December 6, 2021

Why hasn’t there been a 'US variant'? (Hint: 'It’s not because it doesn't exist.')

Daily Briefing

    Most of the major coronavirus variants have been first detected outside of the United States. However, that may not be because the virus isn't mutating in U.S., but rather because the country's viral surveillance system lacks the ability to quickly detect variants, experts say.

    Covid-19 tested national health systems—and they responded largely as designed

    Lack of a unified surveillance system

    Most Covid-19 tests are able to detect the coronavirus but not which variant it is. That’s because the tests detect parts of the virus that don't typically change, TIME reports. To determine which virus variant is present, a sample needs to be sent out to a lab to be genetically sequenced.

    This has created a blind spot in the United States' surveillance of coronavirus variants, experts say, leaving the country to rely mostly on data from elsewhere in the world.

    "There's a reason we haven't heard of something called the United States variant, and it's not because it doesn't exist. It's because we just don't detect these things early," said Kavita Patel, a non-resident fellow at the Brookings Institution. "They're picked up in other places that tend to have better surveillance systems."

    "To the extent we're constantly relying on Israel, Britain, and now South Africa … that is the definition of flying blind," said Zeke Emanuel, vice provost for global initiatives at the University of Pennsylvania. "We're not going to be the first to determine whether vaccine works, what the breakthrough rate is, et cetera, and that's not because we don't have [omicron] here," he added.

    "All of the key questions about the variant are really dependent on us being able to identify the variant here in the U.S. but also tracking how it's spreading and in whom," said Ashish Jha, dean of the Brown School of Public Health.

    Geographic variations

    According to Rick Bright, CEO of the Pandemic Prevention Institute at the Rockefeller Foundation, genetic sequencing is not well distributed geographically, meaning a case in a region with little surveillance could easily be missed.

    "If you're focusing on that sequencing in very limited or few populations, you can get 10,000 sequences a day from New York City and [that] doesn't tell you what's happening in the rest of the country," he said.

    In some states, genetic sequencing can take longer than the 10 days it typically takes CDC to complete sequencing. For example, the Ohio Department of Health said that the process of "collecting the sample, testing it, sequencing it, and reporting it can take a minimum of 3-4 weeks."

    Over the past 90 days, according to GISAID, Vermont has sequenced and shared roughly 30% of its coronavirus cases while Massachusetts has sequenced around 20%. But six states—Alabama, Kentucky, Ohio, Oklahoma, Pennsylvania, and South Dakota—have sequenced less than 3% of their cases.

    The first omicron case in the United States was picked up in San Francisco because scientists quickly ran a molecular test of a sample taken from a person who recently returned from South Africa and was experiencing mild Covid-19 symptoms.

    California Gov. Gavin Newsom (D) said the discovery was a result of the state having "the most robust testing program and protocols in the nation."

    In a briefing on Tuesday, CDC Director Rochelle Walensky noted that genetic sequencing has increased significantly in the United States. About 80,000 virus samples, representing around 14% of all positive PCR tests, are now sequenced each week.

    Still, some experts say the United States could improve. "I think the U.S. has the capability to do much better," said Bright. "They need to make a decision now to ramp up their sequencing capabilities and their genomic surveillance capabilities and do much more testing."

    How the US could improve its surveillance system

    One way experts say the United States could improve its tracking of omicron is to utilize PCR tests that are able to spot likely cases of the variant.

    "One of the things about this variant is that there is a tell in laboratory tests, so you don't even have to do the full genetic sequencing," said David Kessler, chief science officer for the federal Covid-19 response. Some PCR tests can pick up a signature called an S gene target failure, and in those cases "there is an ability to do an early, quick analysis," Kessler said.

    Jha said it's important that labs start looking for this signature. "Most labs don't look at that automatically," he said. "But that information is in the labs that are doing regular testing, and we've got to be sending the word out that they need to look for that and they need to report that to state health departments and the CDC."

    Experts also say communication between CDC, states, labs, and clinicians should improve. "We have a lot of capability and different public health labs across the United States, but we're not fully leveraging all of the sequencing capability in our academic sectors and our private sectors, and we're not yet linking all of that together to get as much information as possible," said Bright.

    Another way the country can improve its viral surveillance is by tracking breakthrough infections. Currently, CDC only tracks breakthrough infections that cause serious illness and death. According to Bright, the United States is "missing the opportunity to look at the changes in those viruses that could be leading to those severe cases and stopping it before it gets there."

    "There's a lot of information being left on the table by not looking into those cases," Bright added. (Park, TIME, 11/30; Stein/Wroth, "Shots," NPR, 11/30; Owens, Axios, 12/2; Anthes, New York Times, 12/2; Owens, Axios, 12/3; Karlamangla, New York Times, 12/2; Lin et. al., Los Angeles Times, 12/2)

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