A Public Health Alerts report today describes the detection of measles virus in wastewater in the Chicago area that was linked to a single measles case in the community that same day, “demonstrating that untargeted metagenomics appeared to detect a single measles infection in a large municipal wastewater stream,” according to the authors.

The report could serve as a template for using untargeted wastewater surveillance for identifying infectious diseases in the surrounding community, say the authors, from the University of Illinois at Chicago, the Illinois Department of Public Health, the University of Missouri, and elsewhere.

Public Health Alerts, a collaboration between NEJM Evidence and CIDRAP, fills a gap in reliable data, offering expert-reviewed reports that translate frontline observations into actionable public health evidence. An NEJM Evidence editorial explains the initiative further.

Part of surveillance efforts in 10 states

In the report, the researchers say they have been carrying out weekly untargeted ultra-deep metagenomic sequencing (MGS) of wastewater from 30 sites across 10 states, including four in the Cook County, Illinois, area as part of the Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs (CASPER), a wastewater MGS network for detecting pathogens like viruses and bacteria.

MGS data from samples collected from a large wastewater treatment plant in Cook County on September 14, 2025, showed measles virus after analysis on October 3. Scientists then notified local public health departments.

Also in September, five months after a previous case was reported in the county, the Cook County Department of Public Health confirmed a second measles infection in an unvaccinated child in a Chicago suburb. The case was tied to international travel.

The detection of measles RNA through ultra‑deep MGS of municipal wastewater appeared to capture a single case within the population of more than 1 million people.

The patient’s home and the hospital at which he or she sought care lay within the catchment area of the positive wastewater sample. The patient’s symptoms began on September 12, and the child still had a fever and symptoms on September 14, the day the wastewater sample was collected. No other measles cases were confirmed in that area at this time.

Polymerase chain reaction (PCR) testing demonstrated that samples from the child and from wastewater closely matched.

The authors conclude, “The detection of measles RNA through ultra‑deep MGS of municipal wastewater appeared to capture a single case within the population of more than 1 million people and wastewater flow exceeding 300 million gallons per day.”