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Tracking COVID in wastewater is the future — but not in Florida

Flushing the toilet can help scientists track surges of COVID-19. Florida is behind other states in utilizing the technology.
Pinellas County Utilities senior chemist Albert McAfee pours one liter of a wastewater sample taken from the South Cross Bayou Water Reclamation Facility into a 250-milliliter container. The sample was sent to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system.
Pinellas County Utilities senior chemist Albert McAfee pours one liter of a wastewater sample taken from the South Cross Bayou Water Reclamation Facility into a 250-milliliter container. The sample was sent to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system. [ DIRK SHADD | Times ]
Published May 5|Updated May 5

As COVID-19 testing continues to recede in Florida, it is far behind other states in tracking the virus with promising technology that relies on wastewater.

The Florida Department of Health received more than $1.2 million from the federal government last summer to build a statewide system to detect the virus in wastewater. Eight months later, the state won’t say whether such a program exists.

A department spokesperson said federal money “mostly went towards increasing lab capacity” but did not elaborate.

Pinellas County Utilities senior chemist Albert McAfee shows off the 10-liter wastewater sampler located on the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Pinellas sends wastewater samples to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system.
Pinellas County Utilities senior chemist Albert McAfee shows off the 10-liter wastewater sampler located on the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Pinellas sends wastewater samples to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system. [ DIRK SHADD | Times ]

Without a state wastewater testing network, 12 of Florida’s 67 counties turned to outside help to track the virus. Pinellas County’s program is funded by the federal government. Others, such as in Hillsborough, are paid for by a private company.

But that patchwork approach has limitations.

On April 15, testing in Pinellas and five other counties ended when federal funding expired. Data collected by the six counties went dark just as the state’s average daily infections jumped 80 percent in two weeks.

“This is our best early warning sign,” said University of Miami microbiologist Helena Solo-Garbiele. But without it: “We lose our ability to detect surges.”

Related: Most Americans — and 75% of children — have gotten COVID, says CDC

While the Centers for Disease Control and Prevention says testing will resume, it took three months to restart after the last interruption of funding.

Colorado, however, wasn’t affected. It took advantage of the same federal grant that Florida received to build its network and now tests 60 percent of the state’s population. That system still functions as infections rise across the U.S.

• • •

‘You’re in the sample’

The strength of wastewater surveillance is that it doesn’t rely on human behavior: No one has to decide to get tested for COVID-19. Nor is anyone prevented from being tested by factors beyond their control.

Infected individuals shed the SARS-CoV-2 virus in their waste, sending virus particles into sewage water. Researchers can determine in real-time whether infections are spreading through a community by sampling its wastewater.

”It doesn’t matter if you get tested or not, if you’re symptomatic or asymptomatic,” Solo-Gabriele said. “If you poop, you’re in the sample.”

That helps health officials quickly detect viral surges because at this point in the pandemic, she said, the official case count is likely missing a lot of infections. Every day, the CDC reports the number of positive COVID-19 cases detected across the country, but that count includes only test results that are reported to state and federal health agencies.

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A view of the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Pinellas sends wastewater samples taken from the plant to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system.
A view of the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Pinellas sends wastewater samples taken from the plant to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system. [ DIRK SHADD | Times ]

As public testing sites disappear, Floridians have turned to at-home tests — the results of which are not reported to health officials — or have foregone testing altogether.

That makes CDC data less reliable. In the past month, Florida recorded the fewest test results since June 2020.

The limitation of wastewater tracking is that it cannot reveal exactly how many infections are in a community at a given time. Public health officials still need data from testing sites, hospitals and other facilities to find that out and to calculate positivity rates.

Related: COVID-19 infections once again on the rise in Florida

But public health officials can use wastewater tracking to gain a holistic understanding of the pandemic and react to rapidly changing conditions, said Edwin Oh, a microbiologist at the University of Nevada, Las Vegas.

“The more important question here is: What is the trend over the last two or three weeks?” he said. “If we start seeing those trends (rise), we will definitely start seeing cases showing up in the hospital soon after.”

Nevada started analyzing sewage in February 2020, when clinical tests were still scarce. Health officials detected COVID-19 in wastewater “basically at the same time that we had our first confirmed case,” Oh said.

When omicron hit the state in December, he said, the variant was identified using wastewater data. Researchers tracked its spread from high-tourist areas around Las Vegas to the rest of the state by looking at where the variant appeared in sewage water.

Related: Racial split on COVID-19 endures as restrictions ease in U.S.

But for tracking to work, health officials have to use the data to deploy testing and vaccination resources quickly enough. That didn’t happen in Nevada, Oh said.

“We’ve been fighting each surge as a sort of catch-up game,” he said. “The next time this happens, hopefully public health organizations are a little bit more prepared (and) a little bit more ready to believe in the data.”

• • •

‘200,000 people in one shot’

Two Pinellas treatment plants may be the county’s best early-warning system to track the growing BA.2 wave and the ones that will come later.

Tucked away in a residential neighborhood between St. Petersburg and Pinellas Park, the South Cross Bayou water plant is one of two county utilities that monitor residents’ infection levels. The other is the William E. Dunn Water Reclamation Facility in Palm Harbor.

Related: He was healthy, vaccinated, then had a heart attack. Was it COVID?

South Cross Bayou serves about 220,000 residents. The William E. Dunn plant serves about 82,000. Together they cover almost a third of Pinellas’ nearly 1 million residents. Earlier this month, Tampa Bay Times reporters toured the South Cross Bayou plant. More than 20 million gallons of raw sewage that is flushed, rinsed and poured down Pinellas drains flows daily through the plant’s pipes.

For every 1,000 gallons of sewage, about one teaspoon is sucked up by the plant’s sampling equipment and deposited into a refrigerated plastic jug atop a beige building on the plant’s outskirts. Twice a week, samples from that jug are decanted into small bottles and shipped to a lab.

“You’re looking at 200,000 people in one shot,” said Pinellas County microbiologist Bina Nayak, gesturing toward the murky gray liquid accumulating in the jug. “Can you imagine testing 200,000 people versus just one wastewater sample?”

Pinellas County Utilities senior chemist Albert McAfee poured one liter of a wastewater sample taken from the South Cross Bayou Water Reclamation Facility into a 250-milliliter container. The sample was sent to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system.
Pinellas County Utilities senior chemist Albert McAfee poured one liter of a wastewater sample taken from the South Cross Bayou Water Reclamation Facility into a 250-milliliter container. The sample was sent to a lab to detect coronavirus levels. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system. [ DIRK SHADD | Times ]

Nayak was coordinating research projects for Pinellas County Utilities when she heard about the CDC’s wastewater testing. She urged county officials to join.

“We had to step up to the plate,” Nayak said, “for the sake of the community, our customers, and the public health agencies that would use the data.”

In total, 11 Florida wastewater plants serving portions of six counties are part of the CDC program. That means wastewater surveillance only tests 1 out of every 5 Floridians.

On April 15, the last date that data was available, viral levels at the two Pinellas plants were the highest since early March.

Related: Florida adds 26,574 COVID cases in past week, positivity rates rise

During the tour of the South Cross Bayou plant, Nayak climbed the two-story metal staircase to the top of the headworks building where samples are collected. She weaved through a maze of tubes and instruments, toward a metal box that holds the sampling equipment.

Beneath her, a 20-foot metal screen removed leaves, diapers and other “non-processables” from the 300 gallons of raw sewage that rushed past each second. Every time the screen cycled through the muck, the machinery burped up a dizzying bouquet of odors.

“It smells like gold to me,” Nayak joked, adjusting her neon blue hardhat in the unseasonably muggy April heat. “There is so much good data in there, as long as you actually use it.”

• • •

‘Patchwork of programs’

The federal program that funds testing in Pinellas County was meant to be temporary while states built their own capability, said Amy Kirby, a CDC microbiologist who leads the surveillance system.

Researchers have been looking for pathogens like polio and influenza in wastewater for years, Kirby said, but “the effort to build the infrastructure has never been worth the return on investment until COVID-19 came along.”

The pandemic left state and local health agencies scrambling to roll out testing as quickly as possible. “So now there’s this patchwork of programs and funding,” she said, “and not all the wastewater surveillance activities in the U.S. are linked to the national system.”

Related: Better ventilation can prevent COVID. Will employers pay for it?

One of the largest players in the private testing market is Biobot Analytics, an MIT start-up that wants to market the technology.

Last year the company raised $20 million. It already has contracts with more than 700 municipalities in all 50 states, according to the Boston Globe, including Hillsborough County. But Biobot does not report that data to the CDC. Instead the company shares the data on its website, using its methodology.

Biobot, which collects data from six Florida counties, said it’s up to local governments to share COVID-19 data with the CDC.

Pinellas County Utilities senior chemist Albert McAfee, left, talks with Pinellas County microbiologist Bina Nayak, right, about testing wastewater for coronavirus levels while on the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system.
Pinellas County Utilities senior chemist Albert McAfee, left, talks with Pinellas County microbiologist Bina Nayak, right, about testing wastewater for coronavirus levels while on the roof of the head works building at the South Cross Bayou Water Reclamation Facility. Wastewater surveillance is a promising technology that scientists can use to detect surges of COVID-19 in communities. But Florida is behind other states in building a statewide tracking system. [ DIRK SHADD | Times ]

The company started collecting Hillsborough’s data in June 2021. A county spokesperson said they haven’t received any reports from Biobot.

The amount of coronavirus detected in Hillsborough’s wastewater has doubled in the past month, according to Biobot’s website. It’s an estimate based on the county’s Northwest Regional Water Reclamation Facility and the city of Tampa’s Howard F. Curren facility.

It’s unclear if Biobot’s data-sharing policy will affect the nation’s wastewater surveillance program. The company took over the federal program on April 15, when it was awarded a $10.2 million contract to oversee the next year of testing.

That contract covers 500 utility providers across the country, according to the CDC. But Biobot and the CDC say the company won’t share COVID-19 data from the 700 utilities not covered by the contract.

Related: White House: U.S. will lose COVID treatments without more funding

The federal government hoped to avoid this jumble of programs by enlisting state agencies to oversee their own surveillance systems, Kirby said. In August 2021, Florida and 32 other states received federal money to establish their own testing, according to the CDC. So far 14 states have done it.

Colorado used $9.4 million of that funding to increase staffing and capacity through July 2023. Officials hope to expand statewide. Colorado’s Department of Health and Environment reports up-to-date data on its website and shares it with the CDC.

Florida Department of Health spokesperson Jeremy Redfern said Thursday in an email that state labs collect sewage samples to identify COVID-19 variants and that officials “helped the utility companies get this project going so they could report to the CDC.”

The state does not report wastewater data, however, and there is no statewide system for doing so. Last month the Times requested the state’s application to obtain the $1.2 million federal grant. The department has yet to provide it.

Edwin Oh, the Nevada microbiologist, said tracking will become more important as the country dedicates fewer resources to future COVID-19 waves.

”The need for contact tracing is really going away for many public health organizations and testing sites are harder and harder to find,” he said. “And that’s exactly why I truly believe that wastewater surveillance will be here to stay.”

Editor’s note: This story was updated with a response from the Florida Department of Health.

• • •

How to get tested

Tampa Bay: The Times can help you find the free, public COVID-19 testing sites in the bay area.

Florida: The Department of Health has a website that lists testing sites in the state. Some information may be out of date.

The U.S.: The Department of Health and Human Services has a website that can help you find a testing site.

• • •

How to get vaccinated

The COVID-19 vaccine for ages 5 and up and booster shots for eligible recipients are being administered at doctors’ offices, clinics, pharmacies, grocery stores and public vaccination sites. Many allow appointments to be booked online. Here’s how to find a site near you:

Find a site: Visit vaccines.gov to find vaccination sites in your ZIP code.

More help: Call the National COVID-19 Vaccination Assistance Hotline.

Phone: 800-232-0233. Help is available in English, Spanish and other languages.

TTY: 888-720-7489

Disability Information and Access Line: Call 888-677-1199 or email DIAL@n4a.org.

• • •

More coronavirus coverage

OMICRON VARIANT: Omicron changed what we know about COVID. Here’s the latest on how the infectious COVID-19 variant affects masks, vaccines, boosters and quarantining.

KIDS AND VACCINES: Got questions about vaccinating your kid? Here are some answers.

BOOSTER SHOTS: Confused about which COVID booster to get? This guide will help.

BOOSTER QUESTIONS: Are there side effects? Why do I need it? Here’s the answers to your questions.

PROTECTING SENIORS: Here’s how seniors can stay safe from the virus.

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