The United States is experiencing its highest annual measles case count since the disease was declared eliminated here in 2000. As of July 21, 2026, the U.S. Measles Tracker maintained by Johns Hopkins’ International Vaccine Access Center had confirmed 2,295 cases nationwide which means that we have already surpassed the 2,289 cases reported in all of 2025, and the most cases the country has seen in a single year since 1991.
According to the World Health Organization (WHO), measles typically starts with a fever (which can spike above 105°F), cough, runny nose, and red, watery eyes. The WHO reports that symptoms usually begin 7–14 days after exposure, with the telltale rash following 3–5 days later, typically starting at the head and spreading down to the trunk and limbs.
Measles spreads through the air when an infected person coughs, sneezes, or even just breathes and talks, and the virus can remain infectious in the air or on surfaces for up to two hours after that person has left the room. The WHO explains that one infected person can go on to infect as many as 18 others.
Because measles spreads so efficiently, and because unvaccinated pockets of people can be scattered, public health departments need every early signal they can get to plan prevention and response activities which may include organizing community vaccination campaigns, educational and referral materials, and surge staffing at healthcare facilities. This is where wastewater surveillance comes in. Timely wastewater surveillance can provide this early warning signal that is desperately needed. Every day counts, and the Lungfish team’s turnaround time for wastewater surveillance is now less than 7 days from collection to data delivery.
People infected with measles shed the virus in respiratory secretions and, it turns out, in wastewater and they start shedding the virus in urine before the illness is obvious. The CDC notes that infected people are contagious from four days before the characteristic rash appears to four days after it fades, and shedding is often already underway during the earlier days of fever, well before most people would think to see a doctor. That gap between infection and diagnosis is exactly where environmental surveillance can add value: sequencing a community’s wastewater doesn’t depend on someone deciding to get tested, or having access to testing at all.
Detection Before Clinical Reporting
In 2025, the Lungfish team detected measles in nine different locations, some of which didn’t know that they had cases. This early warning gave public health officials precious lead time to respond and to encourage vaccination among hesitant residents, as described in our 2025 annual report.
In April 2026, researchers affiliated with Lungfish and the CASPER wastewater network (Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs) published a case study in NEJM Evidence that demonstrated just how sensitive this kind of surveillance can be.
Another related study, co-authored by Martin Shafer, a researcher affiliated with the CASPER network mentioned above, along with colleagues at the Wisconsin Department of Health Services and CDC, was published in Morbidity and Mortality Weekly Report earlier this month and described two travel-associated measles cases in Wisconsin. Wastewater surveillance detected one case, caused by the D8 genotype, before it was reported to health officials, while a separate case, caused by the B3 genotype, was missed by the standard wastewater assay due to a mutation in the circulating virus. Untargeted metagenomic sequencing helped confirm this gap and prompted developers to update the assay.
Identifying Measles in Urban Environments
In a wastewater sample collected on September 14, 2025, from a treatment plant serving more than a million people in Cook County, Illinois, the team’s untargeted metagenomic sequencing turned up 43 reads matching measles genotype B3 out of more than 900 million total sequencing reads from that sample. That’s roughly 0.000005% of the data. Local health officials were notified.
It turned out those 43 reads corresponded to a single known case: an unvaccinated child from suburban Cook County who had contracted measles during international travel and whose home and treating hospital both fell within the catchment area of that wastewater sample. Because the local health department was already aware of and managing this case, the wastewater detection didn’t change the public health response in this instance. But the finding matters for what it demonstrates: that untargeted metagenomic sequencing can pick out the genetic signal of a single measles infection in the wastewater of an entire metropolitan area, without anyone having told the system in advance what to look for.
Potential for the Future
Measles is making a comeback in places that had gone decades without seeing it, at the same time that vaccine coverage has been sliding and federal support for traditional disease surveillance has been shrinking. Wastewater surveillance can give communities something traditional case reporting often can’t: an early, unbiased read on whether measles is already circulating, before people start showing up sick.