M

Mr._Clark

Audioholic Field Marshall
Here is a virologist's twitter feed that talks about this new strain and has details for those who can understand this stuff.
I noticed a Jeffrey Barret also has some tweets of interest. He seems to be quite knowledgeable (His twitter account says: "Chief Scientific Officer, Nightingale Health. Also leading the Covid-19 genomics initiative @sangerinstitute")

Apologies in advance for the long post, but I thought this was worth a read.

.>>>First the obviously bad stuff (red): nine mutations seen in previous VOCs. There's a lot of overlap already among VOCs (convergent evolution), but this variant has an unprecedented sampling from mutations previously seen in Alpha, Beta, Gamma and Delta separately.<<<


>>>Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)...there is...not much green.
1637955188135.png

In orange are three mutations that are probably meaningful biological changes for the virus, but not previously seen in VOCs. Two from VUI level lineages that likely had modest advantages over original virus, and E484A which is at a key site in the receptor binding domain.

Next eleven things seen rarely or never before (blue) that may be functional and just new to us, or may be a side-effect of whatever process led to so many mutations in this lineage (i.e. either neutral or mildly deleterious). Need more data on these.

In green is just D614G, which has been fixed in all SARS-CoV-2 since early 2020.

Finally, three shades of purple which are new (not in previous VOCs) but have some other data to suggest they may be functional. First is a deletion/substitution/insertion hotspot in the N terminal domain, that may be further remodelling the protein structure there.

Then there's a group of 4 nearby substitutions (3 in the space of 5 amino acids) that have not been seen before, but are so close together that I doubt its coincidence. They are also very close to the (previously conserved) binding site of sotrovimab, a therapeutic antibody.
1637955550032.png

Finally S477N and Q498R, predicted in an experimental evolution paper to substantially increase ACE2 binding together with N501Y, but only seen in the wild separately or rarely. Seeing this full combination now (along with everything else) is grim.
1637955644871.png
<<<

 
M

Mr._Clark

Audioholic Field Marshall
At this time I have to say, I have a bad feel about this development. My advice to members is to do as little travel as possible. I strongly advise against travel outside the US at this time, and avoiding anyone that has travelled outside the US. The nearer you stay home the better pending further evaluation and assessment of this evolving situation.
I also have a bad feeling about this. The recent spike in South Africa may be a coincidence, but it certainly altered my perception of the situation.

1637958013413.png


According to Reuters only about 21% of the population of South Africa is vaccinated so that could be a factor (i.e. it seems to me that a spike in cases could occur even if the vaccines are at least somewhat effective against this variant)

>>>Data shared by South Africa's Department of Health on Thursday showed that B.1.1.529 made up about 75% of cases detected in Gauteng province on November 22, just two weeks after the variant first emerged. Its ascent was much faster than that of the Beta and Delta variants, which each took months to become dominant . . .<<<


The feeling I get reminds me of the title of the Tom Clancy novel "The Sum of All Fears."

Apparently it will be about 2 weeks before preliminary information concerning the effectiveness of the vaccines is available, and modified vaccines could be start becoming available.

 

Attachments

TLS Guy

TLS Guy

Seriously, I have no life.
First of all the the WHO have named this new variant omicron. That is now official, and everyone is very concerned about it.

I watched the BBC news today, and there is a lot of concern and anxiety about this development.

The EU have quarantined the whole of Southern Africa, in lock step with the UK's actions yesterday.

Now to put this in perspective.

It will take about three weeks to know how serious this actually is. It will take that long to determine transmissibility and severity of illness. Although South African epidemiologists, say this omicron variant is outpacing Delta. If confirmed that is very bad news.

What is unknown at this time is the degree of vaccine escape this variant may have. This will take at least three weeks to elucidate. Many virologists feel there will be significant or severe escape. However that is an educated guess, and at the end of the day a guess. The only way to know for sure, is accurate collection of real world data. That will take time.

Many residents are questioning the need for restrictions, before information is definite. The reason is that world restrictions in the past have come far too late.
By the time the whole situation is clear, it is far too late to introduce restrictions.

This is a fluid situation on the ground at present. At this time we know that most cases are across Southern Africa. There must be cases in either Egypt, or Turkey, most likely Egypt. We know there is a case Israel, Belgium and at least one in Hongkong. So more than likely we have missed the boat already for containment. But that is my guess. By past experience I'm not at all confident we can contain it, if it is indeed more transmissible than Delta. Pessimism I feel is justified about this aspect.

I will do my best to keep you updated. On the whole this thread has been ahead of major US news media with crucial reliable information.

At this time where this may well turn out to be a crucial turning point in the pandemic, let us all try and keep this thread free of trivial and nonsense posts. There is nothing funny about this now, if there ever was. I regard this turn of events as very concerning.

As I said in a previous post I would share Dr. Michael Osterholm's conversation with you. This was before any news of omicron obviously.

 
highfigh

highfigh

Audioholic Slumlord
This is now a fast moving story.

This nu variant is worrisome. It has major changes to the principle spike antigen that is the target of the current vaccines. Biontec, who designed the Pfizer vaccine are urgently studying whether the vaccine need to be reformulated.

Unfortunately a case has already been found in Belgium. This was an unvaccinated women who travelled from Egypt via Turkey. She has no connection to any country in the African Southern peninsular where the virus seems to be spreading fast.



If more cases are found, I suspect the UK will seal its borders, which will bring great hardship.
And now, we have the Omicron variant. Great. Do people still think that finding the actual cause of the outbreak is unimportant?

I'm not defending Trump, but a huge part of the US population lost their minds when he wanted to restrict travelers from China and now, Biden has done that with Southern Africa. It would have helped.

Let's see how the EU reacts to GB sealing its borders. I suspect this will help, rather than requiring member countries to have what almost amounts to open borders.
 
Trell

Trell

Audioholic Ninja
And now, we have the Omicron variant. Great. Do people still think that finding the actual cause of the outbreak is unimportant?

I'm not defending Trump, but a huge part of the US population lost their minds when he wanted to restrict travelers from China and now, Biden has done that with Southern Africa. It would have helped.

Let's see how the EU reacts to GB sealing its borders. I suspect this will help, rather than requiring member countries to have what almost amounts to open borders.
You are leaving out the reasons why Trump did that, and intent/reasons matters when deciding/implementing a policy. In the best of worlds the policies should be science and evidence based, and most of us knows that was very far from how the Trump administration handled the pandemic which caused at least tens of thousands preventable deaths in USA.
 
highfigh

highfigh

Audioholic Slumlord
You are leaving out the reasons why Trump did that, and intent/reasons matters when deciding/implementing a policy. In the best of worlds the policies should be science and evidence based, and most of us knows that was very far from how the Trump administration handled the pandemic which caused at least tens of thousands preventable deaths in USA.
Maybe, more people need to trust China (PRC) far less than they do- IMO, it would have been the right thing to do and many other countries did this not long after, but without being skewered.

I think that ignorance on a personal level has caused more deaths than anything else. Maintaining distance and avoiding others is an obvious way to prevent the spread of diseases, but college students had 'Covid parties', resorts/festivals/sports venues had large events with thousands of people and many refused to isolate. Personally, I think many people need to learn to spend time alone and stop needing other people so much for their personal validation. Wanting to be 'part of the group' is killing people at an alarming rate.

What if the travel ban been had allowed to remain and slowed the spread? Which restriction on Chinese travel are you referring to the general ban, or the one on Chinese students? The results may be a bit more important than the intent, at times- he's definitely paranoid and has an extremely high opinion of himself (on the outside), but I think it would have decreased the spread, to some extent.

I agree that the policies should be science/evidence-based, but 'the best of worlds' ship sailed a long time ago and I don't see this as a real possibility anymore unless something fundamentally transformational occurs. While I don't like the idea of one group governing the whole planet, I do think that too many governments that disagree on too many topics are involved.
 
TLS Guy

TLS Guy

Seriously, I have no life.
The UK now reports two cases of omicron. One case is in Chelmsford in Essex, which is one of the home counties on the East side of London. Its South border is the Thames Estuary, right opposite the Kent shore on the South shore of the Thames estuary.

The other case is in Nottinghamshire, a county in the East midlands, bordered by Lincolnshire to the East. Its North border takes you up to the old industrial north. So the counties are far apart suggesting widespread distribution of the virus already. Vigorous contact tracing is underway.

The factor that I find most disturbing is the spread of omicron in South Africa.



The purple is omnicron, the black is beta and the beige is Delta.

The slope of that line frankly gives a cold sweat. I just hope this new strain does not have total virus escape. Professor Andrew Pollard of Oxford university has provided some measure of reassurance. He feels the antigenic structure, probably will not cause total vaccine escape. However he says we will just have to wait a few weeks to know the answer to that.

If a new vaccine is required it could be rolled out in 4 to 6 months, may be. If the regulators want full trial it will be a year at least. In my view if this is a serious as feared, we need to pass it on like tweaks to flu vaccines.

60 people on flight from South Africa to Amsterdam have tested positive for Covid-19. Genome sequencing is in progress.

Germany has identified a case in a traveler from South Africa.

Covid-19 seems to be spreading in Germany, Austria and the neighboring Bohemian countries fast. I suspect they have omicron and just don't know it.

One humorous note. The WHO skipped over Nu and Xi for this variant to avoid offending China's president Xi! I think that was a mistake.
 
Last edited:
Trell

Trell

Audioholic Ninja

>>>
Florida shares deep connections with Puerto Rico as home to the territory’s largest diaspora community on the US mainland. But when it comes to Covid-19, the two places have little in common.

While Florida, like many states in the South, has seen high infection rates and troubling death counts, Puerto Rico has been something of a coronavirus success story. As of November 22, Puerto Rico had fully vaccinated 74 percent of its population — a higher proportion than any other US state or territory — and had among the lowest Covid-19 death rates since the start of the pandemic, with 102 in 100,000 people dying from the virus.

By comparison, Florida’s vaccination rate is far more typical for the US; it has administered two shots to 60.9 percent of its population, slightly above the national average of 59.2 percent. That’s after Florida led the country in total caseloads for months, and after significant loss of life: Florida residents have died of the virus at nearly triple the rate of Puerto Rico residents.

Throughout the US, politics has been a key factor in determining how states have fared during the Covid-19 pandemic. States that embraced the individualistic approach of the Trump administration, sometimes ignoring scientific guidelines and avoiding mandates, have seen worse outcomes than states that took more comprehensive actions to stop the spread of Covid-19.
...
<<<
 
M

Mr._Clark

Audioholic Field Marshall
The UK now reports two cases of omnicron. One case is in Chelmsford in Essex, which is one of the home counties on the East side of London. Its South border is the Thames Estuary, right opposite the Kent shore on the South shore of the Thames estuary.

The other case is in Nottinghamshire, a county in the East midlands, bordered by Lincolnshire to the East. Its North border takes you up to the old industrial north. So the counties are far apart suggesting widespread distribution of the virus already. Vigorous contact tracing is underway.

The factor that I find most disturbing is the spread of omnicron in South Africa.



The purple is omnicron, the black is beta and the beige is Delta.

The slope of that line frankly gives a cold sweat. I just hope this new strain does not have total virus escape. Professor Andrew Pollard of Oxford university has provided some measure of reassurance. He feels the antigenic structure, probably will not cause total vaccine escape. However he says we will just have to wait a few weeks to know the answer to that.

If a new vaccine is required it could be rolled out in 4 to 6 months, may be. If the regulators want full trial it will be a year at least. In my view if this is a serious as feared, we need to pass it on like tweaks to flu vaccines.

60 people on flight from South Africa to Amsterdam have tested positive for Covid-19. Genome sequencing is in progress.

Germany has identified a case in a traveler from South Africa.

Covid-19 seems to be spreading in Germany, Austria and the neighboring Bohemian countries fast. I suspect they have omnicron and just don't know it.

One humorous note. The WHO skipped over Nu and Xi for this variant to avoid offending China's president Xi! I think that was a mistake.
Italy has also reported a case.
 
D

Dude#1279435

Audioholic Samurai
Should I get the booster if I'm 50?
Also, what do you think of gain-of-function with Fauci and Rand Paul's case against him?
 
highfigh

highfigh

Audioholic Slumlord
One humorous note. The WHO skipped over Nu and Xi for this variant to avoid offending China's president Xi! I think that was a mistake.
Or, he could proclaim a special day in his own honor because of it. Then, in a mental lapse due to pride, he could start a speech with "When we invented this disease....".
 
TLS Guy

TLS Guy

Seriously, I have no life.
Should I get the booster if I'm 50?
Also, what do you think of gain-of-function with Fauci and Rand Paul's case against him?
If you are more then two months post J & J vaccine or more then six months past your second dose of the Pfizer, or Moderna vaccine, you should get a booster dose right away. Yes, ASAP.

Rand Paul is an ignorant, rude, loud mouthed nut job.
 
M

Mr._Clark

Audioholic Field Marshall
Various news sites are reporting that 13 people on an airline flight from South Africa to the Netherlands have tested positive for the omicron variant. The testing is apparently not complete so there may be more.
 
TLS Guy

TLS Guy

Seriously, I have no life.
Various news sites are reporting that 13 people on an airline flight from South Africa to the Netherlands have tested positive for the omicron variant. The testing is apparently not complete so there may be more.
Yes, those 13, where from the 60 who tested positive for Covid-19 on a flight from South Africa.

The two UK cases in Essex and Nottinghamshire are connected and both came from a recent flight from South Africa. Contact tracing is in progress. There was a recent football match at Twickenham between an English and South African team with fans from South Africa also. The UK is very concerned about this.

I have found out that Minnesota recently closed its genome testing site a let all the skilled technicians go. There has been abject stupidity in the US during this pandemic. It is mind boggling.
 
mtrycrafts

mtrycrafts

Audioholic Slumlord
Scratching head, how did they get on a flight in the first place?
 
mtrycrafts

mtrycrafts

Audioholic Slumlord
...

I have found out that Minnesota recently closed its genome testing site a let all the skilled technicians go. There has been abject stupidity in the US during this pandemic. It is mind boggling.
Beyond belief.
 
M

Mr._Clark

Audioholic Field Marshall
Hopefully this (mild symptoms) turns out to be true for the majority of cases:

>>>JOHANNESBURG, Nov 28 (Reuters) - A South African doctor who was one of the first to suspect a different coronavirus strain among patients said on Sunday that symptoms of the Omicron variant were so far mild and could be treated at home. . . .
"We have seen a lot of Delta patients during the third wave. And this doesn't fit in the clinical picture," she said, adding she alerted NICD on the same day with the clinical results.

"Most of them are seeing very, very mild symptoms and none of them so far have admitted patients to surgeries. We have been able to treat these patients conservatively at home," she said.

Coetzee, who is also on the Ministerial Advisory Committee on Vaccines, said unlike the Delta so far patients have not reported loss of smell or taste and there has been no major drop in oxygen levels with the new variant.

Her experience so far has been that the variant is affecting people who are 40 or younger. Almost half of the patients with Omicron symptoms that she treated were not vaccinated.<<<

 
newsletter

  • RBHsound.com
  • BlueJeansCable.com
  • SVS Sound Subwoofers
  • Experience the Martin Logan Montis
Top