Wastewater Testing for Influenza A and H5 During the 2024 H5N1 Outbreak in Cattle

In 2024 highly pathogenic avian influenza A(H5N1) spread through dairy cattle and poultry in the United States, and 13 human cases were confirmed from January through August. As part of the response, CDC and state and local health departments began watching wastewater for influenza A virus and its H5 subtype. Wastewater surveillance tracks what a community sheds, whether or not people have symptoms, get tested or see a doctor, and some sites had followed influenza this way for years with results that matched traditional measures. The catch is that current tests cannot tell human virus from animal virus. This MMWR report covers the first 9 weeks of that monitoring, May 12 to July 13, 2024.

How it worked

Influenza A. Samples from about 750 sites in 48 states and the District of Columbia were tested by health departments, a CDC contractor or the academic program WastewaterSCAN, and sent to CDC's DECIPHER data pipeline. This routine testing picks up any influenza A virus, seasonal or H5. Each laboratory measured concentrations by digital polymerase chain reaction with its own optimized assay. For each site, the latest week's normalized concentration was ranked as a percentile against October 1, 2023–March 2, 2024 — the part of the flu season before the outbreak in dairy cattle was reported — and labeled high (80th percentile or above), above average, moderate, low or minimal.

H5. In April 2024 WastewaterSCAN developed a digital PCR test for the H5 hemagglutinin gene and found H5 RNA in wastewater from several places with cattle outbreaks. Routine H5 testing began in May at 193 sites in 41 states (152 sites by July 1), with results on a public dashboard, plus 10 more sites in one state — 203 sites with any H5 testing.

Follow-up. CDC told jurisdictions weekly about high influenza A levels and daily about new H5 detections, and gave them a checklist: review human flu surveillance, and work with wastewater utilities, agriculture departments and others to identify what flows into the sewershed.

Influenza A and H5 testing in wastewater, and sites with high influenza A levels or H5 detections, May 12–July 13, 2024. CDC figure.

High influenza A levels

On average, 309 sites in 38 states had enough data to analyze. Eleven sites in four states — California, Illinois, Kansas and Oregon — had a high influenza A level at least once. In three of those states, six of the sites were in communities where other surveillance showed human flu activity. None of the four states reported human H5 cases or confirmed infected herds or poultry in the relevant sewersheds or counties during the period. Most of the sites had combined (open) sewersheds, and some named possible animal inputs.

H5 detections

Of the 41 states testing for H5, nine — California, Colorado, Idaho, Iowa, Michigan, Minnesota, North Carolina, South Dakota and Texas — had at least one detection, at 24 sites in all. Seven of the nine reported an infected dairy herd during the period and one more had reported one earlier; Colorado and Michigan also reported confirmed human H5N1 cases. Of the 32 states with no detections, 30 (94%) reported no infected herds during the period, and the other two had reported them only earlier.

At 15 of the 24 sites (63%), investigators found animal inputs in the sewershed or county, including milk-processing inputs at 8 sites (33%). Other inputs included meat processing, dairy operations, other livestock waste such as a truck wash, wild birds and domestic poultry farms.

What it means

Most sites had neither high influenza A levels nor H5. Where influenza A ran high, human flu in the community was the most common explanation; where H5 appeared, animal inputs — milk-processing effluent above all — were common. Infected cows' milk carries very high concentrations of the virus, and wastewater investigations suggest milk-processing plants can be a major source of H5 in sewage. That contrast, the authors wrote, is why subtyping matters, and why a One Health approach — health, agriculture, wildlife, food safety, utilities and academic partners working together — is needed to sort animal sources from human ones. Clinical surveillance of people remains essential for catching human H5 infections quickly.

The authors urged programs that monitor wastewater to be ready to add subtype testing, including for seasonal H1 and H3, and to pair any public dashboard with clear explanation of the risk to people and the actions being taken, such as alerts to clinicians or wider access to testing or vaccines, as was done for SARS-CoV-2 and mpox.

Limitations

• Tests cannot separate human from animal sources, and the H5 test is not specific to HPAI H5N1, so a detection may reflect animal infection or low pathogenic avian influenza.
• Little is known about how many infected people shed flu virus in urine or feces, or how shedding varies by subtype and over an illness.
• Wastewater coverage of the population varies widely between states.
• Sewershed inputs were investigated only where there was a signal, so no comparison with other sites was possible.
• The depth of follow-up varied, and source investigations are complicated — milk processed in one state may come from others.

Sources

• Louis S, Mark-Carew M, Biggerstaff M, et al. "Wastewater Surveillance for Influenza A Virus and H5 Subtype Concurrent with the Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in Cattle and Poultry and Associated Human Cases — United States, May 12–July 13, 2024." MMWR 2024;73(37).