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.”
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.
“Sequencing will tell us a lot, but it can’t tell us everything,” says Gregory Armstrong, who leads the CDC’s Office of Advanced Molecular Detection. For example, one of the things public health experts are concerned about is how well people with existing immunity gained through a previous bout with Covid-19 will be able to fend off infections with this new UK strain. To test it, scientists have to be able to assess how well the antibodies found in the blood of Covid-19 survivors attack and neutralize the B.1.1.7 version of the virus. Another alarming possibility is that the vaccines that have been developed and authorized so far won’t be as effective against emerging strains. “We need to have a library of variants in order to get those answers,” says Armstrong.
The NS3 program, which Armstrong expects to be fully up and running by the end of the month, will help with that. But it won’t get the US as much genetic data as public health officials need to track the progress of B.1.1.7 and other emerging strains, like an alarming one that originated in South Africa, through the American populace. That’s why the CDC is also bringing large commercial testing labs on board. In December, the agency signed contracts with LabCorp and Illumina, and it is in the process of negotiating further deals with others that have the capacity to acquire and sequence samples from all around the country. In addition, since September the CDC has granted about $8 million to academic sequencing centers and is currently seeking to bring additional sites online. Data from all these efforts is continuously analyzed by CDC scientists and uploaded to public databases like GISAID for other researchers to use.