A year ago, testing sewage for COVID-19 was a new fringe science with an attention-grabbing gross-out factor. The words “poop” and “coronavirus” were making headlines across the country.
So, what has happened in the interim to all that human-waste sampling and its potential to predict where COVID-19 is spreading?
The short answer is that it is continuing; it has proved helpful; and it now goes by a more-savory moniker. Like a Bobby growing up into a more dignified Mr. Roberts, “poop testing” has become a scientific niche known as “wastewater surveillance” or “wastewater epidemiology.”
More than 65% of Colorado’s population is now under wastewater surveillance. Twenty-two Front Range municipalities, counties and wastewater treatment entities are being monitored under a grant program with the Colorado Department of Public Health and Environment, Metropolitan State University, Colorado State University and the private company GT Molecular. That testing is being done in coordination with the Centers for Disease Control and Prevention.
Another 20 Colorado entities have participated in testing through Biobot Analytics, a Somerville, Massachusetts-based company. A number of Colorado universities are performing their own tests in on-campus labs.
All this testing of the conglomerate waste that is flushed down toilets, ground up in garbage disposals and drained from bathtubs has proved to be a reliable indicator of how much COVID-19 is swirling around in certain geographic locations. It can also be an early warning system because the virus shows up as many as three days before symptoms may occur or tests on individuals show infection.
With all those positives, sewage testing is not viewed as the be-all, end-all test to ferret out a nasty worldwide disease spreader like COVID-19. Instead, it is being referred to as a go-to gadget in the toolbox of COVID-19 tracking methods.
“We believe wastewater monitoring can be a helpful tool in analyzing various disease trends,” wrote Erin Garcia, a spokeswoman for the state health department, in an email response to questions about the state’s experience with sewage testing for COVID-19.
The CDC has deemed sewage testing to be both “a complement to other surveillance systems” and “a leading indicator of changes in COVID-19 burden in communities.” The agency is currently working to partner with more states, tribes and U.S. territories for more widespread surveillance of wastewater. The CDC has set up a national data system for wastewater surveillance.
“Wastewater data can help public health officials understand the true increases and decreases in cases,” wrote Jade Fulce, a public affairs specialist with the CDC, in response to questions. “Several communities have implemented wastewater surveillance in areas where clinical testing was limited and used this data to make decisions about mobile testing and vaccination sites. Public health agencies have also used wastewater data to forecast changes in case counts and hospitalization utilization, providing additional time to prepare for increasing cases.”
Labs flush with information
Testing what goes down the toilet works as a disease tracker because viruses, including the SARS-CoV-2 virus that sparks COVID-19 illness, carry genetic material in each virus particle.
When a sample of wastewater is dipped from a sewage system, filtered, and subjected to sensitive polymerase chain reaction testing by microbiologists and engineering researchers, the RNA genetic material in the SARS-CoV-2 virus reveals itself. The concentration of that genetic material in a liter of sewage water is then calibrated with population numbers. That computation indicates when levels of the virus that causes COVID-19 rise or fall in a given geographic area that feeds a particular sewage system.
A sewage system that yields a COVID-19 level can be as large as an entire community or as pinpointed as a particular college dorm.
Even though this fecal tracking is not a new science, the CDC calls it “a developing field of science.” Wastewater testing has been used in recent years to highlight outbreaks of norovirus, hepatitis-C, polio and other disease-causing pathogens around the world. It has also been used in Australia and in Southern states in the U.S. to measure the levels of illicit drug use, most often focused on opioids.
With all the hype about its helpfulness, some drawbacks to this type of testing remain. About 20% of the nation’s households are not connected to communal sewage systems. And sewage systems can yield skewed results because of the movements of humans linked to commuting or travel. In mountainous areas, runoff can change the makeup of wastewater.
Gunnison County is a good example of a place where wastewater epidemiology is not helpful. The county was one of the earliest places in the state to sample its wastewater for COVID-19 more than a year ago and found out that the movement of vacationers and the spring runoff from the mountains into the sewage ponds both made poop testing an unhelpful metric for that area. Gunnison County is no longer doing wastewater testing.
Colorado authorities had initially planned to test wastewater for a year to see if it might be helpful in tracking the coronavirus. With that $520,000 project ending in July, and with the testing proving to be viable, the state is reupping for another two years. The CDC is funding that next phase.
The state hopes to expand the testing to some Western Slope sewage systems in the coming phase, Garcia wrote.
Currently, Colorado Mesa University is one of the few places – if not the only -̶ on the Western Slope doing COVID-19 testing. The university recently garnered national attention for using that testing along with a number of other tracking systems to pick up on dormitory hotspots for the coronavirus before they turn into widespread outbreaks.
The university has set up its own in-house testing system to process wastewater samples from specific dormitories six days a week. That is accomplished with a team of white-coated engineering students who bicycle around campus hauling a small trailer. The samples go to an on-campus lab managed by a recent graduate student and overseen by a cadre of professors. The in-house system allows the campus to have results in 24 hours and to modify campus gatherings, such as sports practice and competition, based on those results.
“The sooner we know where people are who might be infected, the sooner we might be able to step in in a way that might limit spread,” said CMU Biology professor Kyle McQuade.
“Smart sewers” may be in our future
At CSU, Graduate students take samples from manholes on campus every 15 minutes. Those samples are then combined into a composite sample to test for COVID-19 genetic bits. Two residence halls were quarantined after the testing showed high levels of virus in the sewage from those buildings.
Biobot Analytics, which is working with 400 entities on wastewater testing around the country, predicts that sewage testing for various diseases and drugs will become a routine part of wastewater treatment facilities beyond the COVID-19 pandemic. Newsha Ghaeli, president and co-founder of Biobot, said she envisions wastewater treatment being known as “smart sewers” in the future.
“We want to turn wastewater epidemiology into permanent parts of wastewater systems,” Ghaeli said.
Ghaeli, an architect who partnered with an epidemiologist friend to create Biobot in 2017, said they didn’t have a pandemic in mind when they began testing sewage. The only epidemic they aimed at then was the opioid scourge spreading through Southern states. Levels of opioids they found in sewage systems mirrored opioid use reflected in more conventional measurements like overdoses and arrests.
“Wastewater epidemiology was very much a fringe science before the (COVID-19) pandemic,” Ghaeli said.
Wastewater epidemiology was also an expensive science in the beginning.
Biobot was charging a prohibitive $1,200 per sample early in the pandemic. That fee has now come down to as low as $350 per sample. For entities that have purchased their own equipment, doing the sampling can be much cheaper, and the CDC has signaled that it will help fund wastewater testing.
CSU researcher Carol Wilusz, who is helping to lead that university’s project, said in a CSU internal publication that the testing can be done for pennies per person when an entire population is taken into account.
Ghaeli said she believes wastewater epidemiology will become even more useful post-pandemic to ferret out population-affecting illnesses like influenza outbreaks. In the meantime, it is being tweaked so that it can separate the many variants of COVID-19. Ghaeli said they are already using it to find the UK B.1.1.7 variant.
The Sabeti Lab at Harvard University, which has been working with Colorado Mesa on setting up its tracking system, has identified a possible new strain of COVID-19 in CMU’s wastewater. For now, the lab is calling it “peacock” and is monitoring it to determine if it is indeed a new mutation of the virus.
That kind of detailed virus sleuthing is expected to become a more important part of increasingly sophisticated fecal testing.
The CDC is preparing to publish a report that will lay out its future plans for wastewater surveillance. That report will tackle potentially thorny issues like the ethics of collecting human sewage for testing and the reluctance of some public health agencies to accept its usefulness.
Once those barriers are addressed, the CDC predicts, “the COVID-19 pandemic may be the initiating event that turns this emerging public health tool into a sustainable nationwide surveillance system.”