New Coronavirus News from 27 Nov 2021b

Heavily mutated Omicron variant puts scientists on alert [Nature.com, 27 Nov 2021]

By Ewen Callaway

Researchers are racing to determine whether a fast-spreading coronavirus variant poses a threat to COVID vaccines’ effectiveness.

Researchers in South Africa are racing to track the concerning rise of a new variant of the SARS-CoV-2 coronavirus that causes COVID-19. The variant harbours a large number of the mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa.

A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveller arriving in Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do.

“We’re flying at warp speed,” says Penny Moore, a virologist at the University of the Witwatersrand in Johannesburg, South Africa, whose lab is gauging the variant’s potential to dodge immunity from vaccines and previous infections. There are anecdotal reports of reinfections and of cases in vaccinated individuals, but “at this stage it’s too early to tell anything”, Moore adds.

“There’s a lot we don’t understand about this variant,” Richard Lessells, an infectious-diseases physician at the University of KwaZulu-Natal in Durban, South Africa, said at a press briefing organized by South Africa’s health department on 25 November. “The mutation profile gives us concern, but now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.”

On 26 November, the World Health Organization (WHO) designated the strain, known as B.1.1.529, as a variant of concern and named it Omicron, on the advice of scientists who are part of the WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution. Omicron joins Delta, Alpha, Beta and Gamma on the current WHO list of variants of concern.

Researchers also want to measure the variant’s potential to spread globally — possibly sparking new waves of infection or exacerbating ongoing rises being driven by Delta.

Changes to spike
Researchers spotted B.1.1.529 in genome-sequencing data from Botswana. The variant stood out because it contains more than 30 changes to the spike protein — the SARS-CoV-2 protein that recognizes host cells and is the main target of the body’s immune responses. Many of the changes have been found in variants such as Delta and Alpha, and are linked to heightened infectivity and the ability to evade infection-blocking antibodies.

The apparent sharp rise in cases of the variant in South Africa’s Gauteng province — home to Johannesburg — is also setting off alarm bells. Cases increased rapidly in the province in November, particularly in schools and among young people, according to Lessells. Genome sequencing and other genetic analysis from a team led by Tulio de Oliveira, a bioinformatician at the University of KwaZulu-Natal, found that the B.1.1.529 variant was responsible for all 77 of the virus samples they analysed from Gauteng, collected between 12 and 20 November. Analysis of hundreds more samples are in the works.

The variant harbours a spike mutation that allows it to be detected by genotyping tests that deliver results much more rapidly than genome sequencing does, Lessells said. Preliminary evidence from these tests suggest that B.1.1.529 has spread considerably further than Gauteng. “It gives us concern that this variant may already be circulating quite widely in the country,” Lessells said.

Vaccine effectiveness
To understand the threat B.1.1.529 poses, researchers will be closely tracking its spread in South Africa and beyond. Researchers in South Africa mobilized efforts to quickly study the Beta variant, identified there in late 2020, and a similar effort is starting to study B.1.1.529.

Moore’s team — which provided some of the first data on Beta’s ability to dodge immunity — has already begun work on B.1.1.529. They plan to test the virus’s ability to evade infection-blocking antibodies, as well as other immune responses. The variant harbours a high number of mutations in regions of the spike protein that antibodies recognize, potentially dampening their potency. “Many mutations we know are problematic, but many more look like they are likely contributing to further evasion,” says Moore. There are even hints from computer modelling that B.1.1.529 could dodge immunity conferred by another component of the immune system called T cells, says Moore. Her team hopes to have its first results in two weeks.

“A burning question is ‘does it reduce vaccine effectiveness, because it has so many changes?’,” says Aris Katzourakis, who studies virus evolution at the University of Oxford, UK. Moore says breakthrough infections have been reported in South Africa among people who have received any of the three kinds of vaccines in use there, from Johnson & Johnson, Pfizer–BioNTech and Oxford–AstraZeneca. Two quarantined travellers in Hong Kong who have tested positive for the variant were vaccinated with the Pfizer jab, according to news reports. One individual had travelled from South Africa; the other was infected during hotel quarantining.

Researchers in South Africa will also study whether B.1.1.529 causes disease that is more severe or milder than that produced by other variants, Lessells said. “The really key question comes around disease severity.”

So far, the threat B.1.1.529 poses beyond South Africa is far from clear, researchers say. It is also unclear whether the variant is more transmissible than Delta, says Moore, because there are currently low numbers of COVID-19 cases in South Africa. “We’re in a lull,” she says. Katzourakis says that countries where Delta is highly prevalent should be watching for signs of B.1.1.529. “We need to see what this virus does in terms of competitive success and whether it will increase in prevalence.”

Nature 600, 21 (2021)
doi: https://doi.org/10.1038/d41586-021-03552-w

The Omicron variant upends the global pandemic response. [The New York Times, 27 Nov 2021]

By Isabella Grullón Paz

Britain, Israel and others announced new restrictions as some health experts urged caution.

Governments around the world reintroduced restrictive measures as scientists raced to study a new coronavirus variant and several cases were spotted in Europe days after it was first detected in southern Africa.

Omicron, a new variant first detected in Botswana, sent Europe into high alert after cases were detected in the United Kingdom, Germany, Italy and Belgium. The Czech Republic, Austria, Israel and the Netherlands were all investigating suspected cases of the variant.

Relatively little is known about Omicron. It has mutations that scientists fear could make it more infectious and less susceptible to vaccines — though neither of these effects is yet to be established. Most confirmed cases of the variant are contained to southern African countries, but there are worries the virus could have spread more widely before scientists there discovered it.

“There’s been a window of probably about two weeks conservatively that this virus has been spreading,” Andrew Pekosz, an epidemiologist from Johns Hopkins Bloomberg School of Public Health said in an interview on Saturday. It is likely the variant is already in New York, he said.

“There certainly is a chance that it has already spread globally, but we just don’t know yet,” Mr. Pekosz added.

European leaders, already struggling with a surge in Covid-19 cases that has made it once again the epicenter of the pandemic, tried to strike a balance between increasing caution and avoiding panic.

Sixty-one passengers out of more than 500 on two flights from southern African countries into the Netherlands on Saturday tested positive for the coronavirus and are quarantining in Amsterdam. The Omicron variant is likely to be found in some of those 61 passengers who tested positive, the Dutch authorities said.

The European Union is restricting travel to and from seven countries in southern Africa, Botswana, Eswatini, Lesotho, Mozambique, Namibia, South Africa and Zimbabwe, while the United States and South Korea have targeted those countries and Malawi. Britain initially restricted travel from those eight nations before adding Angola, Malawi, Mozambique and Zambia to its red list.

Canada, Australia, Russia, Thailand, Sri Lanka, Singapore, Saudi Arabia, Oman and Morocco have all announced similar restrictions.

Israel said Saturday it would close its borders to foreign nationals for two weeks.

In a news conference on Saturday evening, Prime Minister Boris Johnson said that to curb the spread of the variant, face masks would be required in stores and on public transportation, a rule the country had ended in July.

Britain will also require travelers from abroad to get a PCR test within 48 hours of their arrival and require contacts of those who test positive with a suspected case of Omicron to self-isolate for 10 days, regardless of vaccination status.

The variant was also detected in Hong Kong, which prompted “the most stringent boarding and quarantine requirements” for travelers coming from southern African countries.

“I think certainly caution is warranted to restrict travel and to watch this closely, but at the end of the day, we really need a lot more data to evaluate this new variant,” Philip A. Chan, an infectious disease doctor at Brown University who has helped lead the Covid-19 response for Rhode Island, said.

What we do know, he said, is that the Omicron variant seems to be overtaking the Delta variant in southern African countries, which suggest Omicron is more contagious and that it can overcome some of the natural immunity and vaccine immunity.

“Neither one of those things are good, obviously. And I think that those are the two reasons that have experts and scientists so concerned,” Dr. Chan said. But he still “urges caution and patience.”

“Let’s wait to see what the data shows. Let’s take appropriate precautions,” he said.

Dr. Chan also cautioned that without a robust global vaccination effort, “we are half-treating the pandemic” and leaving the world open to new and more transmittable variants.

Expert urges vigilance over Omicron COVID variant [ABS-CBN News, 27 Nov 2021]

By Aleta Nieva Nishimori,

MANILA— An infectious disease expert on Saturday urged the public to remain vigilant and strictly adhere to health protocols amid the possible threat of a more highly transmissible COVID-19 variant first detected in South Africa.

“Alam na natin na 'yung Delta mataas ang transmissibility kaya maraming na-admit, marami rin nagkakasakit na naging severe. If this virus ganito kadami ng mutation we presume that the behavior of this virus is more transmissible compared to Delta,” said Dr. Rontgene Solante.
(We know that Delta has a high transmissibility rate that’s why many were admitted and many developed severe illness. We presume that, because of the mutations [in the Omicron variant] the behavior of this virus is more transmissible compared to Delta.)

The World Health Organization (WHO) on Friday classified the B.1.1.529 variant detected in South Africa as a SARS-CoV-2 "variant of concern," saying it may spread more quickly than other forms.

“Obserbahan natin kung talaga bang deadly ito dahil ang information natin is this virus is very highly transmissible,” said Solante.

(Let’s observe if this is going to be deadly because based on our information this virus is very highly transmissible.)

Preliminary evidence on the new variant suggest there is an increased risk of reinfection and there had been a "detrimental change in COVID-19 epidemiology," the WHO said in a statement after a closed meeting of independent experts who reviewed the data.

The B.1.1.529 variant has a "very unusual constellation" of mutations, which are concerning because they could help it evade the body's immune response and make it more transmissible, scientists said this week.

With the threat of the variant, the Philippine government acted swiftly by suspending inbound flights from South Africa and six other countries amid the presence of the B.1.1.1529 COVID-19 variant there. The suspension will be imposed until Dec. 15

“They evaluated fully, nakita nila gaano kadelikado itong mutation sa isang virus na more or less highly transmissible over that of Delta so I think that’s the clincher there na talagang nag-declare kaagad ng border control sa mga bansang meron nang Omicron,” said Solante.

(They evaluated and saw how dangerous this mutation is that is more or less highly transmissible over that of Delta so I think that was the clincher there for them to impose border control on countries where Omicron is present.)

Aside from South Africa, the suspension of inbound international flights covers Botswana, Namibia, Zimbabwe, Lesotho, Eswatini, and Mozambique.

The Bureau of Quarantine has been directed to locate travelers from the mentioned countries who may have arrived in the recent 7 days prior to the temporary suspension of inbound travel. The travelers will be required to undergo 2-week quarantine with a mandatory RT-PCR test on the 7th day.

Solante advised all travelers, not only those coming from South Africa, to report to local authorities and have themselves tested if they experience symptoms. They should also go through the Philippines’ quarantine requirements.

“Walang short cut,” he said.

(There’s no short cut.)

Solante said the public should continue to observe the health protocols, while the COVID-19 vaccination program should also proceed unhampered.

"'Pag bumaba ang kaso nagiging complacent na tayo, hindi na tayo nagpapa-test. I think we need to encourage na 'pag merong mga sintomas part of the surveillance talagang magpapa-test tayo," he said.

(We become complacent and no longer do tests when COVID cases drop. I think we need to encourage the public that part of the surveillance is to get tested when we have symptoms.)

More transmissible than Delta? Expert urges public vigilance over Omicron variant

From patient zero to billions wiped off global shares, the inside story of how the Omicron variant emerged [iNews, 27 Nov 2021]

By Jane Merrick

The case of super-variant Omicron’s “Patient Zero” – a 36-year-old man from Hong Kong – throws troubling light on just how contagious this new strain is, and how the international battle to bring the pandemic to an end has become so much harder.

While the global epicentre of the super-variant is South Africa, with cases believed to date back from early November, the first official record of variant B.1.1.529 emerged in Hong Kong on 13 November.

According to Hong Kong’s Centre for Health Protection (CHP), Patient Zero – case number 12388 – flew to South Africa on 23 October, returning on 11 November on a Qatar Airlines flight QR818.

He tested negative on arrival at Hong Kong airport, but under the territory’s strict quarantine rules he was put up in the Regal Airport Hotel in Chek Lap Kok for the required 21 days.
Two days later he tested positive for Covid-19, with the health authority saying his sample showed signs of a mutation, and the next day, 14 November, he was admitted to hospital with a high viral load.

On 22 November, the patient’s genome sample was uploaded onto GISAID, the global genomic database used by virologists around the world to analyse and compare data.

On that same day, the CHP noticed a link between case 12388 and a second, labelled 12404 – someone who had not been to South Africa but was staying in the same hotel as the 36-year-old. In fact, their rooms were opposite each other on the 5th floor of the Regal Airport Hotel.
Case 12404 had checked into the hotel on 10 November, a day before case 12388, and tested negative twice before being diagnosed with Covid-19 on 18 November. He was also admitted to hospital.
Investigators swabbed the rooms of the two men – room 5111 for case 12404 and room 5112 for case 12388 – and found 25 positive samples of Covid-19 on surfaces and other areas.

The CHP report, published on 22 November and seen by i, reads: “Opinions from experts suggested that case 12404, who had stayed in the room opposite to the room where case 12388 had stayed, might have been infected with the virus while air flowed to the corridor when case 12388 opened his hotel room door without wearing a surgical mask, coupled with unsatisfactory air flow.”

Officials contact-traced everyone who stayed on their corridor between 11 and 14 November. It is believed there are no further cases.

Health experts in this country have told i this level of infectiousness – transmission occurring across a corridor when a hotel door is opened – has occurred with Delta, which is also a highly infectious strain.

But this still suggests it is a high-transmission variant, and the CHP report is one of a number that have been pored over by the UK Health Security Agency and World Health Organisation as they scramble to assess how infectious the B.1.1.529 variant is.

As officials in Hong Kong were investigating the two airport hotel cases, scientists in South Africa were trying to establish what was causing a new wave in the country, with an outbreak centred on Gauteng province.

Cases there had risen from a very low level at the start of November to an exponential growth of cases in the space of two weeks. Less than 1 per cent of people in Gauteng were testing positive at the start of November, but this rose to 6 per cent within a fortnight.

South Africa’s high level of genomic sampling meant scientists there were able to quickly establish something different about these new cases. Since 12 November, they have found 77 samples with what is known as S-gene failure – essentially a gene that is missing in a normal covid genome profile.

Although many scientists in South Africa and internationally were noticing evidence of a new variant, a virologist back in the UK was the first to officially report it.

On 22 November, the first sequences were uploaded onto GISAID – including the pair of travellers from Hong Kong.

The next day, Dr Tom Peacock, a virologist at Imperial College London, posted a Pango lineage request – essentially the internationally agreed system of naming covid variants.

Marking it “urgent”, he labelled it “B.1.1 descendant associated with Southern Africa with extremely high number of Spike mutations”, listing 32 of these changes – twice the number seen in Delta.

On Twitter, Dr Peacock described the profile of the variant as “horrific”. There were just four cases, but over the next 24 hours the online database entry would see more samples added – to around 10, including some from Botswana, South Africa and Hong Kong.

A fellow scientist, a geneticist from Stanford University, speculated in the comments that the virus was so different to the original Wuhan strain, Sars-Cov-2, it could be labelled “Sars-Cov-3” – “essentially restarting the pandemic”.

On the morning of Wednesday 24 November, after reading Dr Peacock’s Pango entry request, the i newspaper contacted officials in the UK government about the variant, which did not yet have a distinct label. The i was told UK Health Security Agency officials were looking into the variant as a “matter of routine”.

In fact, the agency’s top health experts were alerted to Dr Peacock and other scientists’ warnings about the variant, and were investigating it as a matter of urgency, including speaking to and offering assistance to scientists in South Africa.

The number of mutations, associated with everything from vaccine escape, higher transmission and higher viral load, caused serious concern among the UK’s top covid experts.
At lunchtime on Wednesday, the i was the first news organisation in the world to publish a story about the variant, which had just been assigned the label B.1.1.529.

Back in South Africa, it is understood, journalists read the i article and began asking the health department for a full briefing on what they knew about the variant.

By Thursday morning, as South African scientific experts gave their press conference, the full extent of the variant’s spread became clear. There were close to 100 cases in Gauteng, but Professor Tulio de Oliveira, a leading South African covid expert, told the press conference he expected there to be “many more” across South Africa.
It was clear the variant was spreading so fast in South Africa that action had to be taken by other governments.

On Thursday afternoon, senior health officials at the UKHSA advised ministers about the extent of the spread and its apparent superior infectiousness.

Within hours it became clear that – just 48 hours after the variant was first identified – ministers had to take drastic action, and they decided to ban flights from South Africa and five other southern African countries.

A senior health expert said the variant was the worst they had ever seen because the 32 mutations made it so dramatically different to the original Wuhan strain, to which the world is building up immunity.

By Friday, a string of other countries imposed travel bans on South Africa, and nervousness about the new variant’s threat to the pandemic recovery sent global stock markets tumbling.
The World Health Organisation, which took two months to designate Delta a variant of concern, decided B.1.1.529 needed the label just 72 hours after it was identified, giving it the Greek name Omicron.

Around £72 billion was wiped off the value of London’s top shares, while the Dow Jones recorded its worst day in more than a year, closing 900 points lower.

Omicron: 5 things Dr Fauci says about this new variant of Covid-19 [Hindustan Times, 27 Nov 2021]

by Poulomi Ghosh

There is no indication that new Covid variant Omicron is present in the United States, but anything is possible, Dr Anthony Fauci said.

Scientists of the United States are actively communicating with their colleagues in South Africa to get more details about Omicron, the new variant of Covid-19, America's top infectious disease expert Dr Anthony Fauci said. Reports of the new variant have triggered panic and brought back fresh restrictions across the world. The variant is heavily mutated and is thought to be more transmissible than the previous variants.

Here are five things that the White House chief medical advisor said about the Omicron in an interview with CNN. Fauci was asked about the concerns regarding Omcron and whether there is any chance that it has already spread to the United States.

1. There are concerns over more transmissibility and the possibility of the evasion of the immune response. We do not know for sure right now. This is really something in motion.

Shouldn’t let guards down’: WHO tells southeast Asian countries over omicron

2. The variant seems to be spreading at a reasonably rapid rate in the sense of when they do test positivity, it seems to be a bit more widespread than what was previously thought. It is in a fluid motion.

3. Anything is possible. There is no indication that the new variant is present in the United States. There is a lot of travel involved in how the variant spread from South Africa to Hong Kong. And so, we are trying to get the actual molecular make-up of the variant so that we can test for it. And that's something that will take time.

WHO avoids Greek alphabet Xi and names new Covid variant Omicron. Here's why

4. When you look at a mutation, it is going to give you a hint or prediction that it might evade the immune response. You need to get that particular sequence of the virus, put it in a form in the lab where you can actually test the different antibodies so you can have a prediction that it might evade or you can actually prove it. Right now, we are getting the material together.

Omicron cases detected in UK, Germany and Italy

Although epidemiologists say travel curbs may be too late to stop the Omicron variant from circulating globally, many countries around the world - including the United States, Brazil, Canada and European Union nations - announced travel bans or restrictions on southern Africa. This report produced by Jonah Green.

5. You are talking about sort of like a red flag that it might be an issue but we don't know. Once we test, you can tell for sure whether it does or does not evade the antibodies that we make for example against the virus through a vaccine.

Top Botswana health official ‘very concerned’ about Omicron variant [FRANCE 24, 27 Nov 2021]

With a growing number of countries imposing travel restrictions from southern Africa amid the new Omicron variant fears, Botswana’s Covid-19 task force chief Kereng Masupu, told FRANCE 24 his country was taking all necessary public health measures to stem a viral spread.

Botswana, one of the southern African nations facing new travel restrictions, has recorded more than 194,000 total Covid-19 cases and 2,416 deaths since the start of the pandemic.

Speaking to FRANCE 24 on Friday night, Kereng Masupu, coordinator of Botswana’s presidential Covid-19 task force, said the country had detected four confirmed Omicron variant cases and 11 other people were under investigation.

Although public health officials were “very, very worried” about the new variant, Masupu stressed that Botswana is “ready to deal with it”.

Novavax working on vaccine to combat omicron variant | TheHill [The Hill, 27 Nov 2021]

Biotechnology company Novavax is working on a vaccine to combat the new omicron coronavirus variant that was first detected in South Africa.

Public health officials in the U.S. and abroad are worried the omicron variant could be more transmissible and resistant to current vaccines due to the 30 mutations at the spike protein. This protein is the region that interacts with human cells prior to entry.

Novavax said its vaccine would contain the mutated spike protein in the omicron variant so individuals can develop an immune response, a company spokesperson said.

The testing and manufacturing of the shot will likely “take a few weeks,” the spokesperson added.

The company's vaccine received emergency use approval in Indonesia earlier this month and was later approved for emergency use by the Philippines. The company has yet to file for approval in the U.S.

Other vaccine developers said they have already begun evaluating how effective their vaccines are on the new variant. BioNTech said Friday that the company will know in two weeks how effective the vaccine it developed with Pfizer is against the omicron variant.

"We expect more data from the laboratory tests in two weeks at the latest. These data will provide more information about whether B.1.1.529 could be an escape variant that may require an adjustment of our vaccine if the variant spreads globally," a BioNTech spokesperson told Reuters.

The omicron strain has triggered a worldwide scramble to contain the spread, with many countries restricting air travel from several African countries a day after the variant was announced.

The new variant was first found in South Africa and is confirmed to have spread to the United Kingdom, Israel, Hong Kong, Belgium and Botswana.

New York Gov. Kathy Hochul (D) has already declared a state of emergency in preparation for a surge in cases in the state, although there have been no confirmed cases reported in the U.S.

Omicron: What Is the Difference Between ‘Variant of Interest' Vs. ‘Variant of Concern?' [NBC Chicago, 27 Nov 2021]

As the World Health Organization announces that omircon has been classified as a "variant of concern," many are asking about the difference between this categorization and a "variant of interest."

WHO Health Emergencies Programme COVID-19 Technical Lead Dr. Maria Van Kerkhove said early evidence on omicron, known by the technical term B.1.1.529, shows that the variant has a large number of mutations, some of which have concerning characteristics.

Omicron has also shown to have an increased risk of reinfection compared to other highly transmissible variants, indicating that people who contracted COVID and recovered could be more subject to catching it again with this variant.

According to the Centers for Disease Control and Prevention, however, variants of the coronavirus were expected.

"Viruses constantly change through mutation, and new variants of a virus are expected to occur," the CDC's website reads. "Sometimes new variants emerge and disappear. Other times, new variants persist. Numerous variants of the virus that causes COVID-19 are being tracked in the United States and globally during this pandemic."

Variants are categorized into three categories: (1) "variants of interest," (2) "variants of concern" and (3) "variants of high consequence."

The CDC states that a variant is classified as a variant of interest if it shows "specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity."

"We will probably have a variant of what we call a variant of interest identified every few weeks," Chicago Department of Public Health Commissioner Dr. Allison Arwady said Tuesday.
"Like that's how this virus works. Variants of interest just mean we've seen a number of the same genetic mutations emerge and scientists around the world are on the lookout for it every single time. A virus anywhere in the world gets this genetic sequence, it gets updated into a database that's shared internationally, so we can really see what's emerging. When a variant of interest emerges, it says, 'Oh, this is something we should watch a little bit.'"

A variant of concern is one in which "there is evidence of an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures," according to the CDC.

"Once we see a variant of interest clearly have an impact, meaning it is more contagious, it might be evading a treatment, it's clearly making people sicker - that makes it into a variant of concern," Arwady said.

Variants of concern, which include alpha, beta, delta and now omicron, have shown to spread more easily, cause more serious disease, or dent the effectiveness of vaccines and other COVID-fighting tools. They’re more worrying than the variants of interest — like mu and lambda — that have affected aspects like transmissibility and severity of the disease but aren't as transmissible.

Finally, a variant of high consequence "has clear evidence that prevention measures or medical countermeasures have significantly reduced effectiveness relative to previously circulating variants." Or, as Chicago's top doctor put it, a variant in which "the vaccine was not working very well."

Currently there are no variants of high consequence.

"I would say if something became a variant of high consequence that would be a big deal," Arwady said, adding that such variants are ones in which "the vaccine was not working very well."

As of Saturday, no cases of omicron have officially been detected across the U.S., according to health officials. The Chicago Department of Public Health noted, however, that they are "don't know" if the variant has reached America yet.

Omicron has thus far been seen in travelers to the U.K., Belgium, Hong Kong and Israel, as well as in southern Africa.

Biden and Harris briefed as US braces for arrival of Omicron Covid variant [The Guardian, 27 Nov 2021]

By Edward Helmore

US imposes travel restrictions from southern Africa as Anthony Fauci says he would not be surprised if variant were already in US

Joe Biden and Kamala Harris have been briefed on the latest situation regarding the new Omicron coronavirus variant, the White House said on Saturday, as Britain, Germany and Italy reported detecting cases.

Biden, who was spending Thanksgiving with family in Nantucket, Massachusetts, told reporters on Friday: “We don’t know a lot about the variant except that it is of great concern [and] seems to spread rapidly.”

Omicron was first detected in South Africa, leading countries including the US to impose travel restrictions on that nation and at least seven others in the region.

No cases of Omicron have been identified in the US to date, the federal Centers for Disease Control and Prevention said. The agency expects that it would identify the variant quickly if it emerges in the US.

Dr Anthony Fauci, the top US infectious disease specialist and chief White House medical adviser, told NBC on Saturday he “would not be surprised” if the variant were already in the US.

“When you have a virus that is showing this degree of transmissibility and you’re already having travel-related cases that they’ve noted in Israel and Belgium and other places, when you have a virus like this, it almost invariably is ultimately going to go essentially all over,” Fauci said.

Asked about next moves to deal with the Omicron threat, Harris told reporters the administration would take it “one step at a time”.

“For now we’ve done what we think is necessary,” she said.

The White House said senior health officials and its Covid response team were monitoring the latest updates on Omicron and were in regular touch with officials around the world.

In New York, one of the states hit hardest and earliest by Covid-19, the governor announced steps to limit a new winter wave of infections as transmission rates approach those of April 2020.

New York has recorded more than 2.7m cases of Covid-19 and more than 57,000 deaths, the fourth highest state death toll, behind California, Texas and Florida.

Late on Friday, Governor Kathy Hochul said: “While the new Omicron variant has yet to be detected in New York state, it’s coming.”

The next day, the banner headline on the front page of the New York Post tabloid said simply: “Omi-God, Not Again.”

Hochul also issued an executive order postponing elective surgeries, a move designed to protect hospital capacity until at least 15 January, and a disaster emergency declaration.

Covid hospital admissions in New York have increased to more than 300 a day. Hospitals with less than 10% staffed bed capacity, or those designated by the state, will be authorized to screen patients and restrict admissions.

Hochul said: “We’ve taken extraordinary action to prevent the spread of Covid-19 and combat this pandemic. However, we continue to see warning signs of spikes this upcoming winter.”

The governor urged New Yorkers to mask up in indoor public venues, get tested when appropriate and to stay home when ill.

Two-thirds of New York state residents are fully vaccinated and close to 80% have received at least one dose, according to the governor’s office. But New York state is divided between intensively vaccinated downstate areas, including New York City, and upstate areas that have lower vaccination rates and higher rates of infection.

According to the state health department, Buffalo and western New York has a 9.67% Covid positivity rate. The positivity rate in New York City is 1.65%, less than half the 3.84% state average. Vaccination rates in some regions are as low as 52%. In New York City, 97% of Queens adults and 94% of Manhattan adults have had the jab.

Hochul urged New Yorkers to get the vaccination, noting that just under 10% of adults in the state have not.

“The vaccine remains one of our greatest weapons in fighting the pandemic and I encourage every New Yorker to get vaccinated and get the booster if you’re fully vaccinated,” she said.
As parts of the US experience Covid surges, intensive care units in Michigan are approaching capacity. New York and other eastern states are watching closely.

On Friday the mayor-elect of New York City, Eric Adams, said the Omicron variant was “a concerning development that we must watch extremely closely, and be prepared to address as a city, state and country. Our health officials must … have response options available should it prove to be significantly more virulent.”

Adams and the outgoing mayor, Bill de Blasio, earlier came together to urge city residents to get the vaccines and booster shots.

Vaccine makers race to stay ahead of new COVID-19 variants [NPR, 27 Nov 2021]

By DUSTIN JONES

A new strain of COVID-19 first discovered in South Africa was declared a variant of concern by the World Health Organization on Friday. Here's how the pharmaceutical industry plans to address the latest coronavirus curve ball.

Vaccine makers are already pivoting their efforts to combat the new variant: testing higher doses of booster shots, designing new boosters that anticipate strain mutations, and developing omicron-specific boosters.

In a statement sent to NPR, Moderna said it has been working on a comprehensive strategy to predict variants of concern since the beginning of 2021. One approach is to double the current booster from 50 to 100 micrograms. Secondly, the vaccine maker has been studying two booster vaccines that are designed to anticipate mutations like those found in the omicron variant. The company also said it will ramp up efforts to make a booster candidate that specifically targets omicron.

"From the beginning, we have said that as we seek to defeat the pandemic, it is imperative that we are proactive as the virus evolves," said Moderna CEO Stéphane Bancel. "The mutations in the Omicron variant are concerning and for several days, we have been moving as fast as possible to execute our strategy to address this variant."

Pfizer and BioNTech told Reuters that it expects more data about the omicron variant to be collected within two weeks. That information will help determine whether or not they need to modify their current vaccine. Pfizer and BioNTech said that a vaccine tailored for the omicron variant, if needed, could be ready to ship in approximately 100 days.

Johnson & Johnson said in a statement sent to NPR that it too is already testing its vaccine's efficacy against the new variant.

The omicron variant was first reported to the WHO on Nov. 24, the WHO said. Preliminary evidence indicates the variant poses an increased risk for reinfection due to the large number of mutations. Until recently, cases across South Africa have predominantly been from the delta variant, an earlier strain that has pushed health care systems to the max since early summer.
But omicron infections have been on the rise in recent weeks, the WHO reported.
More concerning, omicron cases have emerged across the globe. Al Jazeera reported that cases have been confirmed in the United Kingdom, Italy, Germany, Belgium, Israel and Hong Kong.

News of the rapidly spreading variant led to a new set of air travel restrictions from South Africa and seven other countries, implemented by President Joe Biden, that go into effect Monday. The president made the announcement the day after Thanksgiving, one of the busiest travel periods of the year.

Unlike last year, when millions of people traveled against the advice of health experts, the Centers for Disease Control and Prevention and chief medical advisor to the president, Dr. Anthony Fauci, more or less condoned Thanksgiving get-togethers for vaccinated Americans.
And, according to an American Automobile Association travel forecast, over 53 million people were expected to travel for Thanksgiving — an 18% jump compared to last year — including more than 4 million by air.

As of Friday, the CDC said that no cases of the omicron variant had been identified in the United States. However, Fauci said on Saturday that he would not be surprised if the variant is already here.

"We have not detected it yet, but when you have a virus that is showing this degree of transmissibility and you're already having travel-related cases that they've noted in Israel and Belgium and other places ... it almost invariably is ultimately going to go essentially all over," he said in an interview on the Today show.

As Americans prepare to transition from one busy holiday to the next, the CDC is predicting that coronavirus cases, hospitalizations and deaths will increase over the next four weeks.
More than 776,000 people in the U.S. have died of COVID-19 to date, according to Johns Hopkins University's tracker, and the country is projected to surpass 800,000 deaths by Christmas.

WHO avoids Greek alphabet Xi and names new Covid variant Omicron. Here's why [Hindustan Times, 27 Nov 2021]

The new variant of Covid identified first in South Africa has been named omicron by the World Health Organization on Friday. The variants of SARS-CoV-2 are named after Greek alphabets, but for naming omicron, the experts skipped two letters Nu and Xi and chose omicron instead. In fact, Nu started trending on social media platforms after the news of a new Covid variant came out as Nu was the possible choice for the name of this new variant, which is believed to be more transmissible than the other variants.

Omicron comes next to Nu and Xi, the alphabets WHO experts have cautiously avoided.
According to experts, Nu has been avoided as this alphabet is confusing with the English word new. And Xi has been avoided so that the name is not misconstrued as a reference to Chinese premier Xi Jinping.

Omicron Covid variant: What do we know about risks, symptoms, tests

Paul Nuki, senior editor of the Telegraph shared a quote from a source in WHO who said the alphabets have been deliberately avoided. "Nu had been skipped to avoid confusion with the word new and Xi had been skipped to avoid stigmatising a region," the court read, without mentioning the region.

Omicron cases detected in UK, Germany and Italy

Although epidemiologists say travel curbs may be too late to stop the Omicron variant from circulating globally, many countries around the world - including the United States, Brazil, Canada and European Union nations - announced travel bans or restrictions on southern Africa. This report produced by Jonah Green.

"If the WHO is this scared of the Chinese Communist Party, how can they be trusted to call them out the next time they're trying to cover up a catastrophic global pandemic?" Senator Ted Cruz tweeted.

Omicron is the 15th letter of the Greek alphabet. The letter is derived from the Phoenician letter ayin.

"Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron," the WHO said on Friday.

World is put on high alert over the Omicron coronavirus variant [CNN, 27 Nov 2021]

By Ivana Kottasová

(CNN)Europe is frantically imposing travel bans, scrambling to ramp up its coronavirus sequencing abilities after several countries on the continent reported suspected cases of the newly identified and potentially more transmissible coronavirus variant known as Omicron.

As of Friday, the variant was found in South Africa, Botswana, Hong Kong and Belgium, and the European Centre for Disease Prevention and Control said Friday there was a "high to very high" risk the new variant would spread in Europe.

By Saturday afternoon, two cases were confirmed in the United Kingdom, two others in Germany and one in Italy. Dozens more are suspected in the Netherlands and the Czech Republic. The top infectious disease expert in the United States, Dr. Anthony Fauci, also said it was possible the new variant was already in his country but was yet to be detected.

UK's Secretary of State for Health Sajid Javid said the two cases detected in the UK were linked to travel to southern Africa, the region where the Omicron variant was first detected.
"These individuals are self-isolating with their households while further testing and contact tracing is underway," he added.

The German cases, identified in Munich, are two passengers who arrived from Cape Town on November 24, the Bavarian Ministry of Health said in a statement on Saturday.

"The individuals have been in domestic isolation since Nov. 25 following a positive PCR test. Following reports of the new variant, the two individuals had the foresight to arrange for themselves to be tested for the variant," authorities said.

The Italian case is in the southwestern region of Campania, a passenger who arrived from Mozambique, Italy's health ministry said in a statement. It didn't disclose the date of the passenger's arrival or nationality.

Earlier on Saturday, German authorities had identified a "suspected" case of the Omicron variant in Frankfurt from another passenger who returned from South Africa. The local health department said it should be able to confirm the full sequencing of the virus in this patient on Monday.

Similarly, health authorities in the Czech Republic are investigating a suspected case of the Omicron variant in a traveller who has recently arrived from Namibia, the Czech National Institute of Public Health said in a statement emailed to CNN.

The institute said that that a PCR test indicated the infection could have been caused by the Omicron variant, but added that a full sequencing of the sample needs to be completed in order to confirm this. It said the sequencing work is underway.

Dutch health authorities are investigating whether 61 people traveling from South Africa who tested positive for Covid-19 on Friday were infected with the new variant.

The Centers for Disease Control and Prevention (CDC) said that to date no known Omicron cases have been identified in the United States, and that if the variant emerges, the agency expects that cases would be quickly identified through the nation's variant surveillance system.
Fauci, the CDC Director, told NBC Saturday, "I would not be surprised if it is [in the US], we have not detected it yet, but when you have a virus that is showing this degree of transmissibility and you're having travel-related cases they've noted in other places already, when you have a virus like this, it almost invariably is going to go all over."

The World Health Organization (WHO) said late on Friday that early evidence suggest the Omicron variant, first identified in South Africa, could pose an increased risk of reinfection and said that some of the mutations detected on the variant were concerning.

GGD Kennemerland, the municipal health service responsible for the Amsterdam Schiphol airport, said the positive test results would be examined as soon as possible. Those who tested positive were sent into isolation at a nearby hotel, the Dutch authorities added.

The discovery of the new variant has sparked fears around the world. A number of countries have imposed travel bans and the global markets plunged.

But while WHO designated the Omicron a "variant of concern" on Friday, it stressed that more research is needed to determine whether the variant is more contagious, whether it causes more severe disease, and whether it could evade vaccines.

"This variant has a large number of mutations and some of these mutations have some worrying characteristics," Maria Van Kerkhove, WHO's technical lead for Covid-19, said in a statement on Friday.

"Right now there are many studies that are underway ... so far there's little information but those studies are underway so we need researchers to have the time to carry those out and WHO will inform the public and our partners and our member states as soon as we have more information," she added.

Lawrence Young, a virologist and a professor of molecular oncology at Warwick Medical School in the United Kingdom, said the Omicron variant was "very worrying."

"It is the most heavily mutated version of the virus we have seen to date. This variant carries some changes we've seen previously in other variants but never all together in one virus. It also has novel mutations," Young said in a statement.

The variant has a high number of mutations, about 50 overall. Crucially, South African genomic scientists said Thursday more than 30 of the mutations were found in the spike protein -- the structure the virus uses to get into the cells they attack.

South Africa cut off
The discovery of the variant sparked a fresh round of travel restrictions across the world, with many countries shutting their borders to travelers from several southern African countries.

The United States, the European Union, the United Kingdom, Australia, Japan, Russia, Brazil, Saudi Arabia, Israel, Egypt, the Philippines, Thailand and a number of other countries already announced or proposed bans on flights from the region.

Most, including the US, have restricted travel from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi.

The South African government has taken an issue with the travel bans, pointing out in a statement that the Africa Centres for Disease Control and Prevention "strongly discourages" travel bans for people originating from countries that have reported the variant.

"Over the duration of this pandemic, we have observed that imposing bans on travelers from countries where a new variant is reported has not yielded a meaningful outcome," the statement said.

Scientists have praised South African health authorities for their quick reaction to a Covid-19 outbreak in the country's Gauteng province, which led to the discovery of the new variant.

When cases in the province started to rise at a higher rate than elsewhere, health experts focused on sequencing samples from those who tested positive, which allowed them to quickly identify the B.1.1.529 variant.

Peacock said the South African health ministry and its scientists "are to be applauded in their response, their science, and in sounding the alarm to the world."

She added the development shows how important it is to have excellent sequencing capabilities and to share expertise with others. That message was reinforced by WHO, which has on Friday called on countries to enhance their surveillance and sequencing efforts to better understand coronavirus variants.

But Dr. Richard Lessells, an infectious diseases specialist at the University of KwaZulu-Natal in Durban said South Africa was being "punished" for its transparency and ability to pick up the variant quickly and flag the issue to the international health authorities.

"What I found disgusting and really distressing ... was not just the travel ban being implemented by the UK and Europe but that that was the only reaction or the strongest reaction. There was no word of support that they're going to offer to African countries to help us control the pandemic," he told CNN.

The southern German state has also imposed a lockdown on all districts