Last Friday, only a day after South African scientists first introduced the invention of the Omicron variant, Europe reported its first case: The new coronavirus variant was in Belgium. Before the weekend was out, Australia, Britain, Canada, Denmark, Germany, Israel, Italy and other nations had all discovered cases.
But within the United States, scientists saved looking.
“If we start seeing a variant popping up in multiple countries across the world, usually my intuition is that it’s already here,” stated Taj Azarian, a genomic epidemiologist on the University of Central Florida.
On Wednesday, American officers introduced that scientists had discovered it — in a California affected person who had lately returned from South Africa. By then, Canada had already identified six cases; Britain had discovered greater than a dozen.
The United States recognized a second case, in Minnesota, on Thursday, and extra are nearly actually lurking, scientists stated. So why haven’t we discovered them but?
Multiple elements could also be at play, together with journey patterns and stringent entrance necessities that might have delayed the variant’s introduction to the United States. But blind spots and delays within the nation’s genomic surveillance system might have been elements, too, specialists stated. With many labs now conducting a focused seek for the variant, the tempo of detection might rapidly choose up.
Since the start of the pandemic, scientists have been sequencing the genetic materials from samples of the virus, a course of that permits them to identify new mutations and establish particular variants. When achieved 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 United States, this sort of broad genomic surveillance obtained off to a really sluggish begin. While Britain rapidly harnessed its nationwide health care system to launch an intensive sequencing program, early sequencing efforts within the United States, primarily based primarily out of college laboratories, had been extra restricted and advert hoc.
Even after the C.D.C. launched a sequencing consortium in May 2020, sequencing efforts had been stymied by a fragmented health care system, an absence of funding and other challenges.
In January, when cases had been surging, the United States was sequencing fewer than 3,000 samples per week, according to the C.D.C.’s dashboard, far lower than 1 p.c of reported cases. (Experts suggest sequencing at the very least 5 p.c of cases.)
But in current months, the state of affairs has improved dramatically, because of a mix of new federal management, an infusion of funding and an rising concern in regards to the emergence and unfold of new variants, specialists stated.
“Genomic surveillance really has caught up in the U.S., and it is very good,” stated Dana Crawford, a genetic epidemiologist at Case Western Reserve University.
The nation is now sequencing roughly 80,000 virus samples per week and 14 p.c of all positive P.C.R. assessments, Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, stated at a White House briefing on Tuesday.
The downside is that the method takes time, particularly when achieved in quantity. The C.D.C.’s personal sequencing course of typically takes about 10 days to complete after it receives a specimen.
“We have really good surveillance in terms of quantity,” stated Trevor Bedford, an professional on viral evolution and surveillance on 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 sort of delay shouldn’t be unusual in nations that have a variety of samples to sequence, Dr. Bedford stated.
In some states, the timeline is even longer. The Ohio Department of Health notes that, from begin to end, the method of “collecting the sample, testing it, sequencing it and reporting it can take a minimum of 3-4 weeks.”
But now that scientists know what they’re on the lookout for, they need to be capable of expedite the method by prioritizing samples that appear probably to be Omicron, scientists stated.
In one small little bit of luck, Omicron generates a distinct genetic sign on P.C.R. assessments than the Delta variant, which at present accounts for basically all coronavirus cases within the United States. (In quick, mutations within the new variant’s spike gene means that Omicron samples check destructive for the gene, while testing positive for a distinct telltale gene.)
Many labs at the moment are expediting these samples, in addition to samples from people who lately returned from overseas, for sequencing.
“All of the agencies that are involved with genomic surveillance are prioritizing those recent travel-associated cases,” Dr. Azarian stated.
That might have been how the California case was flagged so rapidly. The affected person returned from South Africa on Nov. 22 and started feeling sick on Nov. 25. The individual examined positive for the virus on Monday and scientists then sequenced the virus, asserting that they’d 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 stated.
As a lot as surveillance has improved, there are nonetheless gaps that might sluggish the detection of extra cases within the United States, together with huge geographic variation.
“Some states are lagging behind,” stated Massimo Caputi, a molecular virologist on the Florida Atlantic University School of Medicine.
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Over the final 90 days, as an example, Vermont has sequenced and shared greater than 30 p.c of its virus cases and Massachusetts has sequenced greater than 20 p.c, according to GISAID, a global database of viral genomes. Six states, on the other hand — Kentucky, Pennsylvania, Ohio, South Carolina and Alabama — have every sequenced and reported fewer than 3 p.c of their cases, in keeping with GISAID.
Moreover, scientists can solely sequence samples from cases that are detected, and the United States has typically struggled to carry out sufficient testing.
“Testing is the weakest part of our pandemic response,” stated 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 for the reason that early days of the pandemic, it’s nonetheless extremely uneven. And while fast, at-home assessments have many benefits, the shift of some testing from the lab to the house might current new challenges for surveillance.
“With increasing at-home rapid diagnostic tests, if that isn’t followed up with, like, a P.C.R. test, those cases won’t get sequenced,” stated Joseph Fauver, a genomic epidemiologist on the University of Nebraska Medical Center. The downside shouldn’t be insurmountable, he added, however “maybe there’s a little blind spot there.”
There are other, extra optimistic causes that scientists have not detected extra cases, though they continue to be theoretical.
“Perhaps infected patients have mild symptoms, and hence are not getting tested and are not subject to genomic surveillance,” stated Janet Robishaw, the senior affiliate dean for analysis on the Florida Atlantic University College of Medicine.
(It continues to be far too early to know whether or not Omicron causes illness that is any kind of extreme than other variants, scientists stress. Even if the cases are disproportionately gentle, which shouldn’t be but clear, that might be as a result of the variant has largely contaminated younger or vaccinated people up to now, who’re much less prone to develop extreme illness.)
It can also be attainable that there may be not but a lot neighborhood unfold of the variant within the United States. If the cases are largely remoted, and tied to overseas journey, they may fly underneath the surveillance radar.
“We’re kind of looking for a needle in the haystack if we’re looking for just single cases that are unrelated,” Dr. Azarian stated.
Although it isn’t but clear where Omicron emerged, the primary outbreaks had been detected in South Africa, where the variant is now widespread.
There are fewer flights between southern Africa and the United States than between that area and Europe, where other early Omicron cases had been detected, Dr. Caputi stated.
And till early November, the United States had banned worldwide vacationers from the European Union and South Africa, he famous. Even when officers lifted the ban, vacationers from these areas had been nonetheless required to supply proof of each vaccination and a current destructive Covid check. These measures might have postponed Omicron’s arrival.
“It is conceivable that Omicron spread is lagging behind in the U.S.,” Dr. Caputi stated in an e-mail.
Either means, he added, he anticipated scientists to seek out extra cases quickly.