Smruthi Karthikeyan, an environmental engineer, had only spent a few days in her lab at the University of California San Diego when the state implemented its first coronavirus lockdown. This was in March 2020.
She’d been brought on as a postdoc by biologist Rob Knight to develop new techniques for studying how microbes in complex ecosystems shape human health and vice versa. The COVID-19 epidemic quickly gave a new twist to this mission.
Soon the lab shifted to support coronavirus response. Karthikeyan said that infections were exceeding the county’s testing capabilities. The university wanted to keep its campus open for the 10,000 students and 25,000 employees. Karthikeyan and his colleagues realized that there had to be a way for infection monitoring without having to test thousands of people all the time.
Public health experts had tested wastewater for pathogens in the past to monitor the movement of infectious agents within communities. Symptoms such as diarrhea, fever, and paralysis can all be detected in stool, which could indicate a potential outbreak. However, no one has ever implemented such a system for tracking a respiratory virus at scale that could reach tens or thousands of people.
Karthikeyan was up to the challenge.
Bold idea
Karthikeyan and his colleagues created and implemented a wastewater monitoring system at UC San Diego. This was reported July 7, 2007. NatureIt processes more than 200 samples each day. Her previous methods could only process eight samples per day, she said. What’s more, the system has identified Coronavirus variants can be spread up to two days earlier than previously thought.Using clinical testing, we accurately predicted the mixture of viruses that would infect students and staff.
School officials have had more time to act to reduce infection rates. Karthikeyan said that less than one percent of all positive clinical tests occurred during the study period between November 2020 and September 2021. This is significantly lower than other campuses in the region.
Among the key players in the team’s monitoring system are 131 robots that collect wastewater samples throughout each day from 360 university buildings. Back at the lab the samples are screened and analyzed for viruses. The results are then fed into a public database. online dashboardAs part of the project.
Karthikeyan’s team isn’t the only one COVID-19 is possible by using human waste. But the scale of the monitoring “is a bit unprecedented,” says Ameet Pinto, an environmental engineer at Georgia Tech in Atlanta. Karthikeyan, along with his colleagues, processed almost 20,000 samples over the course of the study. “That’s amazing,” he says.
Positive results trigger a notification sent to the entire campus via a smartphone app. Everyone who lives in a dormitory is required to test for COVID-19. Those who have been recently in the same building are strongly encouraged to do so.
The team used candy from vending machines to swap for test kits at home and placed test drop boxes inside the buildings. This increased access to the tests. Karthikeyan’s team processes the tests and sends results within a day.
Anybody who tests positive for coronavirus will be moved to an isolation dorm, or told to isolate at home if they are not on campus. If the coronavirus shows up in the next day’s wastewater test, the building’s remaining occupants will receive a notification to test again.
To figure out which variants are causing infections at the university, Karthikeyan’s team built a freely available computational tool called Freyja. It makes use of a variety of genetic markers that allow it to distinguish between well-known and unknown variants in the water. Karthikeyan and co-workers report that Freyja discovered the new delta variant 14 days before clinical testing did.
Increasing the effort
San Diego County officials based on the success of the university asked the researchers for a modified version to be tested. Point Loma Wastewater Treatment PlantThe, which has more than 2.2 millions residents and 17 public schools. Karthikeyan laughed as elementary school students named the robots. They were called Sir-Poopsa-Lot and Harry Botter, respectively.
The team reported that the system detected the emergence the omicron variant at the county-level 11 days before clinical testing. Nature. A detailed analysis of the public school data hasn’t yet been published.
Karthikeyan and colleagues’ methods have been adapted by researchers at the state, national and international levels. The example of the U.S. Centers for Disease Control and PreventionThe Food and Drug Administration uses FreyjaYou can track the variations of wastewater in different parts of the country.
The system is being used to monitor monkeypox and the team is currently working on ways it can detect other pathogens, which may go unnoticed. Pinto states that the work could have a major impact on wastewater epidemiology.
Karthikeyan plans to open her lab at Caltech in 2023. She will use these tools to monitor groundwater. She says that the microbes living there can act as sensors, flagging pollution and climate change, and other disturbances. “My whole thing is to look at a much larger system from a very tiny lens.”
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