Three days before Thanksgiving, a plane loaded with passengers from South Africa landed in San Francisco. One was a woman who was in the early stages of a Covid-19 infection, although she won’t know for almost a week.
It happens to be the same day that scientists 10,000 miles away in Botswana and South Africa started alerting the world to a new, highly mutated version of the virus that causes Covid-19.
Alexandria Boehm, a professor of civil engineering at Stanford University, learned about the usual pattern of mutations in the yet-to-be-named variant and sprang into action.
For more than a year, Boehm and his 45-person team at the Sewer Coronavirus Alert Network, or SCAN, have been collecting and testing sludge samples daily from wastewater treatment plants in Northern California, looking for fragments of the new coronavirus.
Wastewater-based epidemiology has proven so reliable in dozens of pilot projects across the United States that the government has invested millions to create the National Wastewater Surveillance System, or NWSS, a network of 400 testing sites across 19 states and coordinated by the US Centers for Disease Control and Prevention.
Boehm’s SCAN has been part of this network, which has been operating quietly behind the scenes, generating data for public health departments across the country, since September 2020.
For the first time, the CDC will release data on how much coronavirus is showing up in the nation’s sewage. It will add this test data to its Covid-19 dashboard.
Testing shows there has been a decrease in the amount of virus at two-thirds of the NWSS’s 400 sites from levels measured 15 days ago, according to a CDC official familiar with the schedule.
More than 500 sites will begin submitting data in the coming weeks, according to the CDC. A press conference on the surveillance system is scheduled for Friday.
Data from anywhere with a sewer connection
SARS-CoV-2, the virus that causes Covid-19, is enclosed in an oily envelope. After invading our bodies and starting to clone themselves furiously, some of these copies are released into our intestines, where the fatty parts of the virus stick to the fats in the stool. When we poop, the genetic material of the virus is flushed down the toilet into the sewage stream, where it can be detected by the same types of tests that labs use to detect the virus from nasal swabs: real-time polymerase chain reaction, or RT-PCR.
This type of test is very sensitive. It can detect the presence of the virus when only one in 100,000 people in a given area, or sewer, is infected.
And because sewage testing doesn’t depend on people realizing they’re sick and seeking a test, or even having any symptoms at all, it’s often the first warning a community has that the wave of Covid-19 infections is on its way.
The CDC estimates it takes five to seven days after a flush to get sewage data into its COVID Tracker, and samples typically turn positive in an area four to six days before clinical cases appear. .
“As long as people use a toilet connected to a sewer, we can get information about these cases in this community,” said Amy Kirby, a CDC microbiologist who leads the NWSS project.
Government investment has taken what was a little-known branch of public health and brought it into the mainstream.
“It really blew up the field,” said Colleen Naughton, a civil engineer at the University of California, Merced, who leads the @CovidPoops19 Twitter account. “We did sewage monitoring for other pathogens before that, like poliovirus, but it’s really, the number of people involved in everything has really increased exponentially.”
Speed is key to making wastewater testing useful. So when Boehm heard the gravity behind the alerts of a new variant emerging 10,000 miles away, she wasted no time.
“It all happened very, very quickly, right around Thanksgiving and the holidays, which is a really awkward time for things to happen,” she said.
SCAN – a partnership between Stanford, Emory University and the University of Michigan – worked long hours to change the monitoring system into a new test.
The Monday before Thanksgiving, Boehm alerted his team to the new variant. On Tuesday, they uploaded the handful of genetic sequences of the new variant that had been sent to GISAID, a website used by researchers around the world to share information about the novel coronavirus. They began designing a test that could pick up many of his telltale changes, including amino acids that were removed from a piece of sites in his spike protein and the addition of three amino acids to another location on his point.
Boehm ordered supplies: the chemical probes they would need to run their new test. She knew delivery could take weeks, but she says they were lucky and got the new chemicals in just seven days.
But it wasn’t just luck. She had done this several times over the past year, first for the Alpha variant, then for Beta, Gamma, Delta, and Mu.
While they waited for the supplies, Boehm dusted off an older test his team had used to find signs of the Alpha variant. Like Omicron, Alpha lacks certain amino acids at a key location on its spike protein. These deletions cause a pattern on lab tests called s-gene target failure.
“We knew Alpha was pretty much extinct. It’s extinct in our area,” she said. This meant that any Alpha test successes were likely the new variant.
Thursday, Thanksgiving, they got their first hit. A sample from Merced tested positive on the old test.
On Friday, the World Health Organization named the variant they were looking for, Omicron, and officially listed it as a variant of concern.
The following Tuesday, another sample — this time from Sacramento — tested positive, and on Wednesday Governor Gavin Newsom and the CDC announced that the first American had tested positive for Omicron in San Francisco.
The woman had recently traveled from South Africa and landed in San Francisco on November 22. She did not seek to get tested until almost a week later, on Monday November 28, four days after the first sewage sample at Merced came back positive.
In the days that followed, more positive samples arrived from Sacramento.
And in Santa Clara County, they got their first hit in Palo Alto on Dec. 7, the same day a person living in the same sewer became that county’s first case.
What started as a trickle of positive samples quickly became a steady stream. On December 16, the Santa Clara County Health Department held a press conference to warn the public based, in large part, on what it was seeing in sewage data.
“When I look around the corner, what I see is a deluge of Omicron. What I see is one of the toughest times we’ve ever had in the pandemic,” said Dr Sara Cody , director of public health for Santa Clara County.
The limits of wastewater analyzes
CDC’s Kirby says the system worked well for Omicron’s arrival in California. Colorado, Houston and New York. She published an overview of these efforts in the Morbidity and Mortality Weekly Report on January 21.
“What we hear most often is that our partners in the health department say it gives them confidence to know what’s going on in their communities. So really, are cases going up or down? And that’s because it’s completely independent of health care and clinical testing,” she says.
Kirby says it’s also a useful tool for letting counties and cities know where to direct limited resources.
“So if you have, for example, mobile testing capacity and you want to decide which communities could use that extra testing capacity the most, wastewater monitoring is really useful for that,” she says.
There are blind spots in the system. Although 80% of homes in the United States are connected to sewers, the remaining 20% rely on septic systems. These homes, which are mostly in rural areas, would not be covered by the tests.
Wastewater analyzes are also more difficult to interpret and less useful in areas where people come and go often, such as tourist destinations.
It is also difficult to compare data between sewer basins because different areas use different sampling methods. Some take samples directly from the water with thin cotton swabs encased in 3D-printed submarines, while others collect and sample biosolids. Sewers can be of very different sizes, which also complicates comparisons. The new CDC dashboard displays data at the zip code level.
Finally, this type of test cannot signal when a community is free of the virus because the detection threshold – how many people need to be positive in an area to show up in a water sample – is not known.
For these reasons, the CDC says wastewater surveillance is best used with case-based surveillance.
To avoid direct comparisons, Kirby says, the dashboard will compare each site to its own past results. The primary measure will be the percentage change in concentration at the same site over the past 15 days. The other metric that people will be able to see is the number of detections in those same 15 days, the number of samples that tested positive.
“As you can imagine, right now it’s not a very useful metric because everywhere is positive. But as cases come down and we see much lower rates, it will become the metric you want to follow up to see if SARS-CoV-2 reappears in your community,” Kirby said.
Kirby says sewage monitoring will be around long after Covid is gone too. By the end of the year, the CDC plans to expand the number of pathogens tracked on the dashboard to include influenza, a fungal superbug called Candida auris, and foodborne threats like E. coli. and salmonella.
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