Why Didn’t the U.S. Detect Omicron Circumstances Sooner?

Final Friday, only a day after South African scientists first introduced the invention of the Omicron variant, Europe reported its first case: The brand new coronavirus variant was in Belgium. Earlier than the weekend was out, Australia, Britain, Canada, Denmark, Germany, Israel, Italy and different international locations had all discovered circumstances.

However in the USA, scientists saved looking out.

“If we begin seeing a variant popping up in a number of international locations the world over, often my instinct is that it’s already right here,” stated Taj Azarian, a genomic epidemiologist on the College of Central Florida.

On Wednesday, American officers introduced that scientists had discovered it — in a California affected person who had not too long ago returned from South Africa. By then, Canada had already recognized six circumstances; Britain had discovered greater than a dozen.

On Thursday, further circumstances have been recognized in Minnesota, Colorado and New York, indicating that extra are nearly actually lurking, scientists stated. Why wasn’t the variant detected sooner?

There are numerous potential explanations, together with journey patterns and stringent entrance necessities that will have delayed the variant’s introduction to the USA. However there are additionally blind spots and delays within the nation’s genomic surveillance system. With many labs now conducting a focused seek for the variant, the tempo of detection might rapidly choose up.

For the reason that starting of the pandemic, scientists have been sequencing the genetic materials from samples of the virus, a course of that enables them to identify new mutations and determine particular variants. When carried out routinely and on a big scale, sequencing additionally permits researchers and officers to maintain tabs on how the virus is evolving and spreading.

In the USA, this sort of broad genomic surveillance acquired off to a really sluggish begin. Whereas Britain rapidly harnessed its nationwide well being care system to launch an intensive sequencing program, early sequencing efforts in the USA, based mostly primarily out of college laboratories, have been extra restricted and advert hoc.

Even after the C.D.C. launched a sequencing consortium in May 2020, sequencing efforts were stymied by a fragmented health care system, a lack of funding and other challenges.

In January, when cases were surging, the United States was sequencing fewer than 3,000 samples a week, according to the C.D.C.’s dashboard, far less than 1 percent of reported cases. (Experts recommend sequencing at least 5 percent of cases.)

But in recent months, the situation has improved dramatically, thanks to a combination of new federal leadership, an infusion of funding and an increasing concern about the emergence and spread of new variants, experts said.

“Genomic surveillance really has caught up in the U.S., and it is very good,” said Dana Crawford, a genetic epidemiologist at Case Western Reserve University.

The country is now sequencing approximately 80,000 virus samples a week and 14 percent of all positive P.C.R. tests, which are conducted in labs and considered the gold standard for detecting the virus, Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, said at a White House briefing on Tuesday.

The problem is that the process takes time, especially when done in volume. The C.D.C.’s own sequencing process typically takes about 10 days to complete after it receives a specimen.

“We have really good surveillance in terms of quantity,” said Trevor Bedford, an expert on viral evolution and surveillance at the Fred Hutchinson Cancer Research Center in Seattle. He added, “But by nature, it lags compared to your case reporting. And so we’ll have good eyes on things from two weeks ago.”

This kind of delay is not uncommon in countries that have a lot of samples to sequence, Dr. Bedford said.

But now that scientists know what they are looking for, they should be able to expedite the process by prioritizing samples that seem most likely to be Omicron, scientists said.

In one small bit of luck, Omicron generates a different genetic signal on P.C.R. tests than the Delta variant, which currently accounts for essentially all coronavirus cases in the United States. (In short, mutations in the new variant’s spike gene mean that Omicron samples test negative for the gene, while testing positive for a different telltale gene.)

Many labs are now expediting these samples, as well as samples from people who recently returned from abroad, for sequencing.

“All of the agencies that are involved with genomic surveillance are prioritizing those recent travel-associated cases,” Dr. Azarian said.

That may have been how the California case was flagged so quickly. The patient returned from South Africa on Nov. 22 and began feeling sick on Nov. 25. The person tested positive for the virus on Monday and scientists then sequenced the virus, announcing that they had detected Omicron two days later.

“The quick turnaround by the U.S. genomic surveillance system is another example of how much better our system has become over the past few months,” Dr. Crawford said.

As much as surveillance has improved, there are still gaps that could slow the detection of more cases in the United States, including enormous geographic variation.

“Some states are lagging behind,” said Massimo Caputi, a molecular virologist at the Florida Atlantic University School of Medicine.

Over the last 90 days, for instance, Vermont has sequenced and shared about 30 percent of its virus cases and Massachusetts has sequenced about 20 percent, according to GISAID, an international database of viral genomes. Six states, on the other hand — Kentucky, Pennsylvania, Ohio, South Carolina, Alabama and Oklahoma — have each sequenced and reported fewer than 3 percent of their cases, according to GISAID.

Moreover, scientists can only sequence samples from cases that are detected, and the United States has often struggled to perform enough testing.

“Testing is the weakest part of our pandemic response,” said Dr. Eric Topol, the founder and director of Scripps Research Translational Institute in La Jolla, Calif. “It has been from day one.”

Although testing, like genomic surveillance, has vastly improved since the early days of the pandemic, it is still highly uneven. And while rapid, at-home tests have many advantages, the shift of some testing from the lab to the home may present new challenges for surveillance.

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