In the past year, over 135 million passengers traveled to the U.S. from other countries. To infectious disease experts, that represents 135 million chances for an outbreak to begin. To identify and stop the next potential pandemic, government disease detectives have been discreetly searching for viral pathogens in wastewater from airplanes. Experts are worried that these efforts may not be enough.

The CDC’s Traveler Genomic Surveillance Program tests wastewater from airplanes, looking for pathogens that may have hitched a ride with passengers on long-haul international flights. This program operates with participating airlines at four major airports: Boston, San Francisco, New York’s John F. Kennedy, and the Washington, D.C., area’s Dulles.

CBS News received exclusive on-site access to this program, which launched in September 2021 and has since expanded, thanks to a federal government grant of $120 million.

In the time it takes to unload checked baggage, technicians collect a sample of wastewater from airplane lavatories. A courier ships these samples to a lab operated by private contractors at Ginkgo Bioworks in Boston. Researchers sift through the genetic material captured in each water sample, searching for infectious pathogens.

“We need to go find that needle in a haystack,” explained Alex Plocik, Ginkgo’s Biosecurity Genomics director. “In theory, we can look at almost anything that is a potential biosecurity threat.” 

One day, metagenomic sequencing, a technique used to analyze all of the genetic material in a sample, could allow researchers to detect new, previously unknown pathogens. 

“These technologies are getting better all the time… that day is coming,” said Plocik. However, for now, they are only testing for seven viruses: COVID-19, influenza A and B, adenovirus, norovirus, RSV, and mpox.

Within 48 hours, wastewater testing can alert scientists if a passenger is carrying one of these viruses. 

Ginkgo shares the results with the Centers for Disease Control and Prevention and they’re posted to a public dashboard to keep scientists around the world informed. (The most recent data posted is from Feb. 17. Neither the CDC nor the White House has commented on the program since President Trump took office.)  

Flight paths are tracked, allowing the CDC to see where the virus came from — information that can be particularly valuable when other countries are reluctant to share public health data. Government officials can use this intelligence to shape their public health response, which could include enhanced monitoring, contact tracing, and the administration of vaccines and preventive medications.

But a dozen public health and national security experts consulted by CBS News expressed concern that the U.S. is not adequately prepared for another significant outbreak. While they are encouraged by technological advancements like airplane wastewater testing, some worry that the current program is too limited to reliably detect every incoming pathogen. At present, the CDC’s airplane wastewater testing program is at only four airports, despite the fact that an estimated 333 international airports across the U.S. receive passengers, according to Department of Transportation data.

Last September, CBS News sat down with Dr. David Fitter, the CDC’s director of global migration health, to discuss the program and its impact. When asked if the U.S. is prepared for another pandemic, he paused for more than 10 seconds before answering. “We’ve learned a lot from COVID. We’ve learned that we need early detection. We’ve learned about surveillance systems. We’ve learned about expanding testing capacity so that we can respond faster. We continue to learn, and I think that we are prepared to go forward,” Fitter said.

The coronavirus made its way to the U.S. on Jan. 15, 2020, when a 35-year-old American businessman disembarked from a flight in Washington state after visiting Wuhan, China. Unaware that he was infected, he became the first confirmed case of COVID-19 in the United States. Public health officials are unsure if he was truly the first case in the country, as no tests were conducted on passengers or airplane wastewater at that time.

“Disease doesn’t know geographic boundaries”

The CDC’s airplane wastewater testing program is designed to act as radar for infectious diseases entering the country. 

“Disease doesn’t know geographic boundaries,” explained Fitter. “Our job is to stop disease from entering the U.S., and I think that’s where it’s helping us: we’re able to detect early, respond faster.” 

The CDC is monitoring various outbreaks around the world — including Marburg in Tanzania, Ebola in Uganda, and mpox in the Democratic Republic of Congo — but of these, currently only has the capacity to test for mpox in airplane wastewater.

As a proof of concept, the CDC’s airplane wastewater testing program successfully detected new COVID variants three weeks before they appeared in municipal wastewater and two weeks before a surge in cases at doctors’ offices. This advance warning provides public health officials and healthcare providers with lead time to prepare.

“Early warning could mean the difference between life and millions of deaths,” said Admiral Brett Giroir, President Trump’s COVID testing czar at the height of the pandemic in 2020 and now an infectious disease adviser to Health and Human Services Secretary Robert F. Kennedy Jr. 

While at DARPA years before the COVID pandemic, Giroir looked at wastewater testing as a surveillance tool to determine whether foreign facilities might be producing bioweapons. But he came to realize that wastewater testing had many potential applications. He was a big advocate for wastewater testing programs early in the COVID pandemic. 

“If we see a spike going on, we don’t wait until 300,000 people are in the emergency room. We know right away to raise the flag to get the vaccines up, to get antivirals, to get testing, to get everything started,” said Giroir.

Recently declassified U.S. intelligence warned that “a pathogen can travel from a remote village to a major city in less than thirty-six hours.” 

A report released last spring by the National Intelligence Council stated that the COVID pandemic “strained” global health systems, “diminished” their ability to detect and respond to outbreaks, and undermined public trust in government, reducing people’s willingness to follow public health guidance. The report further cautioned that while COVID was a once-in-a-century pandemic, odds are that it won’t be the last for this generation, noting a “nearly 28% chance that a pandemic at least as deadly as COVID-19 would occur during the decade.”

In January, one of President Trump’s first official actions was to release a new CIA report suggesting that the COVID-19 pandemic was most likely caused by a lab leak in China. The world may never know for certain whether the pandemic originated from an animal-to-human spillover or a lab leak. However, expanding wastewater testing beyond municipal treatment plants and airplane wastewater could help provide answers in the future.

“The lesson I would like everyone to understand is that it doesn’t matter whether it’s natural or a lab leak… BSL-4 laboratories are a risk,” Giroir said. Wastewater surveillance might be conducted in areas where humans come into close contact with domesticated animals or wildlife. “One might even think of doing wastewater surveillance from the BSL-4 laboratory because if a person’s infected, they use the toilet in that laboratory, and you might be able to detect that bug out of the wastewater knowing immediately that somebody got infected,” Giroir said.