How Is the US Actually Doing on Tracking Variants Like Omicron? We Asked Some Experts.

Back in February—a lifetime ago in pandemic time—I spoke with several experts who warned about the United States’ ability to sequence and track coronavirus variants. At the time, scientists in the United Kingdom had identified the pandemic’s first “variant of concern,” a strain later called Alpha. The UK boasted the “gold standard” of genomic surveillance strategies, sequencing about 6 percent of positive COVID samples in early 2021; the US, meanwhile, was sequencing about 0.3 percent. “We’re blind to what’s happening,” one expert in infectious diseases and vaccinology told me.

“I feel like the sentiment this time last year was, the US doesn’t sequence enough. We’re behind, we’re behind. And I think it was a fair argument. But at this point, I think it’s just a really lazy argument.”

Alpha would eventually be outperformed in the UK (and the world) by another variant, Delta. But its emergence, among the rise of other variants of concern shortly afterward, was a wake-up call: Without a robust genomic surveillance program, researchers warned, the US would fail to monitor variants as they were introduced or to detect new, homegrown ones—leaving us less prepared to fight the virus.

Enter Omicron. First reported to the World Health Organization by South African officials around Thanksgiving, the variant has since been detected in dozens of countries, including the US. And in much of the news media, the prevailing narrative about the US’s genomic surveillance has remained the same: The country “lags behind” our foreign counterparts, has been “slow to the party,” and is at risk of “flying blind.”

But after talking with a few experts last week, it became clear that this isn’t exactly the case anymore. In fact, the US is far from straggling behind. And in a sea of alarming headlines about Omicron, this is truly good news.

“I feel like the sentiment this time last year was, The US doesn’t sequence enough. We’re behind, we’re behind. And I think it was a fair argument. But at this point, I think it’s just a really lazy argument,” says Joseph Fauver, an assistant professor at the College of Public Health at the University of Nebraska Medical Center, which is working with the state to track variants. “I am unapologetically on the side of, we’re doing an exceptional job. That doesn’t mean we couldn’t be doing things better. But there’s so much data being generated right now across the US and across the world.” 

Here, based on my conversations, is what you need to know about Omicron, future variants, and genomic sequencing:

We’ve seen a huge increase in SARS-CoV-2 genome sequencing. Thank federal funding.

Early this year, when experts called for an investment in the country’s ability to track SARS-CoV-2, the Biden administration listened. In February, it announced a $200 million “down payment” to track variants, followed by a $1.7 billion investment in April. “The CDC, with the support of the White House and federal government, really rolled out a robust plan to get genomic surveillance up to speed across the country,” says Bronwyn MacInnis, director of pathogen genomic surveillance in the Infectious Disease and Microbiome Program at the Broad Institute of MIT and Harvard.

The effort was three-pronged: First, federal health officials worked to get the institutions that were doing large scale COVID testing—shops like Labcorp, Quest Diagnostics, Helix, and the Broad Institute, where MacInnis works—to conduct their own sequencing, giving scientists what she calls a “10,000-foot view” of what strains are circulating across the states.

Second, the administration injected funds into local and state labs, giving them the ability to be “more nimble,” MacInnis says, and zoom in on local outbreaks or perform targeted sequencing in places where it was needed.

The third piece, MacInnis says, was to continue to support academic research centers like hers that are using their lab capacity to track SARS-CoV-2. “It’s not perfect,” MacInnis says about the effort as a whole. “It’s also not easy. But it is really strong.”

By Fauver’s estimate, the US has sequenced about as many, if not more, SARS-CoV-2 genomes as we have for all other viruses combined.

The data backs that up: At the start of 2021, the country was sequencing a few thousand genomes per week. In late November, that level hit nearly 100,000 per week. By Fauver’s estimate, the US has sequenced about as many, if not more, SARS-CoV-2 genomes as we have for all other viruses combined.

“At the beginning of this year, we still weren’t sequencing enough to really get a good snapshot of what was circulating in the US,” adds Alexandra Phelan, an assistant professor at the Center for Global Health Science and Security at Georgetown University, whose work focuses on pandemic preparedness and response. “If we look at us now, we are actually in a much, much better position.”

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