Omicron (B.1.1.529) - What scientists know about the new variant

[mister_coffee]

Right now we are in the "don't really know" phase of things, and shouldn't leap to any conclusions one way or the other.

Keep in mind that it isn't surprising that nearly all of the cases we are hearing of are in vaccinated individuals. It is basically impossible at this time to travel internationally without a covid vaccination, so it stands to reason that all of the cases in that population would be in vaccinated folks. That doesn't tell us anything about how well this new variant might evade vaccination.

[Fun CH]

Phizer board member, Dr. Gottlieb just said that he expects a fully boosted mRA vaccinated person to be somewhat protected from this new variant.

But that's from the experts* looking at the Omicrom variant Gene sequence but more testing and real world data is required to obtain the full picture.

He says the third vaccine dose enables the immune system to Target more parts of the virus.

He also says natural immunity from the Delta variant infection also needs to be studied. They use blood plasma from vaccinated and natural immunity individuals as one test against the virus.


*I assume he's talking about actual experts (virologists) not youtube chiropractors or internet posers.

[PAL]

Public safety, for example, with some risk, as in having speed limits are necessary. Making comparisons of unrelated subjects don't work, for me anyway.
We never think that this could wipe out the human species do we? Most probably we won't get wiped out. It's too preposterous to think about even, isn't it?

[Mark58]

See "straw man argument"

[dorankj]

That’s a pretty stupid response! When have I intentionally crashed OR got COVID? As I’ve said before, if we wish to treat other things like we’re handling this, I demand all speed limits reduced to 5 everywhere, breathalyzers in every vehicle before you can start it, ban all tobacco products for everyone and mandatory diets and weight loss for everyone with a BMI over 28. Think of the 100s of thousands of lives I’d save!

[mister_coffee]

It’s literally 99.9x survival rate, pretty reasonable risk!

Auto accidents in the United States have approximately the same survival rate and I don't see many people intentionally crashing into each other or publicly demonstrating against seat belts and airbags.

[dorankj]

It’s literally 99.9x survival rate, pretty reasonable risk!

[PAL]

Well, Ray, we know it's only a matter of time before it comes here. There is no stopping it. So we deal with it with the protocols.
Well stated Mark58. And Ken, well stated, even though I may not agree. The reason for the vaccine that perhaps not as many people will die. Yes, there are deaths of vaccinated people, but not nearly as many, as has been documented in the stats. Not as many filling the hospitals.
Again is there strong scientific evidence that natural immunity is superior? And how long does it last? It would be great if natural immunity works. But that means you'd have to get the virus to find out. Go ahead Ken, get it and let us know.
I'm not wishing on you that you get it. But you seem so certain that is the way. And that is the way for you; yes a choice but read what Mark says again.
I don't wish for gov't mandates. But in the past, weren't vaccines mandated at one time or another?

And now with the new variants, it means altering the vaccine. And how much can it be altered to really make a difference. These are the unknowns. Someday, there may be a pathogen where no vaccine will work. There probably already are, but those pathogens are not on the loose...yet.
Not attacking, just discussing.

[pasayten]

The New York Times
BREAKING NEWS

The U.K. has reported two confirmed cases of the Omicron variant, and they are said to be linked to travel in southern Africa.
Saturday, November 27, 2021 10:44 AM EST

The country’s health agency is now carrying out targeted testing at several locations where the positive cases could potentially have been spread.

https://www.nytimes.com/2021/11/27/worl ... covid.html

[dorankj]

Well, I’m willing to give my life for others I don’t know as a professional firefighter and rescuer. I’ve saved so many lives performing CPR and accurately treating patients for 30 years so I believe I’m ok on your scale. Tell me again how a ‘vaccine’ that doesn’t stop getting, transmitting and even dying from COVID (and is for old variants) is the ONLY way I can be a good citizen? Natural immunity (for those unlikely to have severe issues or death) is far superior and is a reasonable method for this particular affliction.

[Mark58]

Here's the way i look at it. Humans are part of the animal kingdom. In most of the kingdom survival of the species is attained by survival of the individual, and that's all that counts. What, allegedly, sets humans apart is the size of their brains. Those brains allow for acting in a different manner and allow for species survival by ensuring that we survive as a group, not necessarily only by surviving as individuals. So, to the extent that one acts considering the needs of the group rather than the needs of the individual, one is farther along on the evolutionary scale. So the question I ask myself is "where am I on the evolutionary scale?" Every action one takes in a society is a declaration of where you are on that scale, IMHO.

[dorankj]

I’m sorry for your loss but that doesn’t change the principle, if I could force behavior I could prevent so much needless suffering and death but I can’t accept the responsibility. We all have choices and consequences, using government force is something we should all be cautious of! I agree to not force you to behavior I think is right, if you’ll agree to the same.

[PAL]

Ok, then how about cooperation among the community members and the society in which they live? We need to have civility in a society, don't we? I guess I am looking at the good of a social contract, not the fact that we have to agree to a ruler or someone of authority. But as a society we need to get along, cooperate.
And yes, we have these pathogens we live with all the time. But you know what, I have 2 people right now that I dearly love, struggling with Covid and they were healthy. They were exposed by a healthcare worker that came to the home to take care of the daughter's mother in her home. The mother just died last Sunday.
To me, Covid is a different animal. There was some messing around with some pathogens and there was a law, under Obama that stopped it. Then that law was lifted, wasn't it.
Pearl

[dorankj]

This “social contract” game is at the heart of the problem. Every human is constantly battling pathogens throughout life (death is largely the inability to fight off disease anymore). ‘Healthy’ people are all ‘asymptotic’ spreaders as they mainly don’t show what their body is fighting. We have to understand this is part of human life and really for ‘healthy’ people immune system challenges are necessary for overall health. Shaming, mandating and firing healthy people will NOT fix this, protect the vulnerable, stay healthy, live life!

[PAL]

Here is an important reminder Jetalina makes:

Individual-level protection. None of this variant stuff changes what you need to do on an individual-level right now. Unless, of course, if you weren’t doing anything at all. Get vaccinated. Get boosted. Ventilate spaces. Use masks. Test if you have symptoms. Isolate if positive. And encourage others to do the same.

Immunocompromised: It looks like this variant has major implications of virus evolution in immunocompromised hosts. This underscores the need to ensure that immunocompromised people are protected by their communities. Not just for their sake, but for all of ours.

In some posts there seems to be alot of "I". I this and I that, or me, me, me. There is such a thing as a social contract.
Pearl
Top

[pasayten]

The World Health Organization announced Friday it has designated the newly identified coronavirus variant, B.1.1.529, as a variant of concern, named Omicron.

[mister_coffee]

I think it is important to remember that this is still very early days for this new variant and we will likely know a lot more and have a lot more confidence about what we know in the next few days.

[Mark58]

New Concerning Variant: B.1.1.529

Katelyn Jetelina
2 hr ago
61

13


I hope everyone in the States had a fantastic Thanksgiving (even if you’re a Dallas Cowboys football fan). I hate to ruin the holiday, but…

We have a new variant. I’ve not seen this much anxiety ridden chatter among scientists about a COVID19 variant before. Even among the calm, cool, and collected scientists.

What happened this week?

This week we (epidemiologists and virologists) have been closely following a new COVID19 mutation. Three days ago it was designated the name B.1.1.529.

As I write this, the WHO TAG team is convening. They are tasked to do three things:

Review the evidence to determine if B.1.1.529 is, in fact, a threat;

Classify whether the new variant is a “variant of interest” (in other words, hypothesize that this variant is a threat, but we don’t have the evidence yet) or a “variant of concern” (we have scientific evidence that this variant is a threat);

Name the variant. The next Greek name in line is “Nu”.

The name and classification will hit the news cycle once WHO officially announces. Whatever its name, this is what we know thus far…

What is the B.1.1.529 variant?

B.1.1.529 was first discovered in Botswana on November 11. It was then quickly identified in South Africa three days later and identified in two cases in Hong Kong. This morning Israel and Belgium announced that they have cases. The Belgium case was a young, unvaccinated woman who developed flu-like symptoms 11 days after travelling to Egypt via Turkey. She had no links to South Africa. This means that the virus is already circulating in communities. As of yesterday, 100 cases have been identified across the globe (mostly in South Africa). As I write this, no cases have been identified in the United States.

B.1.1.529 has 32 mutations on the spike protein alone. This is an insane amount of change. As a comparison, Delta had 9 changes on the spike protein. We know that B.1.1.529 is not a “Delta plus” variant. The figure below shows a really long line, with no previous Delta ancestors. So this likely means it mutated over time in one, likely immunocompromised, individual (see my P.S. note at the end of the post).
Source: Next Strain here

Nonetheless, we always pay attention to changes on the spike protein because the spike is the key into our cells. If the virus changes to become a smarter key, we need to know. We are particularly interested in mutations that could do any of the following:

Increase transmissibility;

Escape our vaccines or infection-induced immunity; and/or

Increase severity (hospitalization or death).

B.1.1.529 has the potential to do all three. We know this because we’ve seen a number of these mutations on other variants of concern (VOC), like Delta, Alpha, and Gamma. Dr. Jeffrey Barrett listed the mutations in a figure below. Each row represents a different mutation (32 total). The left hand column is the location of the change. The right hand column/color correspond to what we know (or don’t know) about the change.

Red: This means bad. There are nine mutations on B.1.1.529 that we’ve seen in previous Variants of Concern (VOC). P681R is particularly bad news.

Purple: These are new mutations (i.e. not seen in other VOC), but we have lab data to suggest they are a threat.

Yellow: These probably mean something because of their location, but we don’t know what they mean yet. They have not been previously seen in VOC

Blue: We’ve never seen these changes before. They may mean something or may mean nothing. We don’t know yet. We need more data.

Green: This is a mutation that’s been present on all of the variants since early 2020. Not to be of concern.

Twitter: Jeffrey Barrett

Of these, some mutations have properties to escape antibody protection (i.e. outsmart our vaccines and vaccine-induced immunity). There are several mutations association with increased transmissibility. There is a mutation associated with increased infectivity. This slide, from a presentation yesterday from the South Africa Health Ministry, summarized B.1.1.529 nicely.

It will take weeks to understand what these new mutations mean or, more importantly, the combination of so many mutations. Keep in mind that the number of mutations does NOT always equal more severe. While these important lab studies are under way, we can watch carefully what’s happening in the “real world”.

What we’re seeing in the real world?

Individual-level data

We know a lot about the Hong Kong cases because of their impeccable contact tracing. Health authorities published a report of these two cases yesterday.

The first case in Hong Kong was a 36 year old, fully vaccinated (two Pfizer doses in May/June 2021) male. He was traveling through South Africa from October 22 to November 11. Before returning to Hong Kong, he tested negative on a PCR. As per usual, once he landed in Hong Kong he was required to quarantine. On day 4 of quarantine (November 13), he tested positive on a PCR.

Another guest across the hallway was also infected with B.1.1.529. He was Pfizer vaccinated in May/June 2021 too. In both of these rooms, 25 out of 87 swabs were positive for the virus.

These Hong Kong cases tell us two things:

Confirms that COVID19 is airborne (we knew this)

During their PCR tests, the viral loads were VERY high considering they were negative on previous PCR tests. They had a Ct value of 18 and 19 value. So, this tell us that B.1.1.529 is likely highly contagious.

Population-Level Data

There are preliminary signs that B.1.1.529 is driving a new wave in South Africa. Health officials are looking particularly at a region called Gauteng. In just one week, test positivity rate increased from 1% to 30%. This is incredibly fast.

If we zoom out on South Africa as a whole, we see cases starting to exponentially increase. On Tuesday there were 868 cases, Wednesday there were 1,275 cases, Thursday there were over 3,500 cases. We do not know if these cases are all B.1.1.529, but the timing of explosive spread is suspect.

The rate in which these cases are spreading are far higher than any previous variant. Disease modeling scientist Weiland estimated that B.1.1.529 is 500% more transmissible than the original Wuhan virus. (Delta was 70% more transmissible). John Burn-Murdoch (Chief Data Reporter at Financial Times) also found that B.1.1.529 is much more transmissible than Delta. He plotted the spread below.

There is some good news though

First, we can detect B.1.1.529 on a PCR test. This typically isn’t the case. Usually a swab would have to go to a special lab for genome sequencing to know which variant caused the infection. However, it looks like B.1.1.529 has a special signal like Alpha on the PCR directly. For example, when the PCR is positive it lights up two channels instead of three channels, indicating that it’s B.1.1.529. This is amazing news because it means we can track this virus much easier and much quicker around the world.

Second, we caught this virus incredibly early. I can’t stress enough how amazing South Africa has been on communicating and taking hold of the situation. Because of their swift response, scientists around the world are already working together to decode this new threat. Early detection means that we have a surveillance system in place and it’s working.

Third, if we need another vaccine, we can do this incredibly quickly. Thanks to the new biotechnology, mRNA vaccines are really easy to alter. Once the minor change is made, only 2 dozen people need to enroll in a trial to make sure the updated vaccine works. Then it can be distributed to arms. Because the change is small, an updated vaccine doesn’t need Phase III trials and/or regularity approval. So, this whole process should take a max of 6 weeks. We haven’t heard from Moderna or Pfizer if they’ve started creating an updated vaccine, but I guarantee conversations have started behind closed doors.

Bottom Line: There’s still so much that we don’t know but what we do know is incredibly concerning. We are in a lull right now as we wait for scientific evidence to answer two questions as soon as possible:

Does B.1.1.529 escape vaccines like we fear?

Does B.1.1.529 continue to outcompete Delta like we’re seeing in South Africa?

Once we have answers to these two questions, we’ll know the next step. Stay tuned.

Love, YLE

P.S. A few random thoughts I didn’t know where to put above:

Travel bans are not evidence-based: It may seem like travel bans for individual countries are a necessary step, but I cannot stress enough that they do not work. For example, we had a travel ban with China in March 2020, only to be infiltrated with a European strain. Travel bans are a political move; a tool to show the public that the government is responding. Travel bans can do a lot of damage, though, like perpetuate disease related stigma. This variant has already spread. A travel ban is not an evidence-based solution unless you stop all travel from every country.

Individual-level protection. None of this variant stuff changes what you need to do on an individual-level right now. Unless, of course, if you weren’t doing anything at all. Get vaccinated. Get boosted. Ventilate spaces. Use masks. Test if you have symptoms. Isolate if positive. And encourage others to do the same.

Immunocompromised: It looks like this variant has major implications of virus evolution in immunocompromised hosts. This underscores the need to ensure that immunocompromised people are protected by their communities. Not just for their sake, but for all of ours.

“Your Local Epidemiologist (YLE)” is written by Dr. Katelyn Jetelina, MPH PhD— an epidemiologist, biostatistician, professor, researcher, wife, and mom of two little girls. During the day she has a research lab and teaches graduate-level courses, but at night she writes this newsletter. Her main goal is to “translate” the ever-evolving public health science so that people will be well-equipped to make evidence-based decisions, rather than decisions based in fear. This newsletter is free thanks to the generous support of fellow YLE community members. To support the effort, please subscribe.

[pasayten]

Covid Live Updates: Variant Alert From South Africa Prompts Rush to Halt Flights

South African scientists will meet with W.H.O. experts on Friday to discuss a concerning new coronavirus variant. Several countries are already imposing restrictions on travel to and from South Africa and its neighbors.

RIGHT NOWTravel restrictions multiply for African countries over fears of a new variant.
Here’s what you need to know:
What scientists know about the new variant, B.1.1.529.
Hong Kong records two cases of the new variant detected in South Africa.
Europe is being tested by waves of cases that threaten its progress against the pandemic.
Travel restrictions multiply for African countries over fears of a new variant.

An increasing number of countries — including Britain, France, Israel, Italy and Singapore — were moving on Friday to restrict travel from South Africa and other countries in the region, a day after South African authorities identified a concerning new coronavirus variant with mutations that one scientist said marked a “big jump in evolution.”

In the past, governments have taken days, weeks or months to issue travel restrictions in response to new variants. This time, restrictions came within hours of South Africa’s announcement — and hours before health officials from the country were scheduled to discuss the variant with the World Health Organization.

Britain, France and Israel announced bans on flights from South Africa and several neighboring countries on Thursday, citing the threat of the new variant. Britain’s flight ban applies to six countries — South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe — and begins at noon local time on Friday.

“More data is needed but we’re taking precautions now,” Sajid Javid, the British health secretary, said on Twitter.

“While no cases have been detected so far on French territory, the principle of maximum precaution must apply,” Jean Castex, France’s prime minister, said in a statement, adding that anyone in France who had recently traveled to those countries should get tested and identify themselves to the authorities.

The governments of Croatia, Italy, Malta, the Netherlands, Japan and Singapore announced on Friday that they would impose similar restrictions. Markets were down in Japan in response to the variant’s discovery, and officials in Australia and in New Zealand said that they were monitoring it closely.

“Our scientists are at work to study the new B.1.1.529 variant,” Italy’s health minister, Roberto Speranza, said in a statement, using the variant’s scientific name. “Meanwhile we err on the side of caution.”

Ursula von der Leyen, the president of the European Union’s executive arm, also said in a Twitter post on Friday morning that it would propose restricting air travel to European countries from southern Africa because of concerns about the variant.


In the past two days, scientists detected the variant after observing an increase in infections in South Africa’s economic hub surrounding Johannesburg. So far only a few dozen cases have been identified in South Africa, Hong Kong, Israel and Botswana.

A number of variants have emerged since the onset of the pandemic. One underlying concern about them is whether they will stymie the fight against the virus or limit the effectiveness of vaccines. South African scientists will meet with the World Health Organization technical team on Friday to discuss the new variant, and the authorities will assign it a letter of the Greek alphabet.

In a statement posted on Friday on a government website, South Africa said it would urge Britain to reconsider its travel restrictions, saying: “The U.K.’s decision to temporarily ban South Africans from entering the U.K. seems to have been rushed, as even the World Health Organization is yet to advise on the next steps.”

In December last year, South Africa was the first nation to report the appearance of the Beta variant, which has now spread to nearly 70 countries. Scientists have been concerned that some clinical trials have shown that vaccines offer less protection against the Beta variant. Since then, the more virulent and aggressive Delta variant has spread all over the world and is believed to be fueling the latest surge in cases.

With over 1,200 new infections, South Africa’s daily infection rate is much lower than that in Germany, where new cases are driving a wave. However, the density of mutations on this new variant raises fears that it could be highly contagious, leading scientists to sound the alarm early.

“This variant did surprise us — it has a big jump in evolution, many more mutations than we expected, especially after a very severe third wave of Delta,” said Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform.

[pasayten]

Scientists are still unclear on how effective vaccines will be against the new variant flagged by a team in South Africa, which displays mutations that might resist neutralization. Only several dozen cases have been fully identified so far in South Africa, Botswana, Hong Kong and Israel.

The new variant, B.1.1.529, has a “very unusual constellation of mutations,” with more than 30 in the spike protein alone, according to Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform.

On the ACE2 receptor — the protein that helps to create an entry point for the coronavirus to infect human cells — the new variant has 10 mutations. In comparison, the Beta variant has three and the Delta variant two, Mr. de Oliveira said.

The variant shares similarities with the Lambda and Beta variants, which are associated with an innate evasion of immunity, said Richard Lessells, an infectious diseases specialist at the KwaZulu-Natal Research and Innovation Sequencing Platform.

“All these things are what give us some concern that this variant might have not just enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” Dr. Lessells said.

The new variant has largely been detected among young people, the cohort that also has the lowest vaccination rate in South Africa. Just over a quarter of those ages between 18 and 34 in South Africa are vaccinated, said Dr. Joe Phaahla, the country’s minister of health.

While cases of the variant are mainly concentrated in the country’s economic hub, particularly in the country’s administrative capital, Pretoria, it is “only a matter of time” before the virus spreads across the country as schools close and families prepare to travel for the holiday season, Dr. Phaahla said.

— Carl Zimmer NY Times