Robots Are Predicting COVID-19 Outbreaks by Sifting through Your Poop

Karthikeyan at Point Loma

Erik Jepsen

Key Takeaways

  • Testing wastewater for COVID-19 is an effective way to track potential outbreaks.
  • Thanks to an improved method, this type of surveillance can be done faster, more efficiently, and cheaper.
  • The improvement in the process allows dozens of samples from sewers and sewage treatment plants to be tested each day rather than only a handful.
  • Rapid wastewater testing may also be used to detect and track other viral outbreaks in the future.

Early on in the pandemic, scientists turned to wastewater as a warning system for COVID-19 outbreaks. Testing wastewater samples for the presence of the virus has proven useful in singling out a building or area where COVID-19 is already present, even if carriers are asymptomatic. The method has been implemented everywhere from colleges to local communities.

But this method has one significant flaw: its speed. Now, a team at the University of California at San Diego (UCSD) School of Medicine has found a way to speed up the detection process and provide accurate data more rapidly.

The original process was slow because samples of wastewater or sewage are diluted and must be concentrated, which takes many steps and uses plenty of resources, Smruthi Karthikeyan, PhD, an environmental engineer and postdoctoral researcher at UCSD School of Medicine, tells Verywell. Karthikeyan is the lead author on a report of the process published this month in the journal mSystems.

Speeding Up the Process

Unlike a nasal swab, which takes a small sample of mucus, a wastewater sample from a sewer or sewage treatment plant is diluted after having sloshed around with everything else that went down the drain.

Wastewater samples need to be concentrated so that SARS-CoV-2, the virus that causes COVID-19, if present, is easier to find. But there was a need for a faster method to concentrate those samples and find RNA from the virus. Researchers were specifically interested in finding a method that could be done simultaneously on many samples and could deliver accurate, same-day results. 

To speed the process up, Karthikeyan and her team turned to some robotic assistance she already had in her lab. Before the pandemic started, her research focused on the gut microbiome, an area of study that also involves examining sewage samples. By modifying that system, they were able to rapidly extract RNA from the wastewater samples and run a polymerase chain reaction (PCR) to search for signature genes of COVID-19.

In systems previously used for wastewater surveillance, the water samples were concentrated using filtration or precipitation methods, which took time and many resources to run tests.

Instead, this high-throughput system uses magnetic beads that preferentially link to bits of the virus, Karthikeyan explains. The robotic processor then picks up the beads using a magnetic head, leaving everything else behind.

“This way you select for only the virus and not pick up all the junk,” she says. “It increases your chances of finding the virus even in a dilute system.” The concentrated samples are then tested for three different gene targets on the COVID-19 genome using PCR testing.

What Is High-Throughput Screening?

High throughput screening uses automated equipment to rapidly test thousands to millions of samples for biological activity at the organism, cellular, pathway, or molecular level.

The improved system greatly increases the speed of testing.

“[Previously] I couldn’t do more than 10 samples in a day. It took me hours to do the same thing,” Karthikeyan says. “With this, we can do 120 samples in 4.5 hours from receipt of sample to the actual PCR detection.”

This process has the added benefit of being cheaper since it requires fewer resources and fewer people to run the testing, she adds. The testing can be done on wastewater samples as small as 10 milliliters in volume.

The accuracy of the results with this method is also high. Rapid testing allows the researchers to predict what will be happening with the spread of COVID-19 a week in advance with good accuracy and three weeks in advance with fair accuracy, according to a statement from UCSD School of Medicine.

What This Means For You

Wastewater surveillance for COVID-19 is a reminder that the virus can spread even when individuals aren't experiencing symptoms. It's important to keep taking the necessary safety precautions like wearing a mask, social distancing, and washing your hands to keep yourself and your community safe.

A Success Story

Testing wastewater from dormitories and other buildings at UCSD has been underway since July 2020. A team led by Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at UCSD, discovered the technique.

A month after the school began surveilling wastewater, they detected a positive asymptomatic case and the university was able to send out alerts to people in the affected buildings. This facilitated targeted testing of individuals in a given area rather than attempting to test everyone on campus. The screening results are now made available on a public dashboard.

Other universities, such as the University of Arizona are using wastewater testing to track the spread of COVID-19. New York City even monitors COVID-19 in samples from its 14 wastewater treatment plants.

The UCSD system allows more water samples to be tested rapidly, giving public health officials a look at the spread of the virus before people may be clinically ill. “I don’t think anyone is doing it on a scale like this,” Karthikeyan says.

The system being used at UCSD can detect even just one case of COVID-19 in a building with more than 400 residents. In a young population, such as the student body at UCSD, infected people are often asymptomatic, but are still shedding the virus, Karthikeyan says. By the time an asymptomatic carrier turns symptomatic or spreads the virus to someone who shows symptoms of infection, the virus could have spread exponentially.

Karthikeyan and her colleagues are currently testing wastewater samples for San Diego County. The wastewater treatment facility at Point Loma processes sewage for more than 2.2 million people, allowing samples to be collected at one location for the whole service area. It is difficult and expensive to conduct testing for the virus on the whole population, but using wastewater testing as a surveillance technique allows public health officials to narrow down the areas where testing is crucial.

San Diego County wants the UCSD team to not only detect the virus but also sequence the virus genome to see which variants of the virus may be circulating, Karthikeyan says. “Now we are going to do large-scale genome sequencing," she adds.

This type of wastewater surveillance can be adapted to conduct surveillance for any virus that is shed in feces, Karthikeyan says, adding that it could be used in many types of epidemics of infectious disease and might help detect future pandemics earlier.

The information in this article is current as of the date listed, which means newer information may be available when you read this. For the most recent updates on COVID-19, visit our coronavirus news page.

3 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Farkas K, Hillary LS,2 Malham SK, McDonald JE, Jones DL. Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19. Curr Opin Environ Sci Health. 2020;17:14–20. doi: 10.1016/j.coesh.2020.06.001

  2. Karthikeyan S, Ronquillo N, Belda-Ferre P, et al. High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego County. mSystems. 2021;6(2). doi: 10.1128/mSystems.00045-21

  3. University of California San Diego Health Sciences. Sewage-handling robots help predict Covid-19 outbreaks in San Diego. March 3, 2021.

By Valerie DeBenedette
Valerie DeBenedette has over 30 years' experience writing about health and medicine. She is the former managing editor of Drug Topics magazine.