Detection of an infectious sub-variant of Omicron in Santa Clara County – CBS San Francisco

SANTA CLARA (CBS SF/AP) — Santa Clara County health officials confirmed Tuesday that they have discovered descendants of the highly contagious omicron variant in two people, but are unaware of the new dangers. that this version of coronavirus can cause.

Santa Clara County Deputy Health Officer Dr. George Han told reporters that “early indications that it may be acting like the omicron BA.1 substream, but it’s hard to say because of the number of fields. small case so far.”

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According to the World Health Organization, the omicron variant has four lines called B.1.1.529, BA.1, BA.2 and BA.3. The most common is BA.1. The person currently discovered in Santa Clara County is BA 2.

“The BA.2 subline is much rarer, but has begun to appear in places including California and Santa Clara County and elsewhere in the world,” said Dr. Han.

Scientists and health officials around the world have been monitoring BA2 as it has now been detected in at least 40 countries. BA.2 is considered by many to be stealthier than the original version of omicron because specific genetic traits make it harder to detect. Some scientists worry it may also be more contagious.

But they say there’s a lot they still don’t know about it, including whether it better evades vaccines or causes more severe illness.


Since mid-November, more than three dozen countries have uploaded nearly 15,000 BA.2 genetic sequences to GISAID, a global platform for sharing coronavirus data. As of Tuesday morning, 96 of the cases in that sequence came from the United States

“So far, we haven’t seen it begin to take hold” in the US, said Dr Wesley Long, a pathologist at Houston Methodist in Texas.

Mutants appear more often in Asia and Europe. In Denmark, it accounted for 45% of all COVID-19 infections in mid-January, up from 20% two weeks earlier, according to the Statens Serum Institut, part of the Danish Ministry of Health.


BA.2 has a lot of mutations. About 20 of them in the mutant protein attached to the outside of the virus are shared with the original omicron. But it also has additional genetic changes not seen in the first version.

Dr. Jeremy Luban, a virologist at the University of Massachusetts Medical School, said it’s still unclear how important these mutations are, especially in a population that initially encountered the omicron.

Currently, the original version, called BA.1 and BA.2 are considered subsets of omicron. But global health leaders may give it its own Greek letter name if it is seen as a “worrying variant” globally.

The rapid spread of BA.2 in some places raised concerns that it could lose its effectiveness.

“We have some indications that it might be more contagious or maybe a little more contagious than the (original) omicron because it could compete with it in some areas,” says Long. “But we don’t necessarily know why.”

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An initial analysis by scientists in Denmark showed no difference in hospitalizations for BA.2 compared with baseline omicrons. Scientists are still looking at how infectious this version is and how well current vaccines work against it. It’s also not clear how well the treatments will work against it.

Doctors also don’t know for sure whether someone who has been infected with COVID-19 caused by omicrons can develop a relapse of BA.2 disease. But they are hopeful, especially that an earlier infection of the omicron could reduce the severity of the disease if someone later develops BA.2.

The two versions of omicron have much in common: the possibility that infection with the initial mutation “will help you fight BA.2”, said Dr. Daniel Kuritzkes, an infectious disease specialist at Brigham and Women’s Hospital .

Scientists will conduct tests to see if antibodies from the initial omicron infection “can neutralize BA.2 in the lab and then extrapolate from there,” he said.


The World Health Organization classifies overall omicron as a variant of concern, its most severe designation for coronavirus mutations, but it does not indicate BA.2 with a separate indication. However, given its rise in some countries, the agency said that investigations into BA.2 “should take precedence”.

Meanwhile, the UK Health Security Agency has designated BA.2 as “variant under investigation”, citing increasing numbers found in the UK and internationally. However, the original version of the omicron still prevailed in the UK


The early version of omicron had specific genetic features that allowed health officials to quickly distinguish it from delta using a certain PCR test because of what is known as an “S gene target error.” .

BA.2 does not have this same genetic problem. So in the test, Long said, BA.2 looks like delta.

“It’s not that the test didn’t detect it; it’s just not omicron-like,” he said. “Don’t get the impression that ‘omicron stealth’ means we can’t detect it. All of our PCR tests can still detect it.”


Doctors advise them the same number of precautions: Get vaccinated and follow public health guidance about wearing a mask, avoiding crowds, and staying home when you’re sick.

“Vaccines are still providing good protection against severe illness, hospitalization and death,” says Long. “Even if you’ve had COVID-19 before – you’ve had a natural infection – the protection from the vaccine is stronger, longer lasting and really… good for people who have been infected before.”

The latest version is another reminder that the pandemic is not over yet.

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“We all wish it were over,” says Long, “but until we get the whole world vaccinated, we run the risk of new variants emerging.” Detection of an infectious sub-variant of Omicron in Santa Clara County – CBS San Francisco

Dustin Huang

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