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We still have much to learn about the omicron variant. Since Thanksgiving, federal health officials have been working hard to gather crucial information for the U.S. response. The key to this is increasing the country’s ability to detect the variant within the U.S. populace. Experts are certain that the variant will eventually be discovered, but it is a matter of when and not if. Then, it will be vital to track its spread. Dr. Ashish Jha is the Brown School of Public Health’s dean. “All of the key questions regarding the variant are really dependent upon us being able to recognize the variant here in America, as well as tracking how it spreads and in whom,” he said. Jha and other experts worry that the U.S.’s ability to detect and track the variant is limited due to a few major issues that have plagued the pandemic response since the beginning, such as the patchwork and siloed nature our public health capabilities. “There is a reason why we haven’t heard of the United States variant. It isn’t because it doesn’t exist. It’s because we don’t detect them early,” says Dr. Kavita Paltel, a nonresident fellow at Brookings Institution and physician who practices in Washington, D.C.
Rochelle Walensky (director of the Centers for Disease Control and Prevention) gave a briefing Tuesday in which she defended the agency’s efforts to increase efforts to track down and spot new variants. Walensky stated that CDC has been monitoring variants throughout the pandemic and has greatly increased our capacity for genome sequencing over the past nine month. She also noted that the U.S. now sequences more than 80,000 strains of the virus every week, which is one in seven cases of positive. Walensky stated that “We are actively putting in systems with local and state labs to make detection and sequencing even quicker.” He also said that the U.S. is increasing testing in four major airports: New York City, Newark San Francisco, San Francisco, and Atlanta. These are just a few areas where public health experts see potential to improve U.S. surveillance in both the short- and long-term. PCR testing can sometimes identify the variant. The CDC is asking all labs across the country to increase their efforts to track it. Some PCR tests can detect likely omicron cases, which is a good thing. Dr. David Kessler is the chief science officer for federal COVID-19 response. Some tests can detect a type of signature called S gene target fail. Kessler says that these cases “can be quickly and easily analysed” and that it is possible to prioritize the tests for genetic sequencing. According to Scott Becker (chief executive officer of the Association of Public Health Laboratories), 56 state public health laboratories across the country are currently capable of doing this. Other labs that have the capability are being asked to switch to using this test for two weeks. Jha warns that labs need to start looking for this signal. He says that most labs don’t automatically look at this information. “But that information is within the labs that do regular testing, so we have to be sending out the message that they need look for it and that they must report it to the state health departments or the CDC.”
Accelerate genomic sequencing According to David Kessler, this is on the rise in the U.S. He says, “We have increased our genetic sequencing significantly, close to 10,0000 sequences per day.” Many public health experts believe it’s not enough. Rick Bright, CEO of Pandemic Prevention Institute at Rockefeller Foundation, says that the U.S. has the ability to do better. “They must make a decision to increase their sequencing capabilities, their genomic surveillance capabilities, and perform more testing. Bright says that the problem is that current sequencing may not be distributed geographically and could easily miss cases in regions with limited surveillance. He says that if you focus on the sequencing in very few or very small populations, you can get 10,000 sequences per day from New York City. However, it doesn’t tell what’s happening elsewhere in the country. Walensky stated that the agency has received specimens from all 50 US states, Guam, Northern Mariana Islands (Puerto Rico), the Virgin Islands, and the District of Columbia during Tuesday’s briefing. “We’re sequencing samples in these jurisdictions and from different areas across the country, collaborating closely with state labs, academia, and industry partners, but our variant surveillance system demonstrates we can reliably detect novel variants,” she said. Becker, CEO of the Association of Public Health Laboratories, agrees that the U.S. could do more sequencing. He says that the surveillance system will not be able to process as many specimens in areas where there is less testing. It is important that all states cooperate with CDC to conduct surveillance and increase it if necessary. PCR testing speed should be increased. It appears that PCR as well as antigen tests still work to detect positive cases of the new variant. However, Becker says that the FDA is currently analyzing the samples to confirm this. The problem is that the U.S. does not do enough testing and lab turnaround times can be slow. Bright says that “we need to do more testing to be in a position to identify where this virus exists in the United States.” Bright says that one problem is that many families cannot afford the over-the counter antigen tests. He says that most Americans don’t have the means to access these tests. They are $25 for two kits in many places. We’re already ahead of the curve in making sure more people can test quickly to see if there’s an infection and should move on to sequencing. Patel believes the U.S. should focus on testing and shift resources to “really high-throughput PCR testing,” as PCR tests can be sent for genetic sequencing. She also notes that the CARES Act has money available to support testing that has not been spent. Improve communication between CDC and state labs, academic laboratories, and clinicians. However, even if more labs perform PCR tests that can detect omicrons, detection could still be slow. This is because these labs must start routinely notifying CDC about what they find. Patel, Brookings Institution’s director of public health surveillance, said that the U.S. has been behind in detecting variants during the pandemic because of the “silos” within our public health surveillance system. “The labs that are run by the states or the labs run by the academic centers are isolated from the clinical work that is taking place. She says that the two don’t talk. Bright agrees. He says, “We have a lot more capability and different public labs across the United States. But we’re still not fully leveraging all the sequencing capability in both our academic sectors as well as our private sectors, so we’re not yet linking all that together to get the most information possible.” Kessler suggests that you should track all breakthrough infections.
An increase in these infections could indicate that the omicron variant of the virus is spreading and evading protection. He says that if the virus does indeed enter the United States, he predicts that there will be an increase in breakthrough infections. However, more cases does not necessarily mean more severe cases. “That’s still up-and-coming.” Many experts in public health say that the CDC made a huge mistake by focusing on only those cases of breakthrough infections that can cause death or serious illness. Instead of tracking all cases, they should have been closely monitoring all cases. “I feel that it left us a little flat footed. It means that we are now playing catch-up,” Patel says, explaining that more information could have been obtained about who was gaining breakthroughs and why. Although the CDC does not track breakthroughs in a comprehensive way, it does use “cohorts” which Kessler claims offer “highly reliable” data. However, the most complete data relates only to hospitalizations or death. Bright says that this means that “we’re missing an opportunity to examine the changes in viruses that could lead to severe cases and stop it from happening.” He adds that there is a lot of information left if these cases are not investigated. This report was contributed by Will Stone.