A NYC subway stationRichard B. Levine/Levine Roberts/Zuma

This story was originally published by Undark and is reproduced here as part of the Climate Desk collaboration.

It all started when Christopher Mason’s 3-year-old daughter licked a subway pole.

Like any parent, he was horrified, but also keenly curious: What types of microbes might be clinging to a metal pipe gripped by countless commuters every day?

Mason, a geneticist at Weill Cornell Medicine, soon became obsessed with that question. His toddler’s gross interlude inspired him to embark on a journey to unveil the world of bacteria, fungi, and viruses co-mingling with more than 8 million people in New York City’s urban jungle.

In 2013, he launched a project that began dispatching a small army of students shouldering backpacks crammed with latex gloves, vials, and sterile Q-tips. They sampled turnstiles, benches, and kiosks at every open metro stop in the city. It was an expedition into a largely unexplored terrain, like Mars or a deep-sea canyon, brimming with lifeforms both familiar and unknown.

The swabbers were sampling what’s called environmental DNA, or eDNA, representing the assortment of cells that all humans, animals, and microorganisms naturally shed as they go about their everyday lives, leaving genetic fingerprints. The scientists gradually quantified and mapped the unseen biological diversity—the microbiome—of the entire city.

In 2015, they reported that they’d found more than 1,600 different types of microbes, nearly half of which were previously known to science. Most were harmless, associated with human skin and gastrointestinal tracts. About 12 percent were known pathogens, including fragments of genomes similar to Bubonic plague and anthrax, though there was no evidence that these small bits could make anyone sick. They hadn’t found any new deadly viruses lurking in New York’s underground—yet.

Four years later, in late 2019, Mason and his colleagues started hearing about a mysterious pneumonia-like disease circulating in China. “We weren’t immediately worried,” he said, “but by January it was clear that it had jumped across the ocean and was spreading.” Suddenly the subway swabbers became front-line workers monitoring Covid-19’s presence, not only in transit systems, but also in hospitals, and wastewater. “We had a new medical focus,” Mason said, “with protocols and tools that could be deployed anywhere.”

Today Covid-19 has killed nearly 80,000 New Yorkers, almost 1.2 million Americans, and nearly 7 million people worldwide. The pandemic catalyzed a push for new technologies that allow scientists to quickly characterize organisms leaving a genetic trace in the environment. Similar to how city-leveling hurricanes have fueled innovations in weather surveillance and building engineering, the pandemic has helped propel the science of pathogen hunting.

The field of eDNA research has mushroomed in the last 15 years as sequencing, computing technology, and metagenomics—the study of DNA from multiple organisms—has advanced. Now, scientists around the world can sample from a cup of dirt, a vial of water, or even a puff of air, and survey the eDNA present for thousands of microbial species. And while the field at-large has faced concerns about privacy and technical limitations, many scientists see an opportunity to further early detection of emerging pathogens. Wastewater surveillance is the most advanced method for monitoring population-level virus spikes, but other realms are catching up. As a result, health officials are becoming better prepared to detect an outbreak—and quickly take steps to contain it.

Experts say the technology may soon become so advanced that an environmental sample, such as air filtered from a high-risk area—a wet market, a hospital, a conference hotel—could be automatically sequenced in a portable device that will report if a threatening pathogen is present. Researchers are using genomic databases to aid rapid identification of pathogens and other microbes. Scientists are getting close to “being able to monitor these high-risk interfaces in real time,” said Erik Karlsson, a virologist at Institut Pasteur du Cambodge, a nonprofit research institution in Cambodia.

The ultimate goal in virus hunting is an early warning system: to find a pathogen that could spark a disease outbreak before it has the chance to do so. The key, say scientists, is monitoring high-risk areas where animals and people intermingle. Those places are usually on the boundaries between areas where humans live and tropical forests, where people hunt and capture animals for food, pets, and ingredients in medicine, or in markets where animals are slaughtered for consumption.

“We like to say, we’re trying to get left of sneeze,” said Karlsson, who monitors for avian influenza and other pathogens in Cambodia’s live bird markets. That means they’re trying to identify potentially threatening pathogens before they spill over into humans, or before they jump into a different animal type and causes an outbreak. “We want to be able to get ahead of that,” he said.

Studies........

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