Europe reported its first case of the new coronaviruses variant on Friday, just a day after South African scientists first announced the discovery of the Omicron variant. Australia, Britain, Canada, Canada, Germany, Israel, Italy, and other countries had cases before the weekend.
Scientists in the United States continued to search.
Taj Azarian, a genomic epidemiologist at the University of Central Florida, said that if a variant pops up in multiple countries, he usually believes it is already here.
The scientists found it in a California patient who had just returned from South Africa. Britain had found more than a dozen cases, while Canada had identified six.
Scientists said that the United States identified two more cases, in Minnesota and Colorado, on Thursday. Why wasn't the variant detected sooner?
The variant may have been delayed in its introduction to the United States due to travel patterns and entrance requirements. There are some delays in the country's genomic surveillance system. The pace of detection could quickly pick up with many labs now conducting a targeted search.
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The United States had its first case of the Omicron variant at the University of California, San Francisco.
Scientists have been analyzing the genetic material from samples of the virus since the beginning of the epidemic. When done routinely and on a large scale, it allows researchers and officials to keep an eye on how the virus is evolving and spreading.
The United States has a very slow start to this kind of broad genomic research. The United States had limited and ad hoc early sequencing efforts, which were mostly based out of university laboratories.
The C.D.C. launched a consortium of researchers in May 2020, but efforts to sequence the genomes were hampered by a fragmented health care system, lack of funding and other challenges.
In January, when cases were increasing, the United States was only able to sequence fewer than 3000 samples a week. Experts recommend that at least 5 percent of cases be sequenced.
The situation has improved dramatically in recent months, thanks to a combination of new federal leadership, an influx of funding and an increasing concern about the emergence and spread of new variant, experts said.
Dana Crawford, a genetic epidemiologist at Case Western Reserve University, said that genotyping has caught up in the U.S.
Fourteen percent of all positive P.C.R. tests are conducted in labs and are considered the gold standard for detecting the virus, according to the director of the Centers for Disease Control and Prevention.
When done in volume, the process takes a long time. The C.D.C. takes about 10 days to complete its own process.
The Fred Hutchinson Cancer Research Center in Seattle has good surveillance in terms of quantity. It lags compared to your case reporting. We will have good eyes on things from two weeks ago.
In countries with a lot of samples to sequence, this kind of delay is not uncommon.
The timelines are longer in some states. The process of collecting, testing and reporting a sample can take 3-4 weeks according to the Ohio Department of Health.
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Pete Kiehart was a reporter for The New York Times.
Scientists said that they should be able to speed up the process by using samples that seem most likely to be Omicron.
The Delta variant of coronaviruses is the most common in the United States, and Omicron generated a different genetic signal on P.C.R. tests. Omicron samples that test negative for the new variant's spike gene are also tested positive for a different telltale gene.
Many labs are speeding up the process of taking these samples and taking samples from people who recently returned from abroad.
The recent travel-associated cases are being prioritized by the agencies involved in thegenomics surveilance.
The California case was flagged quickly. The patient returned from South Africa and began to feel unwell. The person was positive for the virus on Monday and the scientists were able to sequence the virus and find Omicron two days later.
The U.S. genomic surveillance system has become much better over the past few months, according to Dr. Crawford.
There are still gaps that could slow the detection of more cases in the United States.
Some states are lagging behind, according to a researcher at the Florida Atlantic University School of Medicine.
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Biden has a winter plan. As Omicron reaches the U.S., President Biden announced a new strategy that includes hundreds of family-centered vaccination sites, booster shots for all adults, new testing requirements for international travelers and insurance reimbursement for at- home tests.
Experts have differing views on boosters. Many public health experts have opposed plans to give Covid booster shots to all adults. As Omicron gains ground, researchers are changing their minds and now believe that the shots may be the best defense against the new variant.
According to the international database of viral genomes, Vermont and Massachusetts have shared about 30% and 20% of their virus cases over the last 90 days. Kentucky, Pennsylvania, Ohio, South Carolina, Alabama and Oklahoma have each had less than 3% of their cases reported.
The United States has struggled to perform enough testing because scientists only can sequence samples from cases that are detected.
Dr. Eric Topol, the founder and director of the Scripps Research Translational Institute, said that testing is the weakest part of the response to the swine flu. It has been there from the beginning.
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Testing in Houston. Testing has improved since the early days of the Pandemic, but the United States still struggles to perform enough tests.
Since the early days of the Pandemic, testing has vastly improved, but it is still very different. The shift of some testing from the lab to the home may present new challenges for surveilling.
The University of Nebraska Medical Center's Joseph Fauver said that if rapid diagnostic tests aren't followed up with a P.C.R. test, those cases won't get sequenced. He said that the problem is not impossible, but that there is a little blind spot.
There are other reasons that scientists have not detected more cases.
Janet Robishaw, the senior associate dean for research at the Florida Atlantic University College of Medicine, said that it was possible that patients with mild symptoms were not tested and were not subject to genomic surveillance.
Scientists stress that it is too early to know if Omicron causes disease that is more or less severe. The variant has mostly affected young people who are less likely to develop severe disease, so it's possible that the cases are disproportionately mild.
It is possible that there is not much community spread of the variant in the United States. If the cases are mostly isolated and tied to foreign travel, they could be monitored.
If we are looking for just single cases that are unrelated, we are kind of looking for a needle in the haystack.
The first Omicron outbreak was detected in South Africa, where the variant is now widespread.
There are fewer flights between southern Africa and the United States than between Europe and the United States.
The United States had banned international travelers from the European Union and South Africa. Travelers from those locations were still required to provide proof of both vaccinations and a negative Covid test even after the ban was lifted. Omicron may have been delayed by these measures.
Dr. Caputi said in an email that it is possible that Omicron spread is lagging behind in the U.S.
He expected scientists to find more cases soon.
