CDC names Houston Health Dept, Rice a wastewater epidemiology Center of Excellence

Rice CS' Todd Treangen & CEE's Lauren Stadler developed and maintain a weekly viral genome analysis to screen for SARS-CoV-2 variants of concern

Rice research technician Russell Carlson-Stadler analyzes wastewater samples for signs of the SARS-CoV-2 virus.

A system to track COVID-19 through Houston’s wastewater became the basis of an epidemiology center that has now earned special designation from the U.S. government and $1 million in its first year of federal funding. 

The Houston Health Department, partnering with Houston Public Works and Rice University, has been awarded one of two grants by the Centers for Disease Control and Prevention (CDC) to run a National Wastewater Surveillance System Center of Excellence. The designation announced by Houston Mayor Sylvester Turner on Aug. 3 follows the partnership’s successful development and implementation of a SARS-CoV-2 wastewater surveillance system for Houston. 

The center, dubbed Houston Wastewater Epidemiology, will provide training on wastewater epidemiology to other state and local health departments as well as research on developing statistical tools and metrics to enhance surveillance interpretation. It will also expand wastewater monitoring for new diseases. The other awardee is the Colorado State Health Department. 

“I want to take this moment and congratulate the Houston Health Department for its excellent work in collaboration with Houston Public Works and Rice University,” Turner said at a press conference. “(The grant) places the department center stage as the CDC develops standard methods for this public health tool.”

“This award exemplifies the value of strong partnerships between universities and the communities they serve,” said Rice President Reginald DesRoches. “By working together, experts from Rice University, the Houston Health Department and Houston Public Works found that wastewater-based epidemiology was a powerful approach to combating the COVID-19 pandemic. This knowledge can now be standardized, shared with other communities and used as an overall public health tool.”

The partnership between Rice and the city started in early 2020. It has been supported by funding from Rice, the Houston Health Department, the National Science Foundation, the CDC Foundation, the Rockefeller Foundation and the CDC. 

Rice’s own efforts were kick-started in April 2020 by a COVID-19 Research Fund grant.

The project’s leaders are Loren Hopkins, chief environmental science officer for the Houston Health Department and a professor in the practice of statistics at Rice; Katherine Ensor, the Noah G. Harding Professor of Statistics, and Lauren Stadler, an assistant professor of civil and environmental engineering. Houston Public Works Director Carol Haddock, a Rice alumna, has also been critical to the program’s success.

Rice News reported in September 2020 on the team’s success in establishing one of the nation’s first wastewater early detection programs.

“We were right there at the beginning, and we had the most intensive statistical system that uses spatial sampling, along with temporal sampling, to quantify and assess trends in viral prevalence,” Ensor said. “It really shines because the Houston Health Department acts on the information.”

“After 2 1/2 years of dedication to this initiative, wastewater analysis has become the leading indicator of COVID-19 trends,” Hopkins added. “This has become increasingly important in recent months due in part to the rise in at-home testing, which is widely unreported.” 

Hopkins’ joint affiliation with Rice and the city has played a central role in applied research, the translation of advances in science, engineering and higher education. In March 2022, she was named to the National Academies’ Committee on Community Wastewater-based Disease Surveillance. Her leadership has ensured the program is directly beneficial to the residents of Houston. 

“The center will help us share our expertise with states and municipalities across the nation and as CDC develops guidance for this new public health tool,” said Stadler, who is also working to establish protocols to look for other diseases including influenza and monkeypox in wastewater.

“We now have the technology and the ability to determine levels of monkeypox in the city of Houston through the wastewater system, just like we did for COVID,” Turner said.

Stadler’s lab and the Houston Health Department lab provide weekly measurements from 39 city-owned wastewater treatment plants, which serve more than 2 million people. These 39 weekly measurements form the basis of the real-time tracking system. In addition to these measurements, samples are collected at lift stations around the city, including schools, nursing homes and jails. A total of about 100 locations are sampled every week. 

Versions of those early tools to analyze and consistently track infection dynamics in near real time are still in use today. 

Ensor has led the analytics team with help from the students and faculty of Rice Statistics. Since January 2021, the weekly analysis has been performed by Rebecca Schneider of the Houston Health Department, an alumnus of the university’s Professional Master of Statistics program. Ensor and Schneider ensure the system is working as planned and perform additional research to understand emerging issues. 

A key piece of information provided through wastewater epidemiology concerns variants of COVID-19 that emerge in Houston. Todd Treangen, a Rice assistant professor of computer science, and Stadler developed and maintain a weekly variant analysis. Viral genomes from wastewater samples are sequenced each week to screen for variants of concern.

The Spatial Studies Lab, headed up by Farès El-Dahdah, is responsible for the public-facing dashboard that provides a weekly update. 

“This has become a bold initiative for the city of Houston and for Rice,” Ensor said. “It is a perfect example of a successful city-university partnership built from collaborative research and the translation of results to directly benefit people and our communities.”


* Rice research technician Russell Carlson-Stadler analyzes wastewater samples for signs of the SARS-CoV-2 virus. Photo by Brandon Martin

Shawn Hutchins with Mike Williams