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New COVID Variant 'Omicron' Identified In San Francisco; Here's What You Need To Know

SAN FRANCISCO (CBS SF/AP) -- A person who returned to the San Francisco Bay Area from a trip to South Africa has tested positive for the COVID omicron variant -- the first confirmed case in the United States.

Director of the National Institute of Allergy and Infectious Disease Dr. Anthony Fauci made the announcement Wednesday at the White House. The California and San Francisco Departments of Public Health and the US Centers for Disease Control and Prevention confirmed that the case was caused by the omicron variant through genomic sequencing conducted at the University of California at San Francisco, and confirmed with the CDC.

In a news release, San Francisco officials said the individual was a traveler who returned from South Africa to San Francisco International on November 22.

"The individual, who is a San Francisco resident, is self-isolating and is experiencing mild symptoms," the officials said. "We are continuing to speak with the individual about any persons with whom they have been in contact."

The individual, who was not named, fell ill and sought medical treatment that led to the discovery on Nov. 29.

"This is not a surprise," said Dr. Grant Colfax, the city's director of health at a news conference. "We knew that omicron was going to be here. We thought it was already here. We just hadn't detected it yet. This is a cause for concern but it also certainly not a cause for us to panic. We have been prepared in the city for this."


At a Wednesday news conference, Dr. Grant Colfax, the city's director of health, said San Francisco was well-positioned to respond to variants.

"Our vaccine rate is high. More boosters are going into arms every day...Our masking and vaccine requirements are among the most stringent in the country...There is still a lot we don't know about omicron although there is a strong likelihood that it is more infectious delta."

"We don't know how sick it will make people," Colfax continued. "But that is being studied furiously and we don't know how fully effective the vaccines are in protecting against transmission or serious cases of illness or hospitalizations."

As for putting back in place any restrictions, Colfax said: "At this time, we do not anticipate changing any of our health orders or changing any current restrictions or imposing new restrictions on activity in San Francisco. We obviously are following these developments very closely. We will share additional information as we have it."


It appears to have a high number of mutations — about 30 — in the coronavirus' spike protein, which could affect how easily it spreads to people.

Sharon Peacock, who has led genetic sequencing of COVID-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations "consistent with enhanced transmissibility," but said that "the significance of many of the mutations is still not known."

Lawrence Young, a virologist at the University of Warwick, described the variant as "the most heavily mutated version of the virus we have seen." He said it was concerning that although the variant was only being detected in low levels in parts of South Africa, "it looks like it's spreading rapidly."


Scientists know that the new variant is genetically distinct from previous variants including the beta and delta variants, but do not know if these genetic changes make it any more transmissible or dangerous. So far, there is no indication the variant causes more severe disease.

It will likely take weeks to sort out if the new variant is more infectious and if vaccines are still effective against it.

Even though some of the genetic changes in the new variant appear worrying, it's still unclear if they will pose a public health threat. Some previous variants, like the beta variant, initially alarmed scientists but didn't end up spreading very far.

"We don't know if this new variant could get a toehold in regions where delta is," said Peacock of the University of Cambridge. "The jury is out on how well this variant will do where there are other variants circulating." To date, delta is by far the most predominant form of COVID-19, accounting for more than 99% of sequences submitted to the world's biggest public database.


The coronavirus mutates as it spreads and many new variants, including those with worrying genetic changes, often just die out. Scientists monitor COVID-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus.

Peacock said the variant "may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve," in a scenario similar to how experts think the alpha variant — which was first identified in England — also emerged, by mutating in an immune-compromised person.


Maybe. Travelers arriving in the U.K. from South Africa, Namibia, Botswana, Lesotho, Eswatini and Zimbabwe will have to self-isolate for 10 days. European Union nations also moved quickly to try to stop air travel from southern Africa.

Given the recent rapid rise in COVID-19 in South Africa, restricting travel from the region is "prudent" and would buy authorities more time, said Neil Ferguson, an infectious diseases expert at Imperial College London.

Jeffrey Barrett, director of COVID-19 Genetics at the Wellcome Sanger Institute, thought that the early detection of the new variant could mean restrictions taken now would have a bigger impact than when the delta variant first emerged

"With delta, it took many, many weeks into India's terrible wave before it became clear what was going on and delta had already seeded itself in many places in the world and it was too late to do anything about it," he said. "We may be at an earlier point with this new variant so there may still be time to do something about it."

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