South Africa, Australia and Canada
Tom Tapp
Tue, December 7, 2021
Scientists have identified a new Covid-19 lineage responsible for a number of recent Covid cases in South Africa, Australia and Canada that displays “many of the defining mutations of B.1.1.529 (Omicron) [but does] not have the full set. These cases also have “a number of their own unique mutations,” according to analysis posted on information sharing platform GitHub. The platform is widely used by top researchers to share data and information related to Covid-19.
As a result of those similarities and differences with the original Omicron, which was first identified about two weeks ago, the new sequence is being called BA.2, while the original variant has been dubbed BA.1.
The new lineage is being called “stealth” Omicron by some scientists and news outlets because, while PCR tests do identify it as Covid, the mutations on BA.2 defy a shortcut used by scientists to identify a Covid case specifically as Omicron.
Why does that matter? It makes tracking the spread of Omicron more difficult at a time when surveillance of the new variant is critical to understanding it. Only seven cases of BA.2 have been identified thus far, reported the Guardian, the picture is still far from complete.
Per the Guardian: “To have two variants, BA.1 and BA.2, arise in quick succession with shared mutations is ‘worrying’ according to one researcher, and suggests public health surveillance ‘is missing a big piece of the puzzle.’ ”
It is also unclear exactly how or if the unique mutations in BA.2 will impact its transmissibility and virulence.
The original Omicron (now BA.1) has been identified in 19 states, according to CDC data and over 50 countries, said CDC Director Rochelle Walensky on Tuesday.
Scientists found a 2nd type of Omicron that's harder to track since tests struggle to distinguish it from other variants
Marianne Guenot
Wed, December 8, 2021
A healthcare worker conducts a COVID-19 test on a traveller at O.R. Tambo International Airport in Johannesburg on November 28, 2021.
Phill Magakoe/AFP via Getty Images
Scientists have spotted a version of Omicron that appears harder to track.
BA.2, the new lineage, has been seen seven times across South Africa, Australia, and Canada.
Its genetics mean that it is harder to tell apart from other virus variants via a PCR test.
A new version of the Omicron coronavirus variant was designated on Tuesday that experts say will be harder to track because of its genetics.
The new lineage, called BA.2, has been spotted seven times so far across South Africa, Australia, and Canada.
BA.2 is genetically quite different from the original Omicron lineage, now called BA.1, which has been spreading across the world, said Francois Balloux, the director of the University College London Genetics Institute, per the Guardian.
Crucially, it doesn't have the characteristic S-gene dropout mutation which allows Omicron BA.1 to be easily identified via PCR test results, the main way the variant has been tracked so far.
That means that "the two lineages may behave differently," he said, The Guardian reported.
While the change will make tracking harder, it is "nothing to be scared of yet" said Vinod Scaria, a clinician and computational biologist at the CSIR Institute of Genomics and Integrative Biology, in a tweet.
David Stuart, a professor of structural biology at Oxford University, agreed.
"I don't think there's any reason to think that the new outlier is any more of a threat than the form of Omicron that's knocking around at the moment in the UK," he said, per the Financial Times.
"But it is terribly early," he added.
PCR tests should still pick up this variant but might not be able to distinguish it from others
BA.2 carries "many of the defining mutations" of Omicron, according to Andrew Rambaut, an evolutionary biologist at the University of Edinburgh, UK, who reviewed the mutations in a blog post.
But it also has dozens of mutations BA.1 doesn't have and dropped dozens that do appear on BA.1.
Most notably, BA.2 is lacking the specific mutation that scientists were using as a quick way to track Omicron: the 69/70del mutation on the S gene, as Insider previously reported.
PCR tests check for different markers to see if someone is carrying the coronavirus, one of which targets the S gene.
When someone with the BA.1 lineage of Omicron gets a PCR test, one of the markers won't work: this is called an S-gene dropout.
This was an easy way to separate Omicron from other variants currently circulating, most of which wouldn't cause this S-gene dropout.
But this likely won't be the case for the BA.2 lineage. That means scientists will have to depend on more time-consuming and less widespread sequencing to identify it.
For Emma Hodcroft, an evolutionary geneticist at the University of Basel, that means that "there may be more Omicron than we think," per the Financial Times.
She told that outlet that "from the numbers we have right now, I don't think there's a very large hidden burden from BA.2."
In a tweet, Hodcroft emphasized that PCR tests should still work to detect whether someone has the coronavirus, even with this new lineage.
"This means we can't use this 'shortcut' to find possible Omicron cases for BA.2 only. However, the PCR test itself still works!" she said.
Scientists have spotted a version of Omicron that appears harder to track.
BA.2, the new lineage, has been seen seven times across South Africa, Australia, and Canada.
Its genetics mean that it is harder to tell apart from other virus variants via a PCR test.
A new version of the Omicron coronavirus variant was designated on Tuesday that experts say will be harder to track because of its genetics.
The new lineage, called BA.2, has been spotted seven times so far across South Africa, Australia, and Canada.
BA.2 is genetically quite different from the original Omicron lineage, now called BA.1, which has been spreading across the world, said Francois Balloux, the director of the University College London Genetics Institute, per the Guardian.
Crucially, it doesn't have the characteristic S-gene dropout mutation which allows Omicron BA.1 to be easily identified via PCR test results, the main way the variant has been tracked so far.
That means that "the two lineages may behave differently," he said, The Guardian reported.
While the change will make tracking harder, it is "nothing to be scared of yet" said Vinod Scaria, a clinician and computational biologist at the CSIR Institute of Genomics and Integrative Biology, in a tweet.
David Stuart, a professor of structural biology at Oxford University, agreed.
"I don't think there's any reason to think that the new outlier is any more of a threat than the form of Omicron that's knocking around at the moment in the UK," he said, per the Financial Times.
"But it is terribly early," he added.
PCR tests should still pick up this variant but might not be able to distinguish it from others
BA.2 carries "many of the defining mutations" of Omicron, according to Andrew Rambaut, an evolutionary biologist at the University of Edinburgh, UK, who reviewed the mutations in a blog post.
But it also has dozens of mutations BA.1 doesn't have and dropped dozens that do appear on BA.1.
Most notably, BA.2 is lacking the specific mutation that scientists were using as a quick way to track Omicron: the 69/70del mutation on the S gene, as Insider previously reported.
PCR tests check for different markers to see if someone is carrying the coronavirus, one of which targets the S gene.
When someone with the BA.1 lineage of Omicron gets a PCR test, one of the markers won't work: this is called an S-gene dropout.
This was an easy way to separate Omicron from other variants currently circulating, most of which wouldn't cause this S-gene dropout.
But this likely won't be the case for the BA.2 lineage. That means scientists will have to depend on more time-consuming and less widespread sequencing to identify it.
For Emma Hodcroft, an evolutionary geneticist at the University of Basel, that means that "there may be more Omicron than we think," per the Financial Times.
She told that outlet that "from the numbers we have right now, I don't think there's a very large hidden burden from BA.2."
In a tweet, Hodcroft emphasized that PCR tests should still work to detect whether someone has the coronavirus, even with this new lineage.
"This means we can't use this 'shortcut' to find possible Omicron cases for BA.2 only. However, the PCR test itself still works!" she said.
New data shows GSK-Vir drug works against all Omicron mutations
A GSK sign at the pharmaceuticals company's research centre in Stevenage, Britain
Tue, December 7, 2021
(Reuters) - British drugmaker GSK said on Tuesday its antibody-based COVID-19 therapy with U.S. partner Vir Biotechnology is effective against all mutations of the new Omicron coronavirus variant, citing new data from early-stage studies.
The data, yet to be published in a peer-reviewed medical journal, shows that the companies' treatment, sotrovimab, is effective against all 37 identified mutations to date in the spike protein, GSK said in a statement.
Last week, another pre-clinical data showed that the drug had worked against key mutations of the Omicron variant. Sotrovimab is designed to latch on to the spike protein on the surface of the coronavirus, but Omicron has been found to have an unusually high number of mutations on that protein.
"These pre-clinical data demonstrate the potential for our monoclonal antibody to be effective against the latest variant, Omicron, plus all other variants of concern defined to date by the WHO," GSK Chief Scientific Officer Hal Barron said.
GSK and Vir have been engineering so-called pseudoviruses that feature major coronavirus mutations across all suspicious variants that have emerged so far, and have run lab tests on their vulnerability to sotrovimab treatment.
(Reporting by Pushkala Aripaka in Bengaluru; Editing by Sherry Jacob-Phillips)
A GSK sign at the pharmaceuticals company's research centre in Stevenage, Britain
Tue, December 7, 2021
(Reuters) - British drugmaker GSK said on Tuesday its antibody-based COVID-19 therapy with U.S. partner Vir Biotechnology is effective against all mutations of the new Omicron coronavirus variant, citing new data from early-stage studies.
The data, yet to be published in a peer-reviewed medical journal, shows that the companies' treatment, sotrovimab, is effective against all 37 identified mutations to date in the spike protein, GSK said in a statement.
Last week, another pre-clinical data showed that the drug had worked against key mutations of the Omicron variant. Sotrovimab is designed to latch on to the spike protein on the surface of the coronavirus, but Omicron has been found to have an unusually high number of mutations on that protein.
"These pre-clinical data demonstrate the potential for our monoclonal antibody to be effective against the latest variant, Omicron, plus all other variants of concern defined to date by the WHO," GSK Chief Scientific Officer Hal Barron said.
GSK and Vir have been engineering so-called pseudoviruses that feature major coronavirus mutations across all suspicious variants that have emerged so far, and have run lab tests on their vulnerability to sotrovimab treatment.
(Reporting by Pushkala Aripaka in Bengaluru; Editing by Sherry Jacob-Phillips)
Omicron significantly reduces Covid antibodies generated by Pfizer vaccine, study finds
Joe Pinkstone
Tue, December 7, 2021
Health workers giving out Covid vaccines in Gaza on Tuesday - BLOOMBERG
People who have previously had Covid or been vaccinated have far less protection against omicron than they do for other variants, according to the first data of its kind.
Scientists from South Africa grew live samples of the omicron variant and performed lab experiments to see if, and how, omicron was affected by antibodies in blood samples from 12 people who had been vaccinated. Six of the people also had previously had Covid.
The world has been waiting for these neutralising studies to gauge how pre-existing immunity from both vaccination and prior infection will hold up against omicron.
The study shows how many antibodies are needed in order to stop the virus from replicating and is an early indicator of how effective the worrying new variant is at avoiding our immune system.
In reality, the picture is far more complex as human immune systems have other lines of defence that work in tandem with antibodies, such as T-cells.
The new study is the first to show how omicron compares to previous variants, such as beta and delta, on a level playing field and the preliminary data shows antibodies in blood samples are 41 times less effective for omicron than for the 2020 strain.
“This doesn't mean vaccines will be 40x less effective,” said Dr Muge Cevik, an infectious disease expert at the University of St Andrews who was not involved in the research.
However, it will be several weeks before real-world data is available and more nuanced evaluations are possible.
Before omicron emerged, beta was the variant which scientists had found was most adept at dodging antibodies.
In similar experiments, the team of academics found that beta triggered just a three-fold decrease in the number of neutralising antibodies.
Real-world studies subsequently showed that beta diminished the ability of vaccines to prevent infection by around 40 per cent.
“The results we present here with omicron show much more extensive escape,” the researchers of the new study write.
However, people who had been vaccinated and previously infected with the old coronavirus strain had higher antibody levels than in those who were just vaccinated.
“Previous infection, followed by vaccination or booster is likely to increase the neutralisation level and likely confer protection from severe disease in omicron infection,” the scientists say.
Dr Alex Sigal, one of the authors of the paper, said: “There is a very large drop in neutralisation of omicron by [Pfizer] immunity relative to ancestral virus.
“Omicron escape from [Pfizer vaccination] neutralisation is incomplete. Previous infection and vaccination still neutralises.”
Ash Otter, a research scientist working on the coronavirus for the UK Health Security Agency (UKHSA) said on Twitter that the inferior protection was to be expected, given what we know about omicron’s myriad mutations.
“Key thing to stress is [that the] data is small, but [it] looks like we don't lose complete neutralisation in those with [three time] antigen exposures (eg infection and two doses).”
This, he added, increases confidence in the theory that boosters will be effective against omicron to some degree.
Dr Rupert Beale, head of the cell biology lab at the Francis Crick Institute, agreed, tweeting out: “It looks like three jabs could still be very useful.”
“Those who received two doses of vaccine still retained neutralisation,” said Dr Cevi.
“Hybrid immunity provides much better neutralisation, which means we could expect fairly good results in boosted individuals.”
Joe Pinkstone
Tue, December 7, 2021
Health workers giving out Covid vaccines in Gaza on Tuesday - BLOOMBERG
People who have previously had Covid or been vaccinated have far less protection against omicron than they do for other variants, according to the first data of its kind.
Scientists from South Africa grew live samples of the omicron variant and performed lab experiments to see if, and how, omicron was affected by antibodies in blood samples from 12 people who had been vaccinated. Six of the people also had previously had Covid.
The world has been waiting for these neutralising studies to gauge how pre-existing immunity from both vaccination and prior infection will hold up against omicron.
The study shows how many antibodies are needed in order to stop the virus from replicating and is an early indicator of how effective the worrying new variant is at avoiding our immune system.
In reality, the picture is far more complex as human immune systems have other lines of defence that work in tandem with antibodies, such as T-cells.
The new study is the first to show how omicron compares to previous variants, such as beta and delta, on a level playing field and the preliminary data shows antibodies in blood samples are 41 times less effective for omicron than for the 2020 strain.
“This doesn't mean vaccines will be 40x less effective,” said Dr Muge Cevik, an infectious disease expert at the University of St Andrews who was not involved in the research.
However, it will be several weeks before real-world data is available and more nuanced evaluations are possible.
Before omicron emerged, beta was the variant which scientists had found was most adept at dodging antibodies.
In similar experiments, the team of academics found that beta triggered just a three-fold decrease in the number of neutralising antibodies.
Real-world studies subsequently showed that beta diminished the ability of vaccines to prevent infection by around 40 per cent.
“The results we present here with omicron show much more extensive escape,” the researchers of the new study write.
However, people who had been vaccinated and previously infected with the old coronavirus strain had higher antibody levels than in those who were just vaccinated.
“Previous infection, followed by vaccination or booster is likely to increase the neutralisation level and likely confer protection from severe disease in omicron infection,” the scientists say.
Dr Alex Sigal, one of the authors of the paper, said: “There is a very large drop in neutralisation of omicron by [Pfizer] immunity relative to ancestral virus.
“Omicron escape from [Pfizer vaccination] neutralisation is incomplete. Previous infection and vaccination still neutralises.”
Ash Otter, a research scientist working on the coronavirus for the UK Health Security Agency (UKHSA) said on Twitter that the inferior protection was to be expected, given what we know about omicron’s myriad mutations.
“Key thing to stress is [that the] data is small, but [it] looks like we don't lose complete neutralisation in those with [three time] antigen exposures (eg infection and two doses).”
This, he added, increases confidence in the theory that boosters will be effective against omicron to some degree.
Dr Rupert Beale, head of the cell biology lab at the Francis Crick Institute, agreed, tweeting out: “It looks like three jabs could still be very useful.”
“Those who received two doses of vaccine still retained neutralisation,” said Dr Cevi.
“Hybrid immunity provides much better neutralisation, which means we could expect fairly good results in boosted individuals.”
The AP Interview: CDC chief says omicron mostly mild so far
By MIKE STOBBE
Dr. Rochelle Walensky, director of the U.S. Centers for Disease Control and Prevention, poses during an interview with The Associated Press on Wednesday, Dec. 8, 2021, in Atlanta. More than 40 cases of the omicron variant have been reported in the U.S. so far, with most of them people who were vaccinated and nearly all of them suffering only mild illness, Walensky said Wednesday.
(AP Photo/Brynn Anderson)
ATLANTA (AP) — More than 40 people in the U.S. have been found to be infected with the omicron variant so far, and more than three-quarters of them had been vaccinated, the chief of the CDC said Wednesday. But she said nearly all of them were only mildly ill.
In an interview with The Associated Press, Dr. Rochelle Walensky, director of the Centers for Disease Control and Prevention, said the data is very limited and the agency is working on a more detailed analysis of what the new mutant form of the coronavirus might hold for the U.S.
“What we generally know is the more mutations a variant has, the higher level you need your immunity to be. ... We want to make sure we bolster everybody’s immunity. And that’s really what motivated the decision to expand our guidance,” Walensky said, referencing the recent approval of boosters for all adults.
She said “the disease is mild” in almost all of the cases seen so far, with reported symptoms mainly cough, congestion and fatigue. One person was hospitalized, but no deaths have been reported, CDC officials said.
Some cases can become increasingly severe as days and weeks pass, and Walensky noted that the data is a very early, first glimpse of U.S. omicron infections. The earliest onset of symptoms of any of the first 40 or so cases was Nov. 15, according to the CDC.
The omicron variant was first identified in South Africa last month and has since been reported in 57 countries, according to the World Health Organization.
The first U.S. case was reported on Dec. 1. As of Wednesday afternoon, the CDC had recorded 43 cases in 19 states. Most were young adults. About a third of those patients had traveled internationally.
More than three-quarters of those patients had been vaccinated, and a third had boosters, Walensky said. Boosters take about two weeks to reach full effect, and some of the patients had received their most recent shot within that period, CDC officials said.
Fewer than 1% of the U.S. COVID-19 cases genetically sequenced last week were the omicron variant; the delta variant accounted for more than 99%.
Scientists are trying to better understand how easily it spreads. British officials said Wednesday that they think the omicron variant could become the dominant version of the coronavirus in the United Kingdom in as soon as a month.
The CDC has yet to make any projections on how the variant could affect the course of the pandemic in the U.S. Walensky said officials are gathering data but many factors could influence how the pandemic evolves.
“When I look to what the future holds, so much of that is definitely about the science, but it’s also about coming together as a community to do things that prevent disease in yourself and one another. And I think a lot of what our future holds depends on how we come together to do that,” she said.
The CDC is also trying to establish whether the omicron variant causes milder — or more severe — illness than other coronavirus types. The finding that nearly all of the cases so far are mild may be a reflection that this first look at U.S. omicron cases captured mainly vaccinated people, who are expected to have milder illnesses, CDC officials said.
Another key question is whether it is better at evading vaccines or the immunity people build from a bout with COVID-19.
This week, scientists in South Africa reported a small laboratory study that found antibodies created by vaccines were not as effective at preventing omicron infections as they were at stopping other versions of the coronavirus.
On Wednesday, vaccine manufacturer Pfizer said that while two doses may not be protective enough to prevent infection, lab tests showed a booster increased levels of virus-fighting antibodies by 25-fold.
Blood samples taken a month after a booster showed people harbored levels of omicron-neutralizing antibodies that were similar to amounts proven protective against earlier variants after two doses, the company said.
___
The Associated Press Health & Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.
ATLANTA (AP) — More than 40 people in the U.S. have been found to be infected with the omicron variant so far, and more than three-quarters of them had been vaccinated, the chief of the CDC said Wednesday. But she said nearly all of them were only mildly ill.
In an interview with The Associated Press, Dr. Rochelle Walensky, director of the Centers for Disease Control and Prevention, said the data is very limited and the agency is working on a more detailed analysis of what the new mutant form of the coronavirus might hold for the U.S.
“What we generally know is the more mutations a variant has, the higher level you need your immunity to be. ... We want to make sure we bolster everybody’s immunity. And that’s really what motivated the decision to expand our guidance,” Walensky said, referencing the recent approval of boosters for all adults.
She said “the disease is mild” in almost all of the cases seen so far, with reported symptoms mainly cough, congestion and fatigue. One person was hospitalized, but no deaths have been reported, CDC officials said.
Some cases can become increasingly severe as days and weeks pass, and Walensky noted that the data is a very early, first glimpse of U.S. omicron infections. The earliest onset of symptoms of any of the first 40 or so cases was Nov. 15, according to the CDC.
The omicron variant was first identified in South Africa last month and has since been reported in 57 countries, according to the World Health Organization.
The first U.S. case was reported on Dec. 1. As of Wednesday afternoon, the CDC had recorded 43 cases in 19 states. Most were young adults. About a third of those patients had traveled internationally.
More than three-quarters of those patients had been vaccinated, and a third had boosters, Walensky said. Boosters take about two weeks to reach full effect, and some of the patients had received their most recent shot within that period, CDC officials said.
Fewer than 1% of the U.S. COVID-19 cases genetically sequenced last week were the omicron variant; the delta variant accounted for more than 99%.
Scientists are trying to better understand how easily it spreads. British officials said Wednesday that they think the omicron variant could become the dominant version of the coronavirus in the United Kingdom in as soon as a month.
The CDC has yet to make any projections on how the variant could affect the course of the pandemic in the U.S. Walensky said officials are gathering data but many factors could influence how the pandemic evolves.
“When I look to what the future holds, so much of that is definitely about the science, but it’s also about coming together as a community to do things that prevent disease in yourself and one another. And I think a lot of what our future holds depends on how we come together to do that,” she said.
The CDC is also trying to establish whether the omicron variant causes milder — or more severe — illness than other coronavirus types. The finding that nearly all of the cases so far are mild may be a reflection that this first look at U.S. omicron cases captured mainly vaccinated people, who are expected to have milder illnesses, CDC officials said.
Another key question is whether it is better at evading vaccines or the immunity people build from a bout with COVID-19.
This week, scientists in South Africa reported a small laboratory study that found antibodies created by vaccines were not as effective at preventing omicron infections as they were at stopping other versions of the coronavirus.
On Wednesday, vaccine manufacturer Pfizer said that while two doses may not be protective enough to prevent infection, lab tests showed a booster increased levels of virus-fighting antibodies by 25-fold.
Blood samples taken a month after a booster showed people harbored levels of omicron-neutralizing antibodies that were similar to amounts proven protective against earlier variants after two doses, the company said.
___
The Associated Press Health & Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.
