Wastewater enables early detection of COVID-19

Researchers at the University of Miami have developed an innovative strategy to help predict COVID-19 outbreaks up to four days before a person tests positive for the disease. And this early warning system could prove even more useful as the Delta variant causes an increase in coronavirus cases.

“This knowledge could be invaluable in protecting our students, staff, faculty, and hopefully our communities,” said Helena Solo-Gabriele, professor of environmental engineering who began the research study last summer. with assistance from George Grills, associate director of shared resources at the Sylvester Comprehensive Cancer Center.

By sampling the sewage flowing from campus buildings, Solo-Gabriele said members of his research team are now able to isolate areas where SARS-CoV-2 – the virus that causes COVID- 19 – is present on campus. University leaders are now using the data to plan ahead for more COVID-19 testing, to prepare patients using the student health service, as well as to assess the need for more isolation and quarantine spaces, a said Erin Kobetz, vice-president of research and scholarship, who is leading the University’s COVID-19 testing, tracking and tracing efforts.

“This is another data point that is important to how we assess the level of community transmission of COVID-19 at our university,” Kobetz added. “We use it to inform our approach on where there may be a peak and to logistically and operationally plan to support that.”

The COVID-19 wastewater monitoring project, now funded by a $ 5 million grant from the National Institutes of Health (NIH), was born out of research indicating that humans release COVID-19 particles in their urine, stools and their breath before they have even exhaled. notice the symptoms. Initially, the Solo-Gabriele team investigated whether an early warning model could be created using wastewater. When they learned that asymptomatic carriers of COVID-19 can still infect and make others sick, it catalyzed the project because it indicated that detecting the virus early could help save lives.

Yet, through the project, Solo-Gabriele acknowledged that wastewater monitoring is useful beyond COVID-19.

“This can help determine the rate at which a community is suffering from the disease, and it gives an idea of ​​how many people contributing to this sewage might be sick,” said Solo-Gabriele, who studies water contamination. and beaches in South Florida. “Not only for COVID-19, but many other diseases can be monitored this way. “

Still, Solo-Gabriele couldn’t do it alone. She quickly met Grills, who put her in touch with colleagues at the Miller School of Medicine who were already creating tests to identify COVID-19 in patients, to see if the same tests could be adapted to wastewater. As a molecular biologist with a focus on genetics and genomics, Grills had worked with colleagues at Weill Cornell Medicine to track new pathogens using surface sampling in urban environments.

Based on research conducted around the world, Solo-Gabriele and Grills realized that if University researchers could track high levels of viruses in wastewater at specific locations, it could help predict the locations of emerging epidemics. Their project quickly became a university-wide effort.

“We have professors from all three UM campuses involved in this project, and we are integrating environmental surveillance of the virus with human COVID-19 data to develop a model to predict epidemics and inform decision-making in this area. public health, ”Grills noted. “The tools and methodologies we are developing also have the potential to monitor other types of infectious diseases in the future. “

As they started with weekly samples, Solo-Gabriele said NIH funding has allowed the team to grow and collect samples more frequently to see if they can get an even more detailed early warning. , perhaps even allowing them to estimate the number of infected people in a building.

She pointed out that the whole process was sped up by a new analytical technique – developed by Mark Sharkey, assistant research professor in the Division of Infectious Diseases – called V2G (for “second generation volcano”) polymerase chain reaction. quantitative (or qPCR) which can pick up COVID-19 in wastewater faster than previous methods.

In addition, one of the project’s co-investigators, Chris Mason, professor of physiology and biophysics at Weill Cornell Medicine, and his team also verify wastewater samples for SARS-CoV-2 using ‘a rapid diagnostic tool he developed called loop-mediated isothermal amplification (LAMP). The whole project is described in a new paper recently published in the journal Science of the Total Environment.

Since its launch last summer, the wastewater treatment project has grown significantly and now collects samples using automated devices at 16 sites across the University’s three campuses. Their typical workflow begins with the sampling team, which includes Solo-Gabriele, students and research staff, as well as the University’s team for environmental and environmental health and safety which collects and filters. samples, before passing them on to Sharkey, Mason and Sion Williams. to Shared resource in onco-genomics at the Sylvester Comprehensive Cancer Center for further analysis.

Next, the wastewater data is analyzed by public health professor Naresh Kumar and research analyst Alejandro Mantero, who correlate it with the positivity rates of campus-wide COVID-19 tests to fuel the project’s prediction model. This allows the team to estimate where outbreaks may be occurring. Kumar said their model now suggests the virus can be detected up to four days before a clinical diagnosis of COVID-19. It also shows that the virus persists in sewage for up to five days after a positive diagnosis, he added.

Additionally, as COVID-19 variants are now causing more outbreaks, Solo-Gabriele said they are now also working with Mason to sequence and perform metagenomic analysis of some of the wastewater samples. This will allow them to determine which variants of COVID-19 are circulating on University campuses.

Meanwhile, co-researcher Stephan Schürer, professor of molecular and cellular pharmacology at the Miller School, is also working with team member Dusica Vidovic to streamline the massive influx of data from the sample collection process.

Schurer and Chris Mader, director of applications and systems development for the University’s Institute for Data Science and Computing, use this information to create a dashboard that will provide university leaders with insight into the points. potentially emerging hot COVID-19. Meanwhile, they are also sharing the information with a national database created by the NIH to compare the results of all U.S. institutions that monitor COVID-19 in wastewater.

“We are building the infrastructure, so that all data and results of wastewater analysis are processed, integrated and made accessible through a dashboard,” said Schürer.

As the project progressed, Solo-Gabriele said they were adding more data, such as samples from a Miami-Dade County sewage treatment plant, to correlate with the data. local COVID-19 positivity. This will help refine the computer model and broaden their understanding of local wastewater monitoring. It also allows them to step up their research to see how much virus is present in a sample of up to 800,000 people.

The model could help researchers across the country move forward as another wave of COVID-19 occurs or help them monitor future viruses that may be excreted through sewage, according to Solo-Gabriele.

“Especially in pandemic situations, we need to have real-time data collection, analysis and prediction systems at our fingertips,” she said. “I wish we had this system at the start of the COVID-19 pandemic. But at least now we’ve moved it forward, so if the diseases change, you can watch that through the sewage. “