Of the more than 21.5 million officially reported Covid-19 cases in the United States, samples of only 59,438 people, or less than 0.3%, have been sequenced and analyzed for variants, according to GISAID. In contrast, the United Kingdom regularly sequesters more than 10% of its Covid-19 cases. This allowed UK public health officials to monitor in real time as the B.1.1.7 variant went from a rare discovery in early December to dominating new infections three weeks later. The British could be a shining example in this regard, but they are not alone. According to a recent Washington post analysis, 42 other countries have sequenced more cases than the United States, despite the fact that the Americans account for a quarter of all coronavirus infections worldwide.
“What the United States is doing right now is completely inadequate,” Chiu says. He thinks U.S. government officials should aim for that 10% threshold. But the effort will undoubtedly be complicated by the fracture of the American healthcare system. In the UK, which has a single nationalized health service and a supporting microbiology service, it is relatively easy to transfer samples and data. In the United States, the private sector still dominates the testing market. For a sample to appear 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 reaches him. It may take weeks, if at all. Often by the time an epidemiologist in the public health department discovers a case they wish to investigate with genetics, the original sample has already been discarded. “The rate limiting step is not sequencing; it’s really getting the sample, ”Chiu says. “That’s why we need to empower state and county labs to do this internally, so we can get the data faster.”
Over the past decade, public health laboratories have strengthened their sequencing capabilities as part of their role in tracking foodborne illness outbreaks in the United States. Each state lab, as well as a handful of large regional labs, has the technology readily available, according to Wrobleski. But they haven’t been able to deploy it on a large scale during the pandemic because they had their hands full just trying to lead basic diagnostic tests and contact follow-up, she says. And until a few weeks ago, they weren’t ordered to walk to do anything differently.
But that’s finally starting to change.
In mid-December, the CDC released $ 15 million to public health labs nationwide to boost sequencing releases nationwide. This was part of a multi-pronged effort currently underway at the agency to increase both the number of characterized coronavirus variants and the locations from which they are pulled. The money will help states participate in a dedicated SARS-CoV-2 strain surveillance program, dubbed NS3, that the CDC launched in November. When the program is fully operational, public health labs will need to send 10 randomly selected coronavirus samples to CDC labs in Atlanta every two weeks. Samples should represent patients of different ages, racial and ethnic groups, as well as the geographic diversity of each state. In addition to sequencing them, scientists at the CDC will also use the samples to build a centralized strain library that they can draw on for additional testing.
“Sequencing will tell us a lot, but it can’t tell us everything,” says Gregory Armstrong, who heads the CDC’s Office of Advanced Molecular Detection. For example, one of the things that public health experts are concerned about is how well people immune from a previous fight with Covid-19 will be able to fend off infections with this new British strain. To test for it, scientists must be able to assess to what extent antibodies found in the blood of Covid-19 survivors attack and neutralize version B.1.1.7 of the virus. Another alarming possibility is that the vaccines that have been developed and licensed so far will not be as effective against emerging strains. “We need a library of variations to get these answers,” says Armstrong.
The NS3 program, which Armstrong expects to be fully operational by the end of the month, will help. But the United States will not get 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 native of South Africa, through the American population. This is why the CDC also embeds large commercial testing laboratories. In December, the agency signed contracts with LabCorp and Illumina, and is negotiating further agreements with others who have the capacity to acquire and sequence samples from across the country. Additionally, since September, the CDC has awarded approximately $ 8 million to university sequencing centers and is currently looking to bring additional sites online. The data from all of these efforts is continually analyzed by scientists at the CDC and uploaded to public databases such as GISAID for other researchers to use.