Flushing COVID away: Santa Cruz back to wastewater testing in hopes of creating better virus surveillance
Consistent wastewater testing begins again this week in Santa Cruz in an effort to know more earlier about local COVID trends. How does the testing work and how might it help track the virus faster?
Your waste will soon become far more valuable as we figure out the seemingly eternal question: How bad is COVID right now in Santa Cruz County?
Starting this week, Lookout has learned, the city of Santa Cruz’s Wastewater Treatment Facility will again begin weekly testing to determine the current incidence of COVID-19 locally and to potentially stay ahead of surges and new variants.
Though Santa Clara County has collected samples seven days a week from each of its four wastewater treatment plants — in Palo Alto, Gilroy, Sunnyvale and San Jose — since October 2020, Santa Cruz is just getting restarted on testing after its own emergency funding dried up more than a year ago.
Now, the Centers for Disease Control and Prevention has extended its own program of testing to include Santa Cruz and other locales. It’s called the National Wastewater Surveillance System. That testing will be done at CDC-contracted labs, based on samples sent by the plant.
Wastewater testing is providing an early indicator of whether COVID-19 cases are increasing or decreasing in Santa Cruz...
The goal is simple: faster local tracking of the virus.
UC Santa Cruz epidemiologist Marm Kilpatrick, a professor of ecology and evolutionary biology, says the value of the study is how it informs disease trajectory.
“Sometimes, in some settings, it gives you a look at cases either rising or falling a couple of days before the case data do,” he told Lookout on Tuesday. “Much of the time people get infected and they’re asymptomatic or mildly symptomatic for a little bit, and it takes a few days before they get tested. By that time, they will have been shedding the virus for some time and the sewage data will show that.”
Sometimes, in some settings, it gives you a look at cases either rising or falling a couple of days before the case data do.
Additionally, by tracking how much virus is being transmitted by people in the population, it is possible to determine what exactly is being spread, he explained.
Also, with the big question being what comes after Omicron, Kilpatrick said, “some counties are actually using it to detect new variants or the fractions of different variants out there.”
With the new sublineage of Omicron recently found in Santa Clara County, wastewater testing could prove immediately useful to staying ahead of its likely emergence in Santa Cruz County.
In Santa Cruz County, the program provides the likelihood of local health leaders getting an earlier virus read, with less reliance on trailing 14-day infection and positivity rates.
For almost two years now, city and county health officials have largely relied on that often-dated data. The fast-spreading Omicron variant has made the numbers only more uncertain. Increased use of at-home rapid tests, their possible false positives and negatives, and the uncertainty of individuals self-reporting results have raised even more questions.
Further, as Omicron has been noted to produce a large number of untracked asymptomatic cases, we’ve all begun to take the numbers with a grain of salt.
How the testing works
The City of Santa Cruz’s wastewater treatment facility, located at 110 California St., will send five samples per week, “two liquids and three solids,” to the CDC for testing at contract labs conducting the program’s testing, says Akin Babatola, the wastewater plant’s laboratory manager, who is heading up the work.
Though the expected turnaround time of two days for results still falls short of the 24-hour data return time for Santa Clara County, it’s a step forward in staying ahead of the virus.
“The data will be accessible to us so that we can share it with the local health department,” Babatola said.
The plant collects waste from all the sewered systems in the county; many homes in the county are on their own septic systems. Babatola says the samples will be gathered at the wastewater treatment plant from the system’s separate trunk lines. That collection from separate, incoming lines will enable data collection to target which parts of the county might have greater outbreaks than others. Some sense of where high incidence is occurring will be possible; from somewhere on the Westside, for instance, but not a specific location on the Westside.
“We started with the big episode in March of 2020 when we tested through city funding,” said Babatola. “We were able to track the flow of COVID in the sewer system, which for us includes all of the city and the south part of the county. That initial ‘emergency’ funding ran out in September 2020,” though the city continued some testing into November.
The CDC started a new monitoring program in late 2021, which includes Santa Cruz. As of now, the funding is expected to last one year.
Interestingly, Babatola said, data from early testing showed that Santa Cruz’s usual influx of visitors increased COVID spread — more fodder for anti-tourist Santa Cruzans.
We knew when tourists came into the city during the weekends, the prevalence increased.
“We knew when tourists came into the city during the weekends, the prevalence increased,” he said, adding that when more people moved into Santa Cruz from the mountains to escape the CZU fires in August 2020, the same thing happened, because sewage from mountain residences does not flow to the Santa Cruz wastewater treatment plant.
Santa Cruz follows Santa Clara, Alameda, San Francisco, Marin, Contra Costa and Napa counties in performing consistent, ongoing wastewater studies.
Lessons from around the Bay Area
In Palo Alto, the practice has been refined over time.
“Preliminary treatment comes first and gets rid of any foreign contaminants in the wastewater system,” explained Jamie Allen, manager of the Regional Water Quality Control Plant in Palo Alto. That process screens for objects ranging from plant matter to plastics to paper products.
Then, a substance referred to as “primary sludge” is collected as the sample to be analyzed.
“Primary treatment is a low-energy process to observe what has initially settled from the wastewater,” Allen said. “It is essentially a physical removal of material that can be sampled.”
In Palo Alto, the plant collects samples daily, allowing Bay Area health departments to receive fast, consistent data showing how widespread COVID is in certain areas, as they typically get results back within 24 hours of sampling.
The quick turnaround time of results provided by new testing will be one more important tool in understanding the virus that has transformed social interaction. But it’s just one tool, with its limits as well.
You may not know whether you’re getting a positive signal from Watsonville or Santa Cruz or if an outbreak was from a school or a rock concert. So by itself, it could not replace tracking cases and testing.
“You lose all the detailed information, which is absolutely critical for understanding what’s happening,” said UCSC’s Kilpatrick. Wastewater data, of course, doesn’t indicate age, source or specific geography. “You may not know whether you’re getting a positive signal from Watsonville or Santa Cruz or if an outbreak was from a school or a rock concert. So by itself, it could not replace tracking cases and testing.”