To stop COVID-19, Idaho cities are tracking it in an unusual (smelly) place: your sewage

BOISE — A handful of cities in Idaho — including Boise, Moscow, Coeur d’Alene, Twin Falls, and Lewiston — have been making an effort to provide new COVID-19 information to their health districts through an unusual source: their wastewater.

Sewage captures buttloads of information (pun intended) from the communities it is collected from, and the coronavirus is no exception.

How is the virus detected in wastewater and how is that information being used? We spoke with city officials and scientists in Boise and Moscow to find out.

Why looking for coronavirus in the sewage is a good idea

Residents may not realize it, but sewage systems contain a snapshot of a community’s lives. If you take showers or go the bathroom regularly, the information about the products you use or how healthy you are — together with your neighbors’ — is being accumulated in wastewater.

Although it is a relatively new field, wastewater-based epidemiology — the analysis of raw wastewater to obtain data on community habits — had already proven useful for informing levels of drug use inside districts before the pandemic hit.

With the discovery that about 41% of patients with confirmed coronavirus infections can shed the virus in their feces, wastewater emerged as an incredibly useful tool for city officials to obtain much-needed information about the advance of the pandemic in their communities.

Back in March, a Boston-based company called Biobot Analytics published a method for isolating the virus in wastewater and spearheaded a national campaign that added 400 cities in 42 states to its sewage testing program.

“There were a lot of questions and not a lot of data or answers,” said Haley Falconer, environmental manager within the city of Boise’s public works department.

“The organization who was originally doing the testing is one we had worked with in the past, and we also had citizens emailing us asking us to participate,” Falconer said about what prompted the city to start testing with Biobot.

Boise is testing at two facilities, one on Lander Street and one at the West Boise Water Renewal Facility. Those serve all of the city of Boise as well as Eagle and Garden City.

The city of Moscow also started testing with Biobot back in May, who was offering subsidized testing at the time. According to Tyler Palmer, it was important for the city to establish a baseline for the presence of the virus while University of Idaho students were away to detect how it changes once students are back for the fall semester. Palmer is the deputy city supervisor of public works and services in the city of Moscow.

Moscow has one treatment plan for the entirety of the city.

Though initial analyses were done through Biobot, Boise and Moscow have now changed their service providers — the University of Missouri and the University of Idaho, respectively — in an attempt to reduce the costs of testing.

Protocols for detecting coronavirus in sewage water still in development

The method initially described by Biobot to detect coronavirus in sewage water is relatively simple. However, as people started to adapt it to specific needs, many other ways of obtaining the same results have emerged.

One of the challenges of implementing COVID-19 testing in sewage samples is that there is no standard methodology yet, said Thibault Stalder, research assistant at University of Idaho. Stalder leads the project of wastewater testing at UI, which combines the efforts of microbiologists, virologists, mathematicians and environmental engineers.

Testing for coronavirus in wastewater is definitely not the same as doing it from a freshly taken sample that comes from a patient. In stark contrast to testing using throat swabs, the virus in the sewage water is diluted, extremely dirty and has been partially destroyed. Molecular biologists are not used to working with samples in such poor conditions.

That’s why the initial step in the whole process involves concentrating the genetic material present in the sample — which can come from humans, bacteria and the virus, among others. This is done by filtering the sample and collecting the solids filtrated out of the water. Then, scientists use alcohols to separate the genetic material from the rest.

The genetic material of the coronavirus is RNA — a single-stranded cousin of the double-stranded DNA — so the second step is separating the RNA from the DNA in the sample.

Similar to those meal-kit companies that deliver ingredients and instructions for you to cook at home, scientists use commercial kits with standardized ingredients and instructions that make extracting RNA a straightforward process.

RNA extraction kits also help remove all of the additional ‘dirt’ that can interfere with the next steps in the process — detecting the amount of coronavirus RNA in the sample. This is generally done by a widely used technique called PCR (Polymerase Chain Reaction), a process in which scientists can look for a small piece of the genome of the coronavirus and make thousands of copies of it.

The piece of RNA targeted is only about 90 to 120 letters long — out of almost 30,000 letters in the virus genome — and holds part of the information that creates those lollipop-like spike proteins in the surface of the virus. According to Tanya Miura, virologist at UI, this is a specific region of the viral RNA that is more likely to be preserved in the poor conditions of wastewater.

Finally, scientists can quantify the amount of copies of the coronavirus RNA obtained after doing PCR. This number is proportional to the amount of virus in the sample, which is in turn proportional to the amount of virus in the community.

For now, the process being developed at UI is “not a high throughput process,” said Eva Top, professor at UI and leader of the lab where testing is being developed. They would need more funding to scale up the process, Top said. They have been working with samples from the city of Moscow and the city of Twin Falls.

Results are useful for detecting trends in infections

It is possible to estimate the amount of infections in a community, but neither scientists nor officials think it is an accurate estimation. It is full of assumptions about things that are not known with high certainty.

For example, an estimate of the number of cases depends on how many people and how often are using a particular sewage system. Researchers should know the amount of people shedding the virus in their stool and how much virus can actually be present in someone’s stool. They need to control for how much water is running through the sewage system or for how much of the virus initially present in the sample is lost in the detection process.

However, the variation in time of the number of viral copies present in the wastewater can inform about the infection trends in the community. It is especially valuable because it incorporates data on asymptomatic patients, who can unknowingly spread the infection and are unlikely to get tested.

“The increase in concentration in the wastewater is correlating to an increase in confirmed cases” in Moscow, Palmer said, which “gives us confidence that we are getting good information.” Back in May, “the first three (weekly) tests came back with no technical COVID, and in the fourth test we saw a spike in the COVID concentration,” he said.

The city of Boise is making its COVID wastewater testing information available for the public in a dashboard, where it shows the trends in the number of copies of the virus in the water along with the confirmed cases for Ada County. From there, it is clear that the spikes in confirmed cases can be observed several weeks earlier in the wastewater data.

“We’ve made a really clear decision to not try and translate that virus copies number to a number of cases, because the science isn’t there yet,” said Kyle Patterson, data strategist in the office of innovation and performance of the city of Boise.

Although it has proven useful, wastewater data is not currently “being utilized in a way that directly impacts policy decisions related to COVID-19,” according to Brian Atkins, program manager in family and clinic services division at Central District Health.

“While it certainly can act as an early indicator, it is not likely that it will drive policies similarly to key indicators like testing and hospital data. It can contribute to the larger picture but is not a stand-alone data source that has enough impact to make unilateral decisions,” Atkins said.