New Yorkers know the subway can be nasty, but COVID-19 has made riding the rails dicier than usual.
As I write this, New York City is getting hit harder than any other metropolis. In the past 24 hours, 365 residents died of COVID-19. “The rate in the next few days [will] continue to go up,” Francisco Moya, a New York City councilmen, told The Guardian.
How much coronavirus is out there? Are handrails, Amazon packages, and elevator buttons all contaminated? How would we know?
It turns out that several industries—commercial kitchens and breweries, for example—rely on what’s called “environmental sequencing” of surfaces and door handles. They do this to keep dangerous bacteria and viruses from getting anywhere near your food to begin with. Experts are now applying this technology in the search for the new coronavirus.
I spoke with three such experts this morning during an online town hall I hosted to understand how we can track and respond to coronavirus within our built world. Cornell professor Christopher Mason has swabbed the NYC subway system before with surprising results. Now, with help from Twist Bioscience’s NGS Target Enrichment tools for coronavirus, Chris is sampling the public transit system to see if and where the novel coronavirus is residing. Chris was in conversation with Twist CEO Emily Leproust, as well as Josh Perfetto, founder and CEO of Chai Bio, which makes tools like Open qPCR accessible to researchers everywhere.
Here’s what they had to say.
How do we detect viruses in the environment?
“Everywhere we go is a living ecosystem,” explained Mason, who famously studied astronaut poop to look for differences in the microbes of people living on and off Earth. (Yes, even the International Space Station is home to various germs.)
Mason has been swabbing different parts of the New York City subway since 2013. His motivation? “When my daughter got old enough to ride the subway, she did actually one day lick a subway pole, which I was terrified about. So I really wanted to know what was there.”
Mason is now part of a consortium of scientists who are swabbing urban environments around the world. In 2019 they nabbed 9521 samples from every continent except Antarctica, including 647 samples from New York City. Normally samples are collected as a snapshot every summer. This year, the swabbing has started early.
“We don’t have any good, solid evidence that there is SARS-CoV-2 [the virus that cases COVID-19] in the subway,” Mason reported this morning. “We just have a very limited data set so far, but the collection has ramped up.” Collections to monitor SARS-CoV-2 began two months ago and has expanded to 59 cities.
“We are going to post a lot of this study into a preprint,” he said. Preprints are an increasingly popular way for scientists to quickly share their findings before they have gone through the lengthy peer-review process. “I was hoping it would be online by today, but it is probably going to go on early next week.”
Once collected, samples from the environment can be studied in different ways. Depending on how a lab does the processing, it can take 30 minutes, three hours or up to three days to get a result. Researchers generally scrutinize the genetic material in a given sample, then attempt to back-calculate which microbes or viruses it came from.To detect the presence of SARS-CoV-2 in a subway swab, a so-called RT-PCR protocol is often performed. This test takes a few hours and can give a definitive answer as to whether intact genes from the virus were present at the time the sample was collected. The same technique is used to detect the virus in patients.
“The biggest danger of swabbing in public places is that some people think correctly that you are just collecting a sample [while] other people think you are leaving something, which can be technically a crime.”
Synthetic DNA to the Rescue
Critical to this work are reliable controls. In order for Mason to know that his instruments are working properly, and that their findings can be trusted, the team relies on synthetic DNA molecules made by Twist. If those positive controls fail to produce a signal, something must have gone wrong inside one of the sample processing labs.
“At Twist we have built a platform based on silicon to write DNA,” explained Twist CEO Leproust. “There are a number of applications for that. One of them is in diagnostics, so you can understand the genetic make-up of a sample.”
While widely used RT-PCR tests give researchers and public health professionals a clear yes/no answer about the presence of the virus, “the next step is [that] you may want to know what exactly is that virus — are there any mutations in that virus compared to what is known?”
No environmental sample (especially one from a subway seat) is pure. Each swab draws up a multitude of microbes, most of which are perfectly benign. Human cells can even wind up in the tube. To make sense of all this overlapping genetic material, and to fish out any dangerous viral information, Twist has developed what it calls a ‘coronavirus target enrichment probe.’ This molecular tool acts like a magnet, attracting just the virus’ genes and letting human genetic material and other contaminants wash away during processing. The net effect? A cheaper experiment that produces more reliable sequencing results.
“We’ve compared the Wuhan coronavirus versus the Australian coronavirus, and there are ten bases that are missing in the Australian version,” said Leproust. Bases are the individual letters of the genetic code.
Scientists are still racing to understand what these changes in viral spelling may mean, but now, Leproust says, “we can do this at scale.”
Making Environmental Detection Easier
Chai Bio founder and CEO Perfetto believes in that vision, but doesn’t want costs to stand in the way. “We focus on making [RT-PCR] lower cost and easier to use. For example, we have people using this in food safety applications, in breweries where they look for beer-spoilage organisms [and] water quality — for everything under the sun.”
In response to the global pandemic, Chai Bio has rolled out new products and protocols for wide-spread environmental detection of SARS-CoV-2. These include everything needed to both collect samples and perform experiments at home.
“If you are able to do that, you can then take mitigating actions,” said Perfetto, whose products are intended for research use only and have not been approved for clinical diagnosis.
As is the case with coronavirus infections in people, the true extent of the spread of SARS-CoV-2 is almost certainly much larger than anyone has been able to measure. Expanded environmental sampling would help shed light on the truth of this pandemic.
Do you really want to know?
Knowing which microbes linger on door handles and subway poles can be a little disconcerting. When researchers swabbed a random seat on the Bay Area’s rapid transit system in 2011, they found MRSA and other serious antibiotic-resistant pathogens riding along with passengers, creating headlines. Some felt compelled to stand instead of sit on the train ride home. Chris acknowledges that, generally, people just don’t want to know.
“I prefer to run towards information rather than away from it,” he says. “But at the end of the day, it’s a personal choice.”
Whether individuals choose to look closely at the data, these testing technologies represent important new tools for informed public health policy.
Thank you to Ian Haydon and Kevin Costa for additional research and reporting in this article. I’m the founder of SynBioBeta, and some of the companies that I write about—including Twist Bioscience—are sponsors of the SynBioBeta conference and weekly digest — here’s the full list of SynBioBeta sponsors.