Think of it like an early warning system.
With new and more contagious variants of the novel coronavirus emerging all over the world, the U.S. government needs to set up a nationwide regime for detecting and tracking the biology of the coronavirus, experts told The Daily Beast.
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Among other things, the system could give health officials time to put in place emergency measures to prevent a spike in infections and deaths.
“Without continual surveillance efforts, we are effectively flying blind in terms of the risk from emerging variations of this and other pathogens,” Christopher Mason, a biophysicist at Weill Cornell Medicine in New York, told The Daily Beast.
New and more transmissible SARS-CoV-2 strains that first appeared in the United Kingdom and South Africa in recent months definitely are real, even if reports of a possible “USA variant” appear to have been premature. And they represent harbingers of a possible new phase of the year-old pandemic, one in which the virus mutates faster than our existing health systems can adapt.
The implications are frightening, but don’t count on the administration of outgoing President Donald Trump to take serious action on a nationwide monitoring system to detect and track these mutations. Days after Trump incited a deadly assault on the U.S. Capitol, and just two weeks before the end of his term, the president has all but given up on governing, to say nothing of keeping up with the pandemic.
To health experts, the shortfalls are obvious. “We really need to up our game in genomic screening,” Irwin Redlener, the founding director of Columbia University’s National Center for Disaster Preparedness and a former Joe Biden adviser, told The Daily Beast.
Fortunately, the incoming administration of President-elect Biden has signaled its interest in setting up a viral early-warning system.
“The president-elect supports a national testing program that can help stop the spread of COVID-19 and find variants,” T.J. Ducklo, a Biden spokesperson, told The New York Times. “That means more tests, increased lab capacity, and genome sequencing.”
Broadly speaking, disease monitoring occurs at two levels—individual and population-wide. Going to your local pharmacy for a COVID test is a kind of monitoring, but it mostly has implications for just you and your own decision-making. Do you isolate? Seek medical help?
Population-wide monitoring aims to assess how widespread a pathogen is in a large group—the residents of a city, state, or entire country—in order to drive public health policy. Does a city shutter businesses? Does a state compel out-of-state travelers to quarantine when they arrive? Where does a national government direct emergency resources?
The U.S. Centers for Disease Control and Prevention operates America’s large-scale disease-monitoring programs. The CDC gathers, analyzes, and disseminates population-level data on COVID transmission, infections, and deaths.
But population-level monitoring doesn’t always have a genetic component. And individual testing pretty much never does. That is to say, you might get a rapid test at the corner pharmacy to tell you you’ve got the novel coronavirus in your system, but it’s unlikely the pharmacy is going to collect a sample of your viral load and send it off to a laboratory for sequencing.
The CDC is already doing some genetic analysis on a small but growing number of samples in order to keep loose tabs on various mutations of the novel coronavirus, in particular the U.K. variant that first appeared in the fall. “CDC had already been scaling up U.S. sequencing for COVID-19 when the U.K. variant... came to the attention of U.K. public health officials, and [we] are doing this along several lines,” an agency spokesperson told The Daily Beast.
But to keep pace with more and more new SARS-CoV-2 mutations, the CDC needs to greatly expand its monitoring, experts said.
“Large-scale viral sequencing is absolutely essential, in my opinion,” Niema Moshiri, a geneticist at the University of California, San Diego, told The Daily Beast.
It’s no longer enough to have a sense of how many people are getting sick and where. Now the CDC also needs to know exactly which variant or strain of the pathogen is infecting people, and where.
Recognizing the need for more sequencing is one thing. Setting up a system for addressing that need is another. All the technology is readily available. But harnessing it requires money, expertise, and bureaucratic discipline that, up to this point, have been in short supply in the federal response to the pandemic.
“It is very doable and mostly requires a bit of organization,” Mason said. “It would likely be a mix of industry, government, and academic sites partnering together to share samples, data, and results.”
Getting the samples is the easy part, Mason said. Pharmacy chains such as CVS have centralized sites for holding millions of samples. More come in every day. The CDC could tap that flow of raw samples. “They just need to be sequenced,” Mason said.
Moshiri has ideas for how that mass-sequencing could go down. It all starts with high-output sequencing machines, such as the kind San Diego-based Illumina makes. “They're expensive, but they can be purchased if the state or federal government provided grant funding for this,” Moshiri said.
Mason also mentioned the Illumina machines, which can sell for more than $100,000 apiece.
“The machine itself could sequence samples from roughly 1,000 individuals per day,” Moshiri said. “Then, given the raw data from these 1,000 samples, I have been personally working on acceleration techniques to make the computational side of the analysis feasible, and I've gotten it down to just a couple hours of compute time to get results.”
Once labs have torn apart the samples, sequenced, and analyzed them, they just need to share the data. The easiest way might be for labs to plug into GISAID, the global repository for genetic data on viral pathogens. “We just need funding allocated and people to jump in,” Mason said.
The CDC’s monitoring efforts could expand significantly after Biden’s Jan. 20 inauguration, possibly growing to include the coordination, sequencers, and data-sharing that experts described. The Biden transition team did not immediately respond to an emailed query, but Mason said that his department has been in touch with the team.
Whatever system the Biden administration sets up could be useful even after the end of the current pandemic, experts stressed. An intensive, nationwide pathogen-monitoring system could help to spot any reemergence of the novel coronavirus and, with a simple switch in testing, could monitor and track new pathogens, Lawrence Gostin, a Georgetown University global health expert, told The Daily Beast.
“If we’ve learned one lesson, it’s that we’ve got to prepare,” he said.
