The global search for new variants of Covid reaches the bathrooms of airplanes

At the same time, after a successful test at New York’s JFK Airport, the Centers for Disease Control and Prevention is continuing discussions with airlines and port authorities to begin collecting samples of wastewater from flights long-haul international flights after landing.

The small but growing traveler genomic surveillance program, run by the CDC with a biotech company and a company that collects samples, is seen by administration officials and public health experts as part of an infrastructure revolution of biosecurity and a critical panel of national security in the post-pandemic era. As it expands geographically and looks at new pathogens, it could function as an early warning system for where and when dangerous viruses and bacteria, natural or otherwise, enter the country.

“Just like we have radar to look for planes to make sure we know what’s coming into our country, or we take swabs and samples to make sure someone going through security doesn’t have explosives on their hands, that’s the same for pathogens. or viruses or bacteria,” said Matthew McKnight, the CEO of Ginkgo Bioworks, the biosecurity and public health unit of Concentric by Ginkgo, which is partnering with the CDC on the program along with XpresCheck.

In Omicron’s early days, the program detected both the BA.2 and BA.3 subvariants weeks before they appeared elsewhere in the U.S. In the pilot project at JFK, in which staff collected wastewater samples in flights arriving from Europe in August and In September, the program identified the same sequences of SARS-CoV-2 in the wastewater circulating predominantly in the countries of origin of the flights.

Since the program was stepped up in response to the China outbreak, the CDC says it has found no new variants in viral samples from passengers from China. “So far, reassuringly, we’re seeing BA.5.2 and BF.7, two lineages that have been reported from China, which are nothing new or worrisome,” said Cindy Friedman, chief of the CDC Travelers Health.

The program now covers around 500 flights a day from around 30 countries. It’s voluntary: Arriving passengers, after customs, can stop at a booth, answer a few questions and give a nasal swab to program staff. The samples are then sent to a laboratory in the Ginkgo network for testing; if they’re positive, Ginkgo sequences them, analyzes them and reports that information to the CDC, which shares it in a global database and in the agency’s COVID data tracker.

Participation has grown rapidly since the CDC began monitoring more flights last month. The week of January 2, for example, about 4,500 passengers at the seven airports where the program now operates volunteered to give samples, compared with about 2,700 the previous week.

However, given international flight traffic, it is still relatively low and has the inherent disadvantage of targeting a self-selecting group that may generally be more cautious about Covid.

“Trusting people to volunteer to get tested for Covid at this stage of the pandemic is really challenging,” said Megan Diamond, director of global health partnerships at the Rockefeller Foundation. “You’re going to have a biased sample. “The people who do that are the people who are most likely to get an antigen test before they leave home.”

Expanding to include routine sewage sampling at airports would widen scientists’ lens on bugs entering US soil. It does not require the purchase of passengers, and the operation requires less personnel in the complicated airport environment, so it is less expensive.

Finally, the CDC envisions the two strands of the traveler surveillance program—voluntary sample collection and wastewater monitoring—connecting with other countries that are beginning to do the same, feeding a global system that provides a picture in real time of how travelers . We carry diseases all over the planet.

“We want to know when a new variant arrives or increases rapidly, and these are the tools that will help answer those questions,” said Tom Inglesby, director of the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health. “Otherwise, we’re just waiting for these things to pop up in cities. … This is trying to get that much further ahead to get the signal as quickly as possible.”

“The dream of biosecurity infrastructures”

The CDC program fits into the Biden administration’s broader vision to use lessons learned during the Covid pandemic to strengthen the nation’s defenses.

The administration is already using the extensive network of public health laboratories, testing sites and domestic wastewater surveillance established during the pandemic to collect virus samples and analyze them to learn which variants of SARS-CoV-2 are circulating in the USA wants the White House. . to see that this network, which includes the traveler’s genomic surveillance program, went to work looking for other threats.

Building on that infrastructure will be “really important to the long-term biosecurity of our country,” White House Covid-19 response coordinator Ashish Jha told POLITICO.

The CDC program has already added a new virus to its watch list: the flu. This winter, given the unusual flu season in several countries, Ginkgo began testing passenger samples for influenza A and B viruses, in addition to SARS-CoV-2. It has shared positive samples with the CDC for sequencing — information that could be used in vaccine development for the upcoming flu season.

It’s the kind of pivot that would make the program’s expansion to more airports and aircraft wastewater a national security asset after the pandemic ends, Ginkgo’s McKnight said.

“You want to be able to detect genetic variants of Covid. You want to be able to detect genetic variants of other threatening pathogens that may appear, known and unknown. And you want to have the ability to look for genetically modified organisms released by mistake, or things released on purpose, and then you can deploy it in places where you’re worried about things popping up,” he said. “This is the dream of biosecurity infrastructure. And it’s totally doable.”

Since Beijing abruptly lifted its “zero-Covid” policy last month, several other countries have also begun to think more about landing biological information in airplane toilets.

The European Union recently said it is looking into testing and sequencing aircraft and airport wastewater, and this month Canadian biotech firm LuminUltra announced it was launching a wastewater pilot project at Pearson International Airport in Toronto to test SARS-CoV-2 and mpox variants. in wastewater from airplanes and airport terminals.

Ginkgo recently signed an agreement with the government of Ukraine, which has seen an increase in infectious diseases due to the pandemic and the ongoing war with Russia, to establish a pilot wastewater testing project that will monitor SARS -CoV-2 and the flu. The company is also in the process of developing aircraft wastewater monitoring programs in Rwanda and Qatar.

“It’s pretty cool to see other places emulating what has been a two-year CDC program,” McKnight said. “You start to see these other countries say, ‘Wait, this is a good way to do it.’

“It’s always hard to be the first”

Getting U.S. airlines and airports to agree to let the government examine their customers’ waste will take some effort, the CDC acknowledged.

“We know this works,” said the CDC’s Friedman, who is talking to “global partners” and U.S. airports where the program is already collecting nasal swabs on airplane sewage tests. The JFK pilot project “showed that we could detect sewage sequences,” he said.

But, he added, it is a challenge “to get the cooperation of all the different entities… We are in talks with airlines and airports to get permission to take a sample of the sewage.”

Ginkgo’s McKnight, who is also talking to airlines about the technology, said there hasn’t been an outright backlash from the industry, but airline executives have been cautious.

The Rockefeller Foundation’s Diamond said the airlines involved could be taking a reputational risk because it could focus on the fact that there are people on their flights infected with Covid, or because some passengers can see the analysis of the your waste as a privacy issue.

“It’s always hard to be the first to do something that has pros and cons,” Diamond said.

The government and the airline industry need to make the case to the public, he said, telling people that by letting the government approve their waste, they help keep everyone safer.

“If we do robust monitoring of wastewater, in communities, in hospitals or schools or on an airplane, I have no doubt that we will be better equipped to detect threats, respond to them faster and save more lives,” he said. .

Adam Cancryn contributed to this report.

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