Christine Kelly, Paul Cieslak, David Mickle, Harrison Hall, Ryan Scholz and Melissa Sutton, "Avian Influenza A(H5) Subtype in Wastewater — Oregon, September 15, 2021–July 11, 2024," MMWR, Centers for Disease Control and Prevention; a work of the United States government in the public domain. Numbers in parentheses refer to the report's references.