On a street corner in Chelsea last week, public works employees opened a manhole cover and pulled up a container hanging underground by a rope. Inside, a device had been pumping up samples of the wastewater flowing below every 15 minutes for the past 24 hours. They sucked up some of the cloudy wastewater with what looked like a turkey baster and transfered 50 milliliters into each of 3 test tubes.
As the number of COVID-19 cases in Massachusetts continues to rise — and even as more people get vaccinated — health officials are scrambling to figure out the impact of newer, more contagious variants of the virus.
A company called Biobot is testing weekly to see if COVID-19 is in the wastewater flowing from the homes in this neighborhood. And if it is, they’re checking to see if the virus is B.1.1.7 — a more contagious variant first detected in the U.K. It’s become the dominant strain in the U.S., and it can lead to more severe illness and is less responsive to therapies.
"Yeah, we're providing firsthand evidence on what's under here, on how the current state of Chelsea is doing," said Chelsea public works employee Alex Arroyo as he captured a sample.
What they're finding isn't good.
The coronavirus has been in Chelsea’s wastewater consistently since November. And for the last three weeks that they’ve been checking for it, they’ve found B.1.1.7, the UK variant.
The city is partnering with the Metropolitan Area Planning Council and the nonprofit Center of Complex Interventions to support the wastewater monitoring program.
Not far away from where they gathered that wastewater, Massachusetts General Hospital set up a mobile COVID-19 testing site in Bellingham Square last week.
Dr. Priya Sarin Gupta of MGH took out her phone to show what Chelsea neighborhoods the wastewater testing showed were having coronavirus spikes.
“And that's what informed where we would be this week with the testing van," she said. "If you look at this graph, it shows the spike in Crescent and Hawthorn sewershed areas."
Most communities aren’t doing the kind of localized testing that Chelsea is. Cambridge is one of the few other cities using this technique, and officials there have found B.1.1.7 in the wastewater too. The variant is also showing in tests of the MWRA water system, but the data doesn’t specify which of the 61 cities and towns it’s showing up in.
Right now, researchers don’t really know much about where in the state these dangerous variants are spreading.
Starting this week, Biobot says it will be able to say what percentage of the virus they find is that U.K. variant. And sometime soon, they hope to be able to identify other spreading variants — like the ones from Brazil and South Africa. The new information is coming at a pivotal moment.
"This is a very fragile moment where we are racing to vaccinate people,” said Dr. Regina LaRocque, an infectious disease physician at MGH and an associate professor at Harvard Medical School. “But at the same time, we are seeing a surge in the variants."
As of last Thursday, the state had confirmed 1,110 cases of B.1.1.7, as well as 102 cases of P.1, the Brazilian variant — the highest rate in the country following an outbreak on Cape Cod.
The actual numbers of cases is likely much higher. Another challenge in tracking the surge is that the vast majority of positive COVID tests in the state are not analyzed to see what variant they are.
"We're testing about one, or just over one percent of positive cases in the state,” said Dr. Bronwyn MacInnis, director of Pathogen Genomics Surveillance at the Broad Institute, which the state has contracted to analyze the DNA of tests to detect the variants. “And that is pretty low, lower than we want to be. But it's higher than we were for the rest of the pandemic before that. And the number is increasing quickly."
Even with limited data, the Broad Institute estimates about 18% of Massachusetts’ cases are B.1.1.7.
MacInnis said the U.S. has lagged other countries in doing this kind of genomic testing.
"Certainly there wasn't a real national strategy or significant funding for doing this,” she said. “It was not something that was given a lot of attention through much of the pandemic until recently."
Now that the variants are on the rise, scientists and public health officials are busy trying to catch up.