How sequencing-based wastewater epidemiology detected measles first

In early January 2025, wastewater treatment plants in Houston detected a virus that had not appeared in the city’s influent streams for over 31 months: measles.  

This detection was not prompted by a reported case or clinical testing, it came from an innovative sequencing-based wastewater monitoring program.  

Less than two weeks later, the Houston Health Department (HHD) confirmed two local cases of measles in unvaccinated travellers living within the same sewershed.  

For wastewater monitoring professionals, this event represents a breakthrough in both disease detection sensitivity and instrumentation strategy.

How it happened

On January 7, 2025, nucleic acid extracts from two wastewater treatment plants serving a combined population of over 218,000 underwent a hybrid-capture sequencing protocol.  

The samples were processed using Qiagen RNA extraction kits, then subjected to a comprehensive viral panel developed by Twist Biosciences and sequenced on an Illumina NovaSeq 6000.  

Alignment against the Virus Pathogen Database revealed 53 reads mapping to 11 regions of the measles genome with a 99.4% match to genotype B3 – a wild-type strain, not used in vaccines.

To confirm the finding, the HHD and Rice University applied reverse transcriptase droplet digital PCR (RT-ddPCR), targeting the measles M gene.  

This orthogonal validation technique showed 4 to 8 positive droplets per replicate, equating to approximately 2,600 genome copies per litre of wastewater.  

Critically, measles had not been detected in any of the 821 samples collected from the same area over the prior 31 months.

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Theory into practice

“Because no other cases had been reported and the detections occurred in the same area where the travellers resided, it’s reasonable to conclude the wastewater signal came from those two infected individuals,” said Dr. Anthony Maresso, co-corresponding author and Professor at Baylor College of Medicine. “That underscores just how sensitive this approach really is.”

Sequencing-based surveillance has long been discussed as a theoretical ideal in wastewater monitoring due to its ability to detect viral and microbial threats agnostically, without relying on pre-targeted PCR assays.  

The Houston event demonstrates that such a system is now not only possible but also actionable.  

When properly integrated into public health workflows, this technology can provide early warnings that traditional case reporting systems may miss.

Instrumentation and methodology

The dual-method validation in Houston – hybrid-capture sequencing followed by RT-ddPCR – demonstrates how modern instrumentation and workflows can be layered for both breadth and specificity.  

While sequencing methods offer coverage across hundreds of potential viral targets, they require 72+ hours for processing and significant lab infrastructure.  

Conversely, RT-ddPCR delivers highly specific quantification in shorter timeframes, making it suitable for rapid validation once a potential pathogen is flagged.

For wastewater instrumentation users, this case suggests several key takeaways:

Hybrid-capture sequencing allows detection of viruses not explicitly targeted, ideal for early warnings.

RT-ddPCR, while more narrowly focused, provides robust confirmation and quantification of low-abundance targets.

Longitudinal sample archives (like Houston’s 31-month baseline) are invaluable for distinguishing novel detections from background noise.

Genotyping from sequence data allows differentiation between vaccine strains and circulating wild-type strains, a critical factor in public health decision-making.

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Can this approach be applied to wastewater epidemiology more broadly?

The team has since expanded their monitoring across Texas, including West Texas cities currently experiencing a measles outbreak.  

Their work is publicly accessible via the Texas Early Pathogen Identification (TEPHI) dashboard here, providing weekly viral activity reports to health authorities and the public.

“This is the first time a sequence-based system has detected measles in wastewater ahead of clinical reporting in the U.S.,” said Dr. Michael Tisza, co-first author and assistant professor at Baylor. “We’ve now got a high-throughput platform capable of tracking not only seasonal respiratory viruses like flu and COVID-19 but also rare or emerging pathogens like measles or H5N1 avian influenza.”

This case makes a compelling argument for wider adoption of sequencing-based wastewater epidemiology.  

While costs are still higher per sample than traditional PCR, the ability to monitor many pathogens simultaneously makes it more cost-effective on a per-target basis, especially when outbreaks are unpredictable.  

In highly vaccinated populations, routine measles PCR screening would be cost-prohibitive and statistically unlikely to detect cases. But sequencing, once implemented, offers detection "for free" across all pathogens in the panel.

“With more states exploring centralised, high-resolution wastewater surveillance programs, this approach could soon be the standard for outbreak early warning systems,” noted Dr. Eric Boerwinkle, Dean of the UTHealth Houston School of Public Health.

The Houston measles detection case illustrates how far wastewater instrumentation has come, from monitoring for BOD and COD to tracking virus genomes in real time.

With proper tools and collaborative infrastructure, wastewater professionals are now on the front lines of public health defence, identifying threats before symptoms arise and buying critical time for intervention.

To read the paper in full, click here.

By Jed Thomas