CDC figuring out ‘logistical and legal’ aspects of testing airplane wastewater for coronavirus variants, source says

By Jacqueline Howard, CNN

The US Centers for Disease Control and Prevention is ironing out the “logistical and legal” aspects of testing wastewater from airplanes for coronavirus variants as it continues to explore such an infectious disease monitoring program.

The agency is still “figuring out how to operationalize this program,” a person close to CDC discussions said, adding that there are “logistical and legal” hurdles that need to be sorted out before the program “would be operational.”

Some of the agency’s partners tell CNN that they are poised to help roll out this potential next frontier in the nation’s COVID-19 surveillance effort.

Monitoring sewage for traces of coronavirus variants is a “validated” scientific process — no longer in its pilot phase — and airplanes are a logical next step, said Matt McKnight, general manager at Boston-based synthetic biology company Ginkgo Bioworks. Its Concentric by Ginkgo biosecurity and public health unit has been chosen to partner in the CDC’s traveler-based genomic surveillance program to detect COVID-19 and flu variants among international travelers.

For now, the use of testing services to collect and analyze airplane wastewater for variants “is an active conversation between CDC, the White House and the airlines,” McKnight said.

But the process of testing airplane wastewater itself is “validated methodology, and it is a program that can be run actively,” he added. “The system is ready to go.”

How wastewater monitoring works

Testing aircraft wastewater involves collecting sewage from individual passenger-carrying commercial airplanes.

“You can pull it off the airplane in under two minutes, quickly put it into a lab network, which we manage all of that,” McKnight said.

Once those wastewater samples arrive at a diagnostic lab for testing, scientists scan them for traces of known or unknown viruses, such as emerging variants of SARS-CoV-2, the coronavirus that causes COVID-19. When samples test positive for the virus, scientists conduct genome sequencing to identify exactly which variant that virus is.

“Usually, sequencing takes about five to seven days,” said Casandra Philipson, a researcher and program lead for Ginkgo Bioworks. Then, scientists may analyze their results and submit their findings to the CDC.

“We can do analysis really quickly,” Philipson said, such as in a few days. “And then return results immediately.”

Both McKnight and Philipson said that airplane wastewater surveillance not only can help with detecting emerging coronavirus and influenza variants — serving as a “radar system” — it can alert vaccine makers to which variants our COVID-19 shots might need to target each year.

Advisers to the US Food and Drug Administration are scheduled to meet this week to discuss COVID-19 vaccines becoming annual immunizations, similar to the seasonal flu vaccine.

That process could include streamlining the vaccine composition, immunization schedules and periodic updates of vaccines, according to meeting documents posted Monday. The FDA has said it expects to assess circulating strains of the coronavirus at least annually and decide in June which strains to select for the fall season, similar to the process of updating annual flu vaccines.

“If you give Moderna or Pfizer information early enough, they can make a vaccine really quickly, which we couldn’t do at the beginning of the pandemic,” McKnight said. “The big lesson learned is that you can think about all of these variants of viruses circulating around the world, and it’s kind of like anything else we would have a radar system for, to detect what is out there so you can get an early warning.”

A ‘valuable component’

A report released last week by the National Academies of Sciences, Engineering and Medicine describes wastewater surveillance as a “valuable component” of infectious disease management and notes that wastewater surveillance at major US airports and ports of entry could help identify initial cases for pathogens from other regions among international travelers. The report was produced at the request of the CDC.

A separate study conducted in the United Kingdom, published last week in the journal Plos Global Health, found that the majority of 150 wastewater samples collected from terminals and additional samples from 32 aircraft at three major international airports in the UK in March 2022 tested positive for SARS-CoV-2. The data included three terminals total — one at each airport.

All samples taken from sewers at the arrival terminals of Heathrow and Bristol airports, and 85% of samples taken from sites at Edinburgh airport, were positive for the virus, according to the study.

“I was not surprised that we found SARS-CoV-2 RNA in those wastewater samples. This was a proof-of-concept study: being able to detect the viral RNA in the samples proved that our methodology works, which was a positive outcome,” Kata Farkas, an author of the study and researcher at Bangor University in the UK, said in an email Tuesday.

“In our study, we used PCR-based detection, but other studies have utilised sequencing successfully for these types of samples. Therefore, variants can also be identified in aircraft/airport wastewater, supporting other types of surveillance programmes to better understand which variants are circulating globally,” she wrote. “It is worth noting that the methodology we described can be used for the identification of other viruses that may threaten global public health.”

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