A nurse registered for a nose-picking trial after performing a COVID-19 test in Los Angeles, California. Increased testing can help detect and track new variations such as omicrons.
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A nurse registered for a nose-picking trial after performing a COVID-19 test in Los Angeles, California. Increased testing can help detect and track new variations such as omicrons.
Mario Tama / Getty Images
There’s a lot we need to learn – and fast – about the omicron variation. Federal health officials have been scrambling since Thanksgiving to gather critical information to inform the US response.
The key to that is strengthening the country’s capacity to detect variations in the US population. Once it does appear – and experts believe it’s a matter of when it doesn’t happen if it doesn’t – tracking its spread will be crucial.
“All of the key questions about this variant really depend on whether we can identify the variant in the US but also track how Who does it spread and to whom does it spread?
But Jha and other experts are concerned that the US ability to detect and ultimately track the variant is limited by some of the major problems that have hampered our pandemic response from day one. , including the patchy, fuzzy nature of our public health capacity.
“There’s a reason why we haven’t heard of something called the US variant, and it’s not because it doesn’t exist,” said Dr Kavita Patel, a non-resident. I didn’t spot these early.” Brookings Institution colleagues and practicing physicians in Washington, D.C. “They are selected elsewhere tend to have better surveillance systems.”
During Tuesday’s briefing, Rochelle Walensky, director of the Centers for Disease Control and Prevention, defended the agency’s effort to expand its efforts to detect and track new variants.
“Throughout the pandemic… CDC has continuously monitored variations and greatly expanded our genome sequencing capabilities over the past 9 months,” Walensky said, noting that The United States is currently sequencing more than 80,000 virus samples per week, representing one out of every seven positive test results.
“We are actively bringing the systems in with local and state labs to make detection and sequencing even faster,” said Walensky, adding that the US is growing Increased testing at 4 major airports: New York, Newark, San Francisco and Atlanta
Here are some areas where health professionals see opportunities to improve U.S. surveillance in the short and long term.
Take advantage of PCR testing, which can sometimes identify variation
The CDC is asking labs across the country to step up what they’re doing to try to track the variant. The good news is that some PCR tests can detect possible cases of omicron disease.
“One of the things about this variant is that there’s an announcement in the lab tests, so you don’t even notice,” said Dr. David Kessler, chief scientific officer for the federal COVID-19 program. There is no need to perform full gene sequencing. There is a type of marker – called an S gene target error – that some tests can recognize. In those cases, “there is the potential to do early, rapid analysis,” adds Kessler, and then prioritize those tests for gene sequencing.
According to Scott Becker, executive director of the association, about 56 state public health laboratories across the country are currently able to do this, and other laboratories with capacity will be required to switch to using the facility. Use this test for the next two weeks. Public Health Laboratory.
It’s important that labs start looking for this signal, Jha warns. “Most labs don’t consider that automatically,” he said. “But that information is in the labs that are doing routine testing, and we have to tell them that they need to look for that information and they need to report that to the state health departments and the CDC. .”
Advanced gene sequencing
Accurate identification of an omicron case requires detailed genetic sequencing. According to Kessler, this number is growing across the United States. “We improved our gene sequences dramatically, almost 10,000 per day,” he said.
Some public health experts say it’s not enough. “I think the US is capable of doing much better,” said Rick Bright, executive director of the Institute for Pandemic Prevention at the Rockefeller Foundation. “They need to make decisions now to enhance their sequencing and genome monitoring capabilities and do more testing.”
The problem, Bright explains, is that the sequence currently occurring may not be geographically well distributed and can easily miss cases in an area with little monitoring.
“If you’re focusing on that sequence in a very limited or small population, you can get 10,000 sequences a day from New York City and not tell you what’s going on,” he said. in the rest of the country,” he said.
However, during Tuesday’s briefing, Walensky said the agency had received samples from all 50 states, plus Guam, the Northern Mariana Islands, Puerto Rico and the Virgin Islands and the District of Columbia.
“We sequenced samples from these jurisdictions and from diverse geographies across the country, collaborating with state and academia labs and industry partners, and Our variant monitoring system has proven that we can reliably detect new variants,” she said.
But the Executive Director of the Association of Public Health Laboratories, Becker agreed that the US could proceed with more sequencing.
“In areas of the country where there are fewer tests, you’ll see fewer specimens go through the surveillance system and so we won’t be sequencing a lot of samples from those regions of the country,” he said. country. “It’s important that all states work with the CDC to conduct surveillance and strengthen it if needed.”
Increase and speed up PCR testing
It appears that PCR and antigen tests still work to detect new variant positives, just as they did with older variants, although the FDA is analyzing them to confirm that. , Becker said. But the trouble is, Patel and Bright note, the US doesn’t do enough testing, and lab turnaround times are slow.
“We need to do more testing to be able to locate this virus in the United States,” Bright said. One obstacle, he said, is that over-the-counter antigen tests are too much for many families to pay. “Most Americans don’t have access to those tests,” he said. “In a lot of places, they’re $25 for a two-pack. So we’ve been behind the gun right there to make sure that more people can do a quick test to see if they’re infected. no and should proceed to the next sequencing.”
Patel said the US should emphasize testing and shift resources to “really high-throughput PCR testing,” because the PCR test could then be submitted for gene sequencing. She noted that an amount from the CARES Act to support the inspection was no longer spent.
Improve communication between CDC, government labs, academic labs, and clinicians
Even as more labs perform more tests, including the PCR type that can detect omicrons, detection could still be slow as these labs must begin to regularly notify CDC about what they are finding.
Patel of the Brookings Institution said “our public health surveillance system” has kept the US behind when it comes to detecting variations in the pandemic.
“The labs that the states run or the labs that the academic centers run are separate from where the clinical work is going. So the two just don’t talk,” she said.
Bright agrees. “We have a lot of different capacities and public health labs across the United States, but we’re not taking full advantage of all the sequencing capabilities in the academic and private sector. our staff, and we haven’t linked all of that together to get as much information as possible,” he said.
Start tracking all the breakthroughs
An increase in breakthrough infections will be one of the first signs that the omicron variant is spreading widely in the country and evading the protection of a vaccine, Kessler said.
“If it does make it to the US, I predict that we will see an increase in breakout cases, although more breakouts does not necessarily mean more severe cases,” he said. . “It’s still in the air.”
Many public health experts say the CDC made the big mistake of deciding to closely monitor only those sudden infections that cause severe illness and death, rather than track all mild breakouts.
“I think that put us off a little bit,” said Patel. It makes us play catch-up now,” said Patel, explaining that we can learn more about who hit the break and why.
CDC tracks breakthroughs in a limited way, using a “cohort” that Kessler says provides “highly reliable” data, but the most complete data only concerns hospitalizations and dead.
That means, Bright says, “we’re missing the opportunity to look at changes in those viruses that could lead to those severe cases and stop it before it gets there.”
“There’s a lot of information left on the table when not looking at those cases,” he added.
Will Stone contributed to this report.
