Sequencing-Based Detection of Measles in Wastewater: Texas, January 2025

Abstract

Measles is a potentially deadly viral infection spread via respiratory droplets from infected individuals. Outbreaks occur when vaccine coverage drops below the threshold of herd, or community, immunity. Using a sequencing-based approach, we report the prospective (January 7, 2025) detection of measles in nucleic acid extracts from 2 wastewater treatment plants in Houston, Texas, with a population of more than 218 000 residents. The sequencing data from 2 samples contained 53 unique reads mapping to 11 different regions of the measles virus genome with a 99.4% match to genotype B3. Importantly, no detections were observed from 821 previous samples from the same city spanning nearly 3 years of monitoring. The findings were confirmed using droplet digital polymerase chain reaction. A concomitant investigation identified 2 unvaccinated measles-positive travelers living within the same sewershed as the wastewater detection event. This work suggests that sequencing-based wastewater analysis is valuable as a comprehensive early detection warning system that facilitates more targeted epidemiological investigation. (Am J Public Health. 2025;115(7):1115-1119. https://doi.org/10.2105/AJPH.2025.308146).

FIGURE 1—

Agnostic Hybrid Sequencing Measles Detection in Wastewater: Houston, TX, January 2025 Note. WWTP = wastewater treatment plant. The measles genome showing the reads from probe-capture sequencing (gray) stacked across the L (11 separate regions) and H genes (1 region). A coverage map is displayed in blue, which shows the regions of the measles genome for which we have sequencing data (“agnostic hybrid capture sequencing detection region”). For reverse transcriptase droplet digital polymerase chain reaction (RT-ddPCR), the genomic region where the primers will anneal is shown in pink, which targets the M gene (“ddPCR detection region”).

FIGURE 2—

RT-ddPCR Measles Detection in Wastewater: Houston, TX, January 2025 Note. RT-ddPCR = reverse transcriptase droplet digital polymerase chain reaction; WWTP = wastewater treatment plant. RT-ddPCR results of the 2 replicate wastewater samples that were an equal volume mixture of the 2 Houston sites. The positive control is a synthetic measles nucleic acid RNA amplicon from the M gene of the D8 measles wild-type strain. The negative control is a reaction that has no wastewater sample and no RNA amplicon template. Y-axis = amplitude (strength of detection event); x-axis = event number from 0 to 20 000 in the partition well.

FIGURE 3—

Approximate Timeline for the Clinical Manifestation and Wastewater Detection of Measles: Houston, TX, January 2025 Note. HHD = Houston Health Department; WW = wastewater.