A one-liter bottle of raw wastewater collected from the Yarmouth Wastewater Treatment Plant could represent the next horizon of tracking how the pandemic is unfolding in Maine.

As the omicron variant has overwhelmed Maine’s ability to keep up with positive tests and track COVID-19 trends using case counts, scientists and the general public are looking for other ways to detect its spread and assess the risk of getting infected.

Some answers could be in our wastewater, flushed from households every day and flowing to various sewage treatment plants in Maine. Wastewater testing has been going on in some places since the early days of the pandemic, but it has expanded recently and the results are shining a spotlight on sewage testing as a reliable way to track the fast-spreading omicron variant.

Mike Abbott, environmental health director at the Maine CDC, said wastewater data can’t tell you how many cases there are, but it does a good job showing whether virus levels in a community are up, down or plateauing.

“Nothing is perfect, but it kind of answers the question people have every day: Is it getting better or worse? And where?” Abbott said.

Dr. Yolanda Brooks inspects a water sample in a centrifuge tube at the lab at St. Joseph’s College in Standish on Wednesday. Shawn Patrick Ouellette/Staff Photographer

The state will soon be expanding its wastewater testing footprint to about 20 plants across Maine, with data to be released weekly on wastewater virus levels.

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While a few municipalities in Maine have intermittently tested their wastewater for COVID-19, Yarmouth and Portland have been the most consistent. Yarmouth has been running its testing on a near-continual basis since September 2020. Portland tested its wastewater starting in 2020 through early November, and then stopped until resuming tests this month.

There is not enough widespread testing to know what is happening statewide as the omicron variant spreads into different communities. But there are signs that Portland and Yarmouth have passed the omicron peak. Their results are similar to the trends measured about a week earlier in samples taken from Boston’s wastewater stream.

In just three weeks since it resumed testing, Portland Water District’s virus concentration levels have plummeted more than 50 percent at both its East End and Westbrook plants. Yarmouth, which measured a sharp rise when omicron arrived in Maine, saw levels fall by 50 percent last week.

In Yarmouth’s case, the wastewater sample is ferried by volunteers to St. Joseph’s College in Standish for testing, and results are typically available about two to three days later. Wastewater testing is also being conducted at certain colleges and universities, including the University of Maine System.

The presence of coronavirus and other viruses detected in wastewater and the methods of collecting and testing for the coronavirus are well established in research. The number of users for each wastewater system is relatively steady and not subject to the supply and demand fluctuations with COVID-19 testing. Everyone connected to the sewer system contributes every day.

Testing wastewater finds “people who are symptomatic as well as asymptomatic, people who are tested and not tested,” says Dr. Yolanda Brooks, assistant professor of biology at St. Joseph’s College in Standish. Shawn Patrick Ouellette/Staff Photographer

“Wastewater data does not lie,” said Sheree Pagsuyoin, an associate professor at University of Massachusetts Lowell’s Center for Pathogen Research & Training.

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And Pagsuyoin said the wastewater data can be near real-time, because samples are collected immediately from flushed waste and typically tested for the presence of the virus soon after. That makes it a leading indicator, about a week before pandemic trends show up in COVID-19 testing results.

“It’s a very good predictor of cases occurring in community,” Pagsuyoin said. Each test costs about $350. The federal government will be picking up the cost of the $400,000 program at about 20 treatment plants across the state, once it starts up in a few weeks.

That’s in contrast to daily case counts, which are becoming much less reliable, scientists say.

The accelerated contagiousness of the omicron variant laid bare the mistake of relying on case counts to reflect current conditions. A massive backlog of processing tests at the Maine CDC has led to a lag of days or weeks in reporting out confirmed cases. Other shortfalls skew the ability to reflect trends, including a lack of access to testing and the proliferation of at-home tests, which are generally not included in the counts reported by the state.

YARMOUTH AS PIONEER 

Yarmouth pioneered wastewater testing for COVID in Maine. The science was identified as a priority of the Yarmouth Community Coronavirus Task Force in the early days of the pandemic

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Founded in part by husband and wife epidemiologists, Dr. Gib Parrish and Dr. Sharon McDonnell, the community task force noticed the potential for wastewater testing even before the first COVID-19 case was detected in Maine in March 2020.

McDonnell, who also works at the Maine Department of Health and Human Services in the COVID-19 social supports program, said it all started in 2020 with the premise that they wanted to be as prepared as possible to deal with the looming crisis. More than 100 people pitched in, and Yarmouth has maintained one of the most comprehensive COVID-19 response efforts in the state.

“We had an astonishing amount of initiative and willingness,” McDonnell said. “I think doing something really helps people get through this and to not feel helpless.”

Yarmouth, a coastal community of 9,000 residents north of Portland, came together to respond to COVID-19 in a number of ways, from  sewing handmade cloth masks when masks were in short supply to counting the number of people wearing masks at certain locations to track how well the community was complying public health advice. They also started a quarantine support group to help people get through isolation and quarantine, such as by picking up groceries for people at high risk of infection and illness.

Dr. Gib Parrish, who along with his wife, Dr. Sharon McConnell, both epidemiologists, helped found the Yarmouth Community Coronavirus Task Force, transports wastewater intended for testing. Shawn Patrick Ouellette/Staff Photographer

But one of the central strategies of COVID-19 response is knowing how prevalent the virus is in your town, and that’s where the wastewater testing came in.

“We have felt from the beginning that wastewater data is more consistent, gives us a better sense of what’s going on in town,” said Dan Ostrye, an environmental scientist who has also been working with the Yarmouth committee since 2020. “Our data is most contemporary.”

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The first step is collecting the raw wastewater from household sewage flowing to a small brick building at the treatment facility, which serves a total population of about 10,000. The sampling site collects 150 milliliters of wastewater – about 5 ounces – for every 25,000 gallons coming in.

Water is siphoned 150 milliliters at a time over a 24-hour period and combined in a one-liter bottle stored in a refrigerator at the treatment plant. From there, Parrish picks up the bottle on Tuesday mornings every week and drives it to St. Joseph’s College in Standish.

At Mercy Hall at St. Joseph’s, Dr. Yolanda Brooks takes the sample Parrish dropped off and it goes through a series of processes before tests can determine what levels of virus are in the wastewater.

Brooks said the wastewater data captures samples from all types of infected people, who shed the virus in their feces.

Workers scramble to provide COVID-19 tests at Yarmouth Public Works last week. There isn’t enough testing on a statewide basis to gauge the omicron variant’s spread into different communities. Shawn Patrick Ouellette/Staff Photographer

“This is finding people who are symptomatic as well as asymptomatic, people who are tested and not tested. It’s not dependent on whether people are seeking care,” said Brooks, assistant professor of biology at St. Joseph’s.

It’s as close to a comprehensive picture of how much virus is circulating in a community as scientists can get right now, Brooks said. One limitation, though, is it does not measure virus levels in people who use septic systems instead of public sewer, and that rules out wastewater surveillance in large rural parts of the state.

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ENDLESS POSSIBILITIES

The processes at Brooks’ lab work to find ribonucleic acid, or RNA, the genetic marker for the novel coronavirus. To do so, Brooks uses a centrifuge to isolate viruses from organic matter in the sewage.

“Think of it like a spin cycle, like when you’re washing your clothes,” said Brooks, wearing a white lab coat and standing next to the circular centrifuge, where she inserts the vials containing the raw sewage.

Brooks uses a coagulate so when the viruses – the coronavirus that causes COVID-19 and other viruses found in the wastewater – come out of the centrifuge, they clump together on the side of the vial.

Brian Leighton shakes up a container with wastewater to be tested for COVID-19 at the Yarmouth Wastewater Treatment Facility last week. This testing method is becoming more prevalent nationwide as a more accurate means of measuring pandemic trends. Shawn Patrick Ouellette/Staff Photographer

From there, the material, which includes 5 microliters of viruses and 20 microliters of reagents – chemical substances used during testing – are put into a RT-PCR machine. The machine detects the RNA markers that reveal the presence and concentration of the coronavirus.

The system adjusts for variables like weather conditions, such as rainy periods that may dilute concentrations of the virus, or dry conditions that would do the opposite, to get as true a picture as possible of the presence of the virus.

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Brooks said that wastewater testing has potential beyond the COVID-19 pandemic.

“We can look for hepatitis A, influenza, the presence of opioids,” said Brooks, who writes on a white marker board to help explain the science behind wastewater testing.

Pagsuyoin, the University of Massachusetts Lowell professor, agreed that the spotlight shined on wastewater testing can lead to a number of other uses in the future, even studying the diet of a community.

“The possibilities of what we can do with this testing are almost endless,” Pagsuyoin said.

Wastewater is transferred to a one-liter bottle at the Yarmouth facility, which serves a total population of about 10,000 residents. The sampling site collects 150 milliliters of wastewater – about 5 ounces – for every 25,000 gallons coming in. Shawn Patrick Ouellette/Staff Photographer

SIGNS OF HOPE

While Yarmouth is one of the few places in Maine that has conducted consistent COVID-19 wastewater testing, it is becoming more common in other places around the nation and is increasingly used to measure pandemic trends. One of the leading wastewater testing companies, Biobot, is located in Massachusetts, and testing of the Greater Boston wastewater system is showing steep declines in the coronavirus, likely foreshadowing the crash of omicron variant cases.

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Omicron is the most contagious COVID-19 variant so far, but appears to be less severe. Cases of omicron ramp up sharply in a few weeks, straining hospital and health care systems, but also quickly crash, according to the experience in other countries, such as the U.K., Denmark and South Africa. This phenomenon also appears to be occurring in East Coast cities that have seen early waves of omicron in the United States, including Boston, New York and Washington, D.C.

Declines are starting to show up in cities in Indiana, Delaware, Oregon, Connecticut and Pennsylvania, according to data from Biobot. But in many parts of the country, the omicron wave is still on the upswing.

The Yarmouth data only measures one town in Maine and is not necessarily representative of statewide trends. But it shows a steep ramp up in the presence of the coronavirus in mid- to late-December, about 30 to 50 percent week-over-week increases, followed by an 18 percent increase the first week of January, and then a 50 percent decrease last week.

When Portland resumed testing in early January, the virus’s prevalence started at very high levels, but has since plummeted by more than 50 percent.

Cars line up for COVID testing at Yarmouth Public Works on Tuesday. Shawn Patrick Ouellette/Staff Photographer

“The wastewater data seems to be showing a marked and significant decrease from a very high level,” said Scott Firmin, director of wastewater services for the Portland Water District.

Firmin said with virus levels low in the fall, and cost being an issue, the water district discontinued testing in November, but started back up in January with the omicron surge. Portland will be one of the 12 or 13 locations as part of the Maine CDC program, Firmin said.

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The level of measurement used to determine virus concentration is copies of RNA per liter or milliliter of wastewater. In Portland’s case, it has nosedived from about 4.5 million copies per liter to 1.8 million on Jan. 18 at the East End plant.

Being able to predict where cases of COVID-19 are increasing – an “early warning sign” from wastewater data – can help the state direct resources to areas where cases will likely climb. Even after the omicron wave subsides, having wastewater testing in place will help track the rise of other variants if those variants become a threat.

“It’s a way to give us a bigger and more detailed picture of what’s going on in the pandemic in Maine. This allows us to focus our prevention efforts,” said Lt. Dena Bushman, a medical epidemiologist with the U.S. Public Health Service who is assigned to the Maine CDC.

Bushman said that knowledge means they can potentially set up pop-up testing and vaccine sites, and give supplies and extra staff  to hospitals, nursing homes and other health care facilities in preparation for a surge in cases.

Dr. Yolanda Brooks and biochemistry major Eilidh Sidaway of Dedham work together in the lab at St. Joseph’s College in Standish. Brooks said wastewater samples offer a comprehensive picture of how much virus is circulating in a given community. Shawn Patrick Ouellette/Staff Photographer

In Yarmouth, a COVID-19 testing site that had opened in the fall at the Public Works garage started seeing an exponential increase in demand in December, correlating with the wastewater data showing a jump in virus levels.

The testing site, run by about 30 volunteers with the Yarmouth committee, is another part of the community’s response to COVID-19 and has helped to provide access to testing when other testing clinics are booked up because of skyrocketing demand. The site, operated once per week, usually on Mondays, operates from 8 to 10 a.m.

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“We had days in the fall where it was only 30 to 40 people being tested, then it went to 65 to 80 and now we test 200,” said Dale Shields, who helps coordinate the program.

Meanwhile, of the 20 or so additional sites in Maine that will be testing wastewater, Rockland, Guilford-Sangerville, Boothbay Harbor, Bethel, Wilton and Bath are expected to start soon and are partnering with a Biden administration initiative. On a parallel basis, Maine CDC is using $400,000 in federal dollars to add an additional dozen or more locations for wastewater testing.

All of the data will be sent to the U.S. Centers for Disease Control and Prevention and published at least once a week on the Maine Center for Disease Control and Prevention website. While there’s no official launch date, Bushman said she expects it will be “in the coming weeks.”

The data will be broken down to a county level. Bushman said they selecting a cross-section of locations that represents the varying geographic and demographic areas of Maine.

At St. Joseph’s College, Brooks said she sees the interest level in wastewater testing skyrocket as its usefulness during the pandemic becomes evident.

“I used to know only a few select people who were into this,” Brooks said. “Now wastewater testing programs are at at least one university in every state.”


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