• December 5, 2021

How Fast Can Scientists Find the New Coronavirus Strains?

“We are really behind in terms of having geographically representative data,” says Kelly Wroblewski, the director of infectious disease for the Association of Public Health Laboratories. She sees the failure as the inevitable outcome of the Trump administration’s decision to leave nearly every aspect of the coronavirus response up to individual states—from ramping up diagnostic testing to rolling out vaccines. “There was no national sequencing plan, because there has not been a national much-of-anything plan,” she says.

Of the more than 21.5 million Covid-19 cases officially reported in the US, samples from just 59,438 people, or less than 0.3 percent, have been sequenced and analyzed for variants, according to GISAID. By contrast, the UK is regularly sequencing more than 10 percent of its Covid-19 cases. That allowed British public health officials to monitor in real time as the B.1.1.7 variant went from being a rare find at the beginning of December to dominating new infections three weeks later. The Brits might be an outstanding example in this regard, but they’re not alone. According to a recent Washington Post analysis, 42 other countries have sequenced more cases than the US, despite the fact that Americans account for a quarter of all coronavirus infections globally.

“What the US is doing right now is completely inadequate,” says Chiu. He thinks American government officials should be setting their sights on that 10 percent threshold. But the effort will undoubtedly be complicated by the fractured US health care system. In the UK, which has a single nationalized health service and a supporting microbiology service, it’s relatively easy to flow samples and data. In the US, the private sector still dominates the testing market. In order for a sample to show up in Chiu’s lab, he says, it has to go from a commercial lab to the county lab and then to the state lab before it gets to him. That can take weeks—if it even happens at all. Often, by the time a public health department epidemiologist comes across a case they want to investigate with genetics, the original sample has already been discarded. “The rate-limiting step isn’t sequencing; it’s really getting the sample,” says Chiu. “That’s why we have to empower state and county labs to do it in-house, so we can get the data out faster.”

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Over the last decade, public health labs have built up their sequencing capacities as part of their role in tracking outbreaks of foodborne illness across the US. Every state lab, as well as a handful of large regional ones, has the technology readily available, according to Wrobleski. But they haven’t been able to deploy it widely during the pandemic because they’ve had their hands full just trying to conduct basic diagnostic tests and contact tracing, she says. And until a few weeks ago, they hadn’t been given marching orders to do anything differently.

But that’s finally starting to change.

In mid-December, the CDC released $15 million to public health labs around the country to boost sequencing outputs nationwide. That was part of a multipronged effort now underway at the agency to increase both the number of coronavirus variants being characterized and the locations from which they’re being drawn. The money will help states participate in a dedicated SARS-CoV-2 Strain Surveillance program, dubbed NS3, which the CDC launched in November. When the program is fully operational, public health labs will be expected to send 10 randomly selected coronavirus samples to the CDC’s labs in Atlanta every other week. The samples should represent patients from different age, racial, and ethnic groups, as well as the geographic diversity of each state. In addition to sequencing them, CDC scientists will also use the samples to build up a centralized strain library that they can dip into to perform additional tests.

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