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How SLO County disease detectives study wastewater to track COVID spread

Tribune - 11/14/2022

Nov. 14—It's been two and a half years since the first COVID-19 case was detected in San Luis Obispo County, and for many residents pandemic fatigue has set in.

"A lot of people actually had got to the point where they no longer wanted to be tested," San Luis Obispo County Public Health Department infectious disease epidemiologist Jessie Burmester said. "Some of (the tests) are rather invasive."

Testing fatigue, the loosening of testing requirements for travel, plus the increased availability of new technologies such as at-home antigen tests all contributed to fewer tests being analyzed and counted by Public Health as the COVID-19 pandemic continues.

"Our numbers weren't able to reflect all of these different and up-and-coming ways of testing," Burmester said. "And the numbers didn't really capture the true burden of disease in the community."

As a result, the COVID-19 case numbers Public Health reported out to the community soon came with the caveat that the numbers were an undercount and not representative of the true prevalence of disease locally.

Public Health needed to adapt its disease monitoring strategy to a method that was less invasive than a nasal swab and more big picture than counting individual cases — so the county joined the communities across the United States that turned to wastewater monitoring instead.

Graphs depicting wastewater detection in participating San Luis Obispo County sewersheds were added to the Public Health department's COVID-19 data page in September once enough data was collected to chart trend lines.

"There's so many advantages of wastewater," Burmester said. "For those that decide not to get tested or might not even have testing availability, wastewater surveillance is inclusive, and it's non-biased, so we don't have to rely on someone testing or not testing."

Wastewater surveillance coupled with other data sources such as the COVID-19 test positivity rates, case data and hospitalizations "can really help us paint a picture of what's happening," she said.

Wastewater surveillance allows for easier disease monitoring

Wastewater monitoring allows scientists to detect the presence of a particular virus within a community and detect trends in infection at the community level, according to the Centers for Disease Control and Prevention (CDC).

As people go through the day, their waste — including saliva, sputum, feces and urine — goes down the drains of toilet, sinks and showers and into the community sewershed, where it is cleaned and reintroduced to the environment.

If a community member is infected with a virus such as SARS-CoV-2, which causes COVID-19 disease, the individual will shed the viral ribonucleic acid (RNA) in their waste.

By taking samples of wastewater from a sewershed, then, scientists can measure concentrations of a viral pathogen like SARS-CoV-2 by extracting the RNA of the virus from the sample and then measuring the RNA concentration in the sample, the CDC said.

Wastewater surveillance is not a new concept, though it's getting renewed focus. For roughly 70 years, the United States has used wastewater to detect the presence of viruses in local communities, such as poliovirus.

But during the COVID-19 pandemic, it became clear that wastewater was a vital tool for public health researchers looking for more information about local virus transmission, Burmester said.

"Coupled with existing data, it can really help us paint a picture of what's happening," Burmester said.

How waste goes down the drain and turns into data

The City of San Luis Obispo Public Works Department is one of the sites in the county that collaborates with Public Health on wastewater surveillance for COVID-19.

Every day around the same time, water quality laboratory analysts such as Tanner Duncan with SLO Public Works go out to the wastewater treatment plant to take a sample and monitor water quality trends.

Because humans typically have regular cycles, for example, eating breakfast and showering about the same time every day and producing corresponding bowel movements, the water quality analysts try to sample at consistent times to ensure the analysis is relatively comparable day to day.

"We want to try and even out those curves as much as possible throughout the plant," laboratory manager Matt Anderson said.

Now, about three times a week, local water quality analysts send additional composite samples to various public health laboratories to check SARS-CoV-2 levels in San Luis Obispo wastewater.

Similar time considerations remain in effect for sampling for COVID-19. The water quality analysts try to sample the same day mid-week, when fewer locals are out of town and fewer tourists are in town so as not to skew the data, Burmester said.

Two of those weekly samples go to BioBot Analytics, the vendor contracted by the CDC to implement the National Wastewater Surveillance System (NWSS). The data is sent to the CDC to analyze for trends in SARS-CoV-2 levels and test for variants and is later reported out to the NWSS.

"We just pack it with ice and then send it off on its way," Duncan said while demonstrating the sampling process.

Public Works also ships a sample off once a week to the Cal Poly laboratory to analyze for SARS-CoV-2 levels.

The results of the Cal Poly laboratory analysis are shared with Burmester as raw data.

Burmester then analyzes the data from each of the participating sewersheds in the county for trends in virus concentration and reports the results to the public in the form of a graph on the COVID-19 data dashboard.

What wastewater monitoring can tell us about COVID-19 in SLO County

Wastewater monitoring allows epidemiologists like Burmester to analyze trends in SARS-CoV-2 infection in participating local sewersheds.

One of the biggest benefits of wastewater monitoring for a virus like SARS-CoV-2 is that it is less prone to bias than counting self-reported cases, Burmester said.

"What's really nice too is that as well as being inclusive of the whole population, it's inclusive of asymptomatic and symptomatic individuals, which gives us access to a whole new realm of individuals that have been really hard to quantify," Burmester said.

In January 2021, a study showed that asymptomatic SARS-CoV-2 infection could be responsible for more than half of all disease transmission. Capturing this type of infection is important to understanding the local impacts of the pandemic.

Asymptomatic infections were often missed by COVID-19 tests and case counts, because people without symptoms and no known exposure are not inclined to test for COVID-19.

Wastewater surveillance is also a leading indicator for COVID-19 spread in a community and can detect the shedding of a virus usually two to three days before an individual feels sick, she said.

"We can kind of see changes in patterns before testing even catches up to that," Burmester said.

The CDC said that wastewater surveillance can detect the presence of SARS-CoV-2 virus in the community if the concentration of the virus in the wastewater is above the threshold the test can detect. Like many complex components of wastewater, that threshold is still being determined.

Wastewater monitoring can also be used to assess trends in COVID-19 infection within the community contributing to the sewershed, according to the CDC.

Trends are the result of a statistical analysis of changes detected in the concentration of SARS-CoV-2 virus in the wastewater, which can be compared with past data from the same treatment plant and sometimes with data from other plants.

Wastewater data for SARS-CoV-2 can be particularly illustrative when paired with other COVID-19 data sources, such as test positivity data, Burmester said.

Wastewater can also be paired with other databases, such as COVID-19 hospitalizations and even influenza data derived from wastewater to help determine seasonal respiratory illness trends.

"It allows us to complement existing data sources in a really valid and and beneficial way," she said.

COVID-19 wastewater monitoring is expensive

The biggest barrier to standing up universal wastewater monitoring for virus surveillance is cost, Public Works and Public Health workers said.

In May 2020, the county started a sampling and monitoring program for SARS-CoV-2 and invited the wastewater facilities in the county to participate, Anderson said.

"Then the cost ramped up to over, I think at that time, it was like $1,200 to $1,500 a week, per location," Anderson said. "It's really expensive."

"It is cost prohibitive," Burmester added. She recalled the cost of conducting a test at each site being closer to $3,000.

However, she said recently "the cost for wastewater surveillance has declined."

Most of the wastewater monitoring sites in San Luis Obispo County are participating in a grant-funded program with BioBot and the CDC that covers the cost of shipping and analyzing the samples through the end of 2022.

"That's been a really beneficial thing for us because otherwise it is an extremely cost-prohibitive program," she said.

For local monitoring, once the San Luis Obispo site started working with Cal Poly's lab, the cost of analysis decreased, Anderson said.

Limitations of wastewater surveillance and analysis for public health

Wastewater surveillance can tell scientists a lot about COVID-19, but there are also some limitations.

For one, it cannot be used to predict the total number of COVID-19 cases in a community.

Instead, wastewater data can be thought of as a pooled community sample that can illustrate the presence of and changes to virus levels in a particular location, according to the California Department of Public Health.

The sample also will not include individuals who use household septic systems or facilities such as prisons, hospitals or colleges that treat their own sewage.

In San Luis Obispo city, for instance, the California Men's Colony prison and Cal Poly are not included in the city wastewater surveillance system, and therefore SARS-CoV-2 transmission trends in these locations are not captured in the reporting.

Why wastewater data for SLO County comes without a vertical axis

Another challenge with wastewater monitoring is the lack of standardization across sites.

Instead of making every site follow the same methodology and analysis, county Public Health, on the recommendation of California Department of Public Health, prioritized getting all of the sites onboard as quickly as possible.

"It's still in my mind better to have more widespread collection and use of wastewater surveillance than mandating certain protocol that might not work for wastewater sites," Burmester said.

For example, the wastewater site in Paso Robles doesn't use raw wastewater as part of their sampling. Instead, they produce a sample using the settled solid sludge particles from the wastewater, Anderson said.

Comparing the data from San Luis Obispo city, which uses raw wastewater, and Paso Robles, which uses sludge, would be like comparing apples and oranges — the viral concentrations are not measured the same way.

Not requiring standardization across sites allowed wastewater monitoring to be implemented quickly in many locations nationwide, but now best practices are starting to be assessed by research steering committees with various agencies.

"This has allowed us to have more comprehensive understanding of wastewater surveillance without necessarily the standardization, but now we're backtracking and trying to figure out how we can relate all of this to each other," Burmester said.

The lack of standardization across sites means the units of measurement differ, which is why viral concentrations are not included on the Y or vertical axis of the graphs for local wastewater sites on the county's COVID-19 data page.

"If we were to try and create a standardized unit, it would lead to estimates and it wouldn't show true data," Burmester said.

By omitting the units of measurement from the Y axis, the public can see if SARS-CoV-2 is trending upwards or downwards week after week without getting confused about the differences between measurements across local sites.

"We wanted to make it as accessible as possible so people could just see the trend lines and understand that, regardless of how they're being sampled or the methods behind it, they can still visualize what's happening in those communities," she said.

How San Luis Obispo County became a leader in wastewater surveillance

Six sewersheds are currently participating in wastewater collection in San Luis Obispo County, with three tracked on the website: San Luis Obispo, Paso Robles and the South County Sanitation District, which includes Arroyo Grande, Oceano and Grover Beach, Burmester said.

"I'm really shocked with how many sites have been gung-ho about jumping on this," Burmester said.

Los Osos, Cambria and Nipomo have also been participating in wastewater sampling. Hopefully by the end of November, there will be enough data to capture trends that can be illustrated in graphs online and added to the COVID-19 dashboard, she said. Currently, the three sites are not part of the wastewater section on the website.

Once the additional sites are incorporated in the dashboard, San Luis Obispo County will be one of the counties in California with the most sewersheds participating in wastewater monitoring and analysis.

"We are a medium-sized county yet we have and we're taking on projects that are still new, and it's just really nice to be at the forefront of this effort," she said.


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