In a recent executive order and again in his $1.9 trillion American Rescue Plan, President Biden has pushed a pandemic surveillance program designed to identify emerging virus strains through genome sequencing. In a White House briefing document, the administration described it this way: “The identification of new strains of SARS-CoV-2 in the United Kingdom and South Africa highlight a key vulnerability in our nation’s COVID response: we simply do not have the kind of robust surveillance capabilities that we need to track outbreaks and mutations.”
Scientifically, this is one of the most important measures the U.S. could take to address the raging pandemic. (In fact, Techonomy called this out last March.) Why does genome sequencing matter in fighting COVID-19? All creatures great and small acquire genetic mutations over time; it’s what happens when cells make tiny mistakes copying genetic material when they replicate, as they do relentlessly. Occasional mistakes are inevitable. RNA viruses like SARS-CoV-2 tend to acquire these mutations faster than other organisms, and it’s one of the traits that makes them such wily foes. Since mutations occur randomly, most of them don’t make enough of a difference to matter. But once in a while, one of those mutations will give the virus an advantage it didn’t have before, such as being more transmissible. Given the right conditions, these new versions of the virus — what you’ve heard reporters and public health officials calling new variants — will quickly outcompete the old version.
We saw this happen relatively early in the pandemic, but back then known mutations were mostly unremarkable. But recently we’ve seen worse versions: the highly contagious UK and Brazil variants, and the South African variant that appears to be both more contagious and less susceptible to current COVID-19 vaccines.
Knowing which variants you’re fighting is crucial for a strong public health response, and it’s impossible to get that information without extensive surveillance programs based on genome sequencing. So why has the U.S. been flying blind?
By the numbers, we should have a huge advantage in this area. With just 4% of the world’s population, the U.S. has an enormous share of the world’s DNA sequencing capability and the highest burden of COVID-19 in the world, with about a quarter of all reported cases. We should be churning out more SARS-CoV-2 genome sequences than the rest of the world combined. Instead, we don’t even break into the top 30 countries contributing sequence data to the international GISAID database.
Embarrassingly, it’s not even as though sequencing the virus is all that difficult. Its genome is a measly 30,000 bases long; the human genome, sequenced routinely in labs across the U.S., is one hundred thousand times that size. A grad student in virtually any biology lab in the country has the skills and technology to get this done. Labs have also fine-tuned techniques for sequencing vanishingly small genomic samples, such as what’s left over after a routine COVID-19 molecular diagnostic test has been run.
But in the U.S., the devastating lack of a national pandemic plan throughout 2020 meant that no one was leading a national virus surveillance effort, and little funding was available to help labs that wanted to generate this kind of data. In the UK, by contrast, a national effort that launched in March drove the sequencing of hundreds of thousands of SARS-CoV-2 genomes. It’s why the UK was able to spot the more contagious variant when it emerged and make the decision to go into lockdown to get it under control. In the U.S., the Centers for Disease Control and Prevention announced what sounded like a similar sequencing effort in May, but in practice it amounted to little more than a press release. Laboratories across the country have attempted to take matters into their own hands. Unfortunately, their efforts are no replacement for a targeted national program; our view of viral variants is more like a blind spot.
Last July, the National Academies of Sciences, Engineering, and Medicine reported the findings of a committee tasked with making recommendations for the country’s genomic surveillance needs. “Due to a number of factors including poor funding, coordination, and capacity, the committee concluded that existing data sources and integration efforts for SARS-CoV-2 genome sequence data are patchy, typically passive, and reactive in the United States,” the committee wrote. “As a result, available data do not represent key population features of individuals who are infected with SARS-CoV-2 and cannot adequately answer many pressing questions about the evolution and transmission of this virus.” The committee strongly recommended a national genome sequencing program for the pandemic — a recommendation that did not translate into action under the last administration.
That’s why the early steps taken by the Biden administration are so essential. Through an executive order issued on January 21, he directed the establishment of a Pandemic Testing Board that would expand genome sequencing and support surveillance testing. The COVID-19 relief bill, if passed, would support these efforts with much-needed funding.
Meanwhile, private companies are stepping in to help the U.S. catch up. The genomics firm Helix recently launched a COVID-19 surveillance dashboard to monitor variants of the SARS-CoV-2 virus across the country. Testing behemoth Labcorp announced that it would also ramp up virus sequencing efforts. Both efforts are supported by CDC funding, and new CDC director Rochelle Walensky has said that her team is also accelerating surveillance efforts.
For all the very recent progress, the U.S. still doesn’t have a clear, focused national genomic surveillance program. It’s urgent one is developed to replace the ineffective patchwork response of the past year.