When a Measles Test for Sewage Missed a Case — Wisconsin, February 2026

Testing sewage has become an everyday public health tool. Wastewater surveillance already tracks influenza, COVID-19, respiratory syncytial virus and monkeypox, and it is increasingly used for measles, where the virus's genetic material can show up in wastewater before anyone recognises an outbreak. In February 2026, two unrelated measles cases in Wisconsin showed both what the method can do and how it can fail.

The program

The Wisconsin Department of Health Services (WDHS) Wastewater Monitoring Program routinely tests incoming wastewater at 44 municipal treatment plants, covering approximately 50% of the state's population served by a participating sewershed. It began looking for wild-type measles in June 2025 with an established assay that a large commercial wastewater laboratory and many state public health laboratories also used — one of the most widely used measles wastewater assays in the United States in 2025–2026.

Several commercial and published measles assays, adapted for the two main digital polymerase chain reaction (dPCR) platforms, have appeared since mid-2025. When the Wisconsin State Laboratory of Hygiene ran proficiency testing across laboratories in February 2026, it found that four of the most commonly used measles assays performed very differently.

Patient A: caught early

On February 5, 2026, the program found wild-type measles virus in a sample collected on February 2 at a treatment plant serving approximately 30,000 residents. Later that day, WDHS was told of a confirmed measles case in an adult who had come back to Wisconsin on January 29 from travel within the United States. The rash had begun during the trip, on January 29, and the patient had isolated at home on arrival — a home inside the sewershed where the virus was found — and was still there when the sample was taken.

Patient A's measles was diagnosed clinically, without laboratory genotyping, but was linked to an outbreak in another state caused by genotype D8, the main measles genotype circulating in the United States.

State and local authorities were told of the wastewater finding, and it appeared in a public media release. Wisconsin shares all of its measles wastewater results with local health departments and publishes them on CDC's national measles wastewater dashboard. The local health department notified known contacts and issued notices of public exposure locations. No further cases were linked to patient A, and no measles virus turned up in samples taken before or after the detection, which suggests the introduction was contained.

Patient B: missed

On February 1, 2026, WDHS received laboratory confirmation of measles in another Wisconsin resident, who had been infected abroad, lived in a different county and a different sewershed, and had no link to patient A. Sequencing identified genotype B3, an internationally circulating genotype that accounted for approximately 5%–10% of U.S. cases in 2025. The rash began on January 29, and the patient stayed at home throughout the infectious period, January 25–February 2.

Even so, the standard assay found no measles virus in any of the eight wastewater samples collected from the patient's treatment plant during those dates. Further testing showed that the assay could not detect measles virus in the patient's own clinical isolate, or in a B3 reference strain.

Two independent methods then looked again:

• a different dPCR assay for measles, used by the program's laboratory, run on a sample collected on February 1 from the part of the sewer system where patient B lived;
• shotgun metagenomic viral sequencing of citywide samples — an untargeted method that tries to sequence all the viral genetic material in a sample and can find unexpected pathogens.

Both found measles virus at detectable levels. The metagenomic results for the February 2 sample were identical to the whole-genome sequence of patient B's clinical isolate, strong evidence that patient B was the source. The local health department notified known contacts and issued exposure notices; no further cases were linked to patient B.

Why the test failed

WDHS told CDC and the assay's developers. Using publicly available whole-genome sequences, the developers found a mutation in the N gene of recent B3 viruses, in the stretch the assay's probe binds to — a single adenine-to-guanine change. On March 2, they released a modified assay with an additional probe that matches the mutation.

The original assay had been designed from 97 measles sequences (43 B3 and 54 D8) plus the Edmonston vaccine strain, all taken from the National Center for Biotechnology Information in March 2025, and checked by computer modelling against circulating B3 and D8 viruses. Its design was made public and used in many states from May 2025. At that time, fewer than 2% of available B3 sequences carried the mutation. In the period after release, May 2025–February 2026, 75% (169 of 226) did. The collection dates suggest the variant has been the dominant B3 variant circulating internationally since July 2024.

CDC's own validated wastewater assay for measles targets a different gene, M, so the N-gene mutation did not affect it. But jurisdictions relying on the original assay may have been less able to detect B3 cases or outbreaks until the second probe was added.

Lessons

Patient A's case adds to evidence that wastewater surveillance can pick up measles from a single case — here, one known case in a sewershed of approximately 30,000 people — early enough to prompt action that can prevent further cases.

Patient B's case shows the upkeep that sensitivity requires. Viruses change, and a test designed against last year's sequences can quietly stop seeing this year's. The authors call for:

• regular computer modelling and wet-laboratory checks of assay primers and probes against circulating strains, to catch mismatches before they weaken surveillance;
• performance testing of wastewater assays, which are many and not tested to a common standard, and which may need frequent revalidation as measles evolves;
• an up-to-date public library of whole-genome sequences to support assay development;
• sequencing-based detection, which could follow mutating viruses without the need to keep updating targeted tests.

Sources

Based on "Genotype-Specific Detection of Measles Virus Using Wastewater Surveillance — Wisconsin, February 2026," by Ian Pray and colleagues (CDC; Wisconsin Department of Health Services; Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison), Morbidity and Mortality Weekly Report 75(27), published by the Centers for Disease Control and Prevention; rewritten in hubnx's own words.

• The report's timeline figure is not reproduced.