TRavelers are the conduit and canary in the coal mine for new COVID-19 variables, and US health officials are trying to use these facts to keep pace with the changes coming into the country.
At four US airports — John F. Kennedy in New York, Newark in New Jersey, San Francisco International, and Atlanta Hartsfield — the Centers for Disease Control and Prevention (CDC) is partnering with XpressCheck and Concentric by Ginkgo to test incoming passengers for COVID-19. (Washington Dulles is expected to join the program in November.) The test gives the CDC information about which variants are entering the country and which are new that might gain ground and become a threat to the United States.
Since the program began as a pilot in September 2021, about 12,000 to 15,000 passengers each week have agreed to have their noses cleared in XpressCheck At airports, these samples were pooled together and sent to Ginkgo technicians, who run PCR tests for SARS-CoV-2 and genetically sequence only those positive samples. When Ginkgo Labs detect new changes in the virus, they alert the CDC and scientists are closely monitoring changing trends in those mutations. The information is vital to CDC scientists, as it serves as an early detection system to detect new variants that are entering the country and could pose a threat in the future.
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This is what the CDC scientists were first alert to BA.3, which appeared in an airport sample on December 3 – the first report of its kind in North America, 43 days earlier than any other test site – and Bachelor 2That appeared among the passengers on December 14, seven days before further reports. The show was also among the first to pick up on other variants that became important to watch this winter, including Bachelor 2.75.2and XBB and BQ.1.
At the end of August, Cindy Friedman, director of traveler health at the CDC, received a call from a member of her team alerting her to a new mutation, eventually called BQ.1, which at the time was on the cusp of a rapid spread in Europe. New mutations don’t necessarily mean a new variant that could spread more easily or be more virulent, but it is an alert. The group reported all the new mutations it found in the public database of SARS-CoV-2 genes, GISAIDThe team’s report on BQ.1 was the first to identify the variable. Then CDC scientists began learning more about its features to determine how it compares to previous variants when it comes to virulence and transmissibility.
BQ.1 numbers are starting to rise, and as of the beginning of October, alternative It accounts for about 17% of samples among travelers entering the US which suggests this alternative may become one to watch this winter. These numbers are now part of the CDC’s COVID-19 Data Tracker, in a section dedicated to Genetic monitoring of travelers.
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BQ.1 appeared in one pooled sample – these pools typically contain 10 to 25 swabs. In fact, the goal of this project is not to test and track individual passengers with positive tests, but rather to identify potential trends in the emergence and spread of variants. This means that passengers who volunteer to conduct the survey do not need to provide personal information, only information about their flight, where it originated, and where they have traveled to in the recent past. It also means that more people are willing to participate, which is essential for the CDC to get the data it needs to effectively track SARS-CoV-2.
As more people COVID-19 testing at homeIn hospitals, doctors’ offices, or clinics, fewer tests are done, where results are reported to health officials. So health authorities are no longer getting a clear picture of how many cases of COVID-19 there are. This in turn means that they also lose their ability to keep up with SARS-CoV-2 variants – with fewer testing, experts have fewer. genetic sequence From the virus, and a mysterious look at how the virus has changed to evade immunity from vaccines and natural infections. “To understand emerging variables, we need a test,” says Friedman. “We need to close some monitoring gaps, and travelers are coming in from all over the world, so they can fill in the gaps and blind spots caused by testing refusal, reporting and sequencing.”
The program currently includes about 150 flights per week at the four airports. The flights are chosen to represent different regions of the world in order to provide the broadest set of data available on how SARS-CoV-2 has developed, and include 26 countries. Friedman hopes to expand that soon to 500 flights a week. Since there is such a variance in countries’ ability to test their populations, Friedman says the Traveler Program offers the added benefit of providing valuable information missing about COVID-19 trends in countries where the data is not robust. This program is a good source of samples in the face of the global decline in testing. For countries that don’t have good data, they can look at our publicly available data, and see what variables we find,” says Friedman.
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The program is completely voluntary. Early on, subjects who shared free PCR test kits were offered, then rapid antigen self-test kits, as an incentive to spend a few minutes wiping their noses; It now relies on the altruism of travelers from other countries to agree to stop for a few minutes and submit a sample. “You would be surprised how many people care about public health, who understand that it is a public health tool, and are willing to participate,” says Matt McKnight, chief commercial officer at Ginkgo Bioworks. At the airport, XpressCheck is responsible for sample recruitment and collection, and has strategically set up tables in areas where passengers are likely to wait such as baggage claim, or at Uber pickup areas. Ultimately, says Friedman, if the program continues to prove as successful as it does in identifying new variants early, such screening could become a routine part of immigration processing. This would be an ideal way to monitor current and new public health threats entering the country.
Currently, the number of volunteers is producing enough data to prove that the program is worthwhile. But it won’t stop there. To supplement swabs from travelers, this summer Concentric began taking about 1 liter of wastewater from every international long-haul flight at JFK for testing as well. sewage control It has become a valuable tool in helping cities in the US track cases of COVID-19, too VariablesIt can also be an important part of monitoring for incoming pathogens on flights.
That’s the idea behind the Traveler Program – to eventually use it as a way to monitor the comings and goings of not only SARS-CoV-2 but also other highly infectious insects, including flu and any potential public health threats not yet identified. Ginkgo’s team is also working with the State Department’s Defense Advanced Research Projects Agency to develop models to predict the likelihood that the genetic sequences they’re analyzing were engineered in the lab and not appear in nature, as a way to raise red flags for potential biosecurity. threats. “As in cybersecurity, experts monitor security threats continuously and diffusely, looking for anomalies,” McKnight says. “So why not notice public health threats sooner so that we can develop interventions like vaccines sooner?”
Such programs can become a new line of defense against both natural and man-made health threats. COVID-19 was the catalyst that combined the most advanced genetic sequencing tools with the computational power to “discover pathogens that can be used as an early warning system for the detection of many pathogens other than SARS-CoV-2,” says Friedman. “Imagine if this platform stood up again in 2020, how wonderful. This is a way forward to better prepare for the next outbreak or pandemic.”
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