Covid Variant Omicron (B.1.1.529)

In summary: There's an "extremely high number" of mutations in this variant, some of which could make it more transmissible or undermine the effectiveness of vaccines. UK Health Secretary Sajid Javid has announced that six African countries will be added to the UK's red list from tomorrow at noon local time. Flights from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will be temporarily banned and UK travellers will be required to quarantine.This variant stands 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....
  • #456
bhobba said:
It is getting terrible in Brisbane.
Look on the bright side. Australia got it right, in that the pandemic has only hit once everyone who wants to be vaccinated has been, and with a far less deadly strain of the virus. This is almost as good as you could have hoped for.
 
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Biology news on Phys.org
  • #458
If four works better than three (but not really) then I’m putting my money on five working better than four (but not really).
 
  • #459
Just to be clear
Extra boosters are given to people who have not gotten a useful immune response to the first three shots.
Example: cancer patients, transplant patients - who are immunocompromised.

Moderna is working on testing a new vaccine against new and different epitopes:
https://www.reuters.com/business/he...develop-omicron-booster-weeks-ceo-2021-12-21/

Some focus on what that could mean
Assuming it works and is approved we may well have gotten past the omicron "spike" and variant X is a problem instead. Or omicron settles in and keeps reinfecting people. In which case a new vaccine could be useful.
 
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  • #460
jim mcnamara said:
In which case a new vaccine could be useful.
I believe Pfizer are working on an Omicron-specific vaccine due March.
 
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  • #463
StevieTNZ said:
I mentioned it in post #429, just before you mentioned your article.
Indeed you did.
 
  • #464
chemisttree said:
If four works better than three (but not really) then I’m putting my money on five working better than four (but not really).

I think well before then; we will have second-generation vaccines.

Thanks
Bill
 
  • #465
Astronuc said:
I'm off to get my first test for SARS-Cov-2. My son seems to be recovering. His has ceased coughing and sneezing, but he's sleeping in today. My wife got tested yesterday.

Edit/update: My rapid test was negative (PCR results will be available next week, hopefully Monday), and my wife's PCR test was negative.

I just learned my PCR test result is negative. So, my wife, who also tested negative with PCR, and I dodged the proverbial bullet. I had to call my doctor's office, which casually informed me. I kind of think it's important to know, but then I understand that they are overwhelmed. Still, having to wait 3, 4 or more days for test to determine if one is potentially infected with a highly transmissible virus is rather poor.

My son still has some congestion, but he went to work today. The congestion could be normal, but it's hard to tell.

Meanwhile, many others are encountering the same problem my son did with false negative rapid tests. Apparently, home tests are even more unreliable than clinic tests. So, how many thousands or millions of false negative tested people, symptomatic or asymptomatic, are out there? We probably will never know, and that should concern everyone.

https://news.yahoo.com/relied-rapid-coronavirus-tests-gather-214812046.html
 
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  • #466
Astronuc said:
I just learned my PCR test result is negative. So, my wife, who also tested negative with PCR, and I dodged the proverbial bullet. I had to call my doctor's office, which casually informed me. I kind of think it's important to know, but then I understand that they are overwhelmed. Still, having to wait 3, 4 or more days for test to determine if one is potentially infected with a highly transmissible virus is rather poor.
Glad that you are both negative! PCR labs testing for COVID have been *slammed* from staffing shortages and supply issues. I’ve had to sleep in a hotel twice in the last two weeks, which is definitely an upgrade from sleeping in my car like the last surges. There are 24 hour PCR labs that you may be able to ask your clinic for if you have to test again. I just don’t understand why it is taking 3+ days for some tests. It seems like labs would have scrambled to adjust their setup to test faster when the pandemic started.

Long testing times meant life or death in the beginning of the pandemic. Often, patients weren’t being treated until they had a confirmed diagnosis through testing. Many have died waiting for test results. I hope that they review this aspect later on and we can make some improvements on testing and treatment times. So sad.

It’s odd, more people around me have tested positive than in any of the other surges and the majority of them are vaccinated. Others are getting sick but testing negative on at-home tests or positive for the flu.

The surge *seems* to be declining right now. Hopefully.
 
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  • #467
Astronuc said:
I just learned my PCR test result is negative. So, my wife, who also tested negative with PCR, and I dodged the proverbial bullet. I had to call my doctor's office, which casually informed me. I kind of think it's important to know, but then I understand that they are overwhelmed. Still, having to wait 3, 4 or more days for test to determine if one is potentially infected with a highly transmissible virus is rather poor.

My son still has some congestion, but he went to work today. The congestion could be normal, but it's hard to tell.

Meanwhile, many others are encountering the same problem my son did with false negative rapid tests. Apparently, home tests are even more unreliable than clinic tests. So, how many thousands or millions of false negative tested people, symptomatic or asymptomatic, are out there? We probably will never know, and that should concern everyone.

https://news.yahoo.com/relied-rapid-coronavirus-tests-gather-214812046.html
Glad your son’s illness was brief and that you and your wife dodged it. My own illness is resolving nicely as is my son’s and I’ll return to my telework job tomorrow. Still have a few symptoms that need more time to resolve. My symptoms are mostly what you would expect after a severe cold. Bit of a cough and some nasal congestion. Very different from Saturday and Sunday when it seriously hurt to swallow!
 
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  • #468
  • #470
PCR type testing was used to determine if one had HIV. A big difference in testing for HIV vs COVID, is that the test for HIV uses blood. One does not have HIV in the blood unless one has an active infection.

PCR type testing takes a sample usually from the nostril and then magnifies it many, many times. Therefore you can have one or two COVID molecules in your system/magified sample and the results of the test would be COVID positive. However, since the concentration of the COVID particles is so small because of the multiple magnification, you may neither be infected or able to transmit enough of the virus to infect someone else. Not enough viral load to initiate infection.

This is how so many individuals were asymptotic. They tested positive but did not carry enough of a viral load to actually infect their bodies or transmit the virus.
 
  • #471
morrobay said:
What the heck is going on in Australia @bhobba ?
I'm not bhobba, but it seems that our various state - and especially federal - governments, have decided that omicron is sufficiently benign that even though we're all getting infected, it wouldn't load up the health system (which predominately means hospital ICUs).

From my perspective, it seems to have started with the NSW Premier, who essentially 'opened up' as soon as he stepped into the role (the previous premier resigned due to a corruption enquiry).

That attitude has percolated across the country and I'm actually watching the federal treasurer on the news now talking about employment numbers being firm and the economy being strong...and I think that's the root cause of what's going on Down Under, @morrobay. The economy over health, with the assumption that omicron is a milder case of covid, mitigated by our high vaccination numbers, and those political decisions made with fingers crossed on both hands!
 
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  • #472

New Zealand will not impose lockdown when omicron hits​

https://www.npr.org/2022/01/20/1074310637/new-zealand-no-lockdown-omicron-variant

WELLINGTON, New Zealand — New Zealand is among the few remaining countries to have avoided any outbreaks of the omicron variant — but Prime Minister Jacinda Ardern said Thursday an outbreak was inevitable and the nation would tighten restrictions as soon as one was detected.

But she also said that New Zealand would not impose the lockdowns that it has used previously, including for the delta variant.

"This stage of the pandemic is different to what we have dealt with before. Omicron is more transmissible," Ardern said. "That is going to make it harder to keep it out, but it will also make it more challenging to control once it arrives. But just like before, when COVID changes, we change."

About 93% of New Zealanders aged 12 and over are fully vaccinated and 52% have had a booster shot. The country has just begun vaccinating children aged between 5 and 11.
 
  • #474
The latest in NZ: https://www.stuff.co.nz/national/he...-case-is-omicron-will-not-trigger-move-to-red

"Officials reported potential new Omicron cases in both Auckland and Palmerston North on Thursday, the latter of which was a recent returnee who tested negative five times in MIQ before testing positive on Wednesday."

If they tested negative and were released from MIQ after 14 days, what does that say about detecting the virus in the first 14 days? I assume the nature of the test was a nasal swab analysed by the lab.
 
  • #475
StevieTNZ said:
If they tested negative and were released from MIQ after 14 days, what does that say about detecting the virus in the first 14 days? I assume the nature of the test was a nasal swab analysed by the lab.
Very scary IMO. :frown:
 
  • #476
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  • #477
morrobay said:
What the heck is going on in Australia @bhobba ?
It was a confluence of events. States had strong border controls, but different rules meant different Covid cases in each state. In Queensland, where I am, it was virtually zero, NSW a couple of hundred each day. Everyone was working towards as high a vaccination as possible before reducing precautions. ACT was first, with 99% over 12 double vaccinated. NSW next at 95%. Queensland closed in on 90% but had a partial opening at 80%. It is now 90% and fully open.

But at that exact time, Omicron hit and threw everything into chaos. It spreads like wildfire. The government quickly introduced a program for third dose boosters at five months, now four months, and three months from the end of this month. The booster program is proceeding as quickly as possible. It is known that the chances of going to ICU are reduced 24 times with the third dose. It is also known that being double vaccinated does not protect well against Omicron, while the third dose is at least 80% effective. But two doses, while not reducing getting Omicrom much, is quite effective at ensuring the infection is mild.

The interviews I have seen with immunologists emphasise our high vaccination rate. While we expect an explosion in cases, the vast majority will be mild. The percentage ending up in ICU seem about the same as a bad flu season, but since so many are getting it, even that small percentage is concerning.

All I can do is emphasise getting the booster. It is the best chance you got. Modelling seems to indicate the peak will hit at about months end, with deaths to peak a week or two after that.

My sense is, with high rates of double vaccination, it is like the flu, but with a high R0. The third dose is the best we can do now and will reduce the chance of getting it a lot and ending up in ICU.

People sometimes forget how bad the flu can be. In Australia, the 2017 influenza season had the highest number of laboratory-confirmed influenza notifications, at a rate of 1021.6 per 100 000 population and 29 000 hospital admissions and 745 deaths. With Omicron, combine that with the high R0, and our current emergency is what you get.

Thanks
Bill
 
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  • #478
StevieTNZ said:
My counterpart, Rt Hon Trevor Mallard, Speaker of the House of Representatives, has the following to say about the impending event - https://www.stuff.co.nz/national/po...-people-to-stock-up-ahead-of-omicron-outbreak

He has also offered, if not affected, to run around for groceries and medicine for people who have to self-isolate if they live in Wainuiomata (just over the hill from where I am).

As I mentioned, when double vaccinated, it seems about the same as the flu, but with a very high R0. The best hope is getting that third vaccination. We must proceed with that ASAP. Take precautions to slow the spread as much as we reasonably can, but use the time to get that third booster.

Thanks
Bill
 
  • #479
bhobba said:
…… It is known that the chances of going to ICU are reduced 24 times with the third dose. It is also known that being double vaccinated does not protect well against Omicron, while the third dose is at least 80% effective. But two doses, while not reducing getting Omicrom much, is quite effective at ensuring the infection is mild…
Bill, where are you getting this data? When you say that your chances of going to the ICU are 24 times less with the third dose, that is a relative risk… but relative to what? Double vaccinated or non-vaccinated?
And what does “protect well” mean?

I don’t believe that triple vaccinated folks are effectively protected 80% against getting Covid. Perhaps a relative risk is being reported?
 
  • #480
chemisttree said:
Bill, where are you getting this data? When you say that your chances of going to the ICU are 24 times less with the third dose, that is a relative risk… but relative to what? Double vaccinated or non-vaccinated?
And what does “protect well” mean?

Daily briefings of our Chief Medical Officer in Queensland e.g. (the article is behind a paywall so a precis follows):

'It is expected to peak in the next two weeks, just as school is set to return for the new year. The state recorded 15,122 new COVID-19 cases and another seven deaths on Monday. Health Minister Yvette D’Ath said the official tally of 86,953 active cases was likely to be a lot higher as the omicron variant circulated in the community. Chief Health Officer John Gerrard said Queensland’s omicron wave would peak early next month. The seven dead were mostly older people who had not received a booster shot. “We want the least amount of people in hospitals and that requires people to come and get vaccinated,” she said. “Do not assume you can avoid this virus. It is everywhere.” Ms D’Ath said there were now 702 COVID-19 patients in hospital, including 47 in intensive care and 15 on ventilators.

Queensland Chief Health Officer John Gerrard said he expected the omicron wave to peak on the Gold Coast next week, and then in Brisbane the week after. “So far, it’s heartening, but the numbers will increase,” he said. Dr Gerrard said the unvaccinated in Queensland were 24 times more likely to end up in an intensive care unit than someone who was triple vaccinated. “I’m still concerned there are elderly people who have not received their booster shot, to ensure they don’t end up in intensive care,” he said. Of the 29 dead in Queensland since December 13, only one had received a booster shot. On Saturday, the Palaszczuk government scrapped its border pass system, and the requirement for interstate visitors to produce a negative PCR or rapid antigen test before arriving in the Sunshine State.'

chemisttree said:
I don’t believe that triple vaccinated folks are effectively protected 80% against getting Covid. Perhaps a relative risk is being reported?

My goof - that should be severe Covid:
https://www.bbc.com/news/health-59696499

Thanks
Bill
 
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  • #481
bhobba said:
As I mentioned, when double vaccinated, it seems about the same as the flu, but with a very high R0. The best hope is getting that third vaccination. We must proceed with that ASAP. Take precautions to slow the spread as much as we reasonably can, but use the time to get that third booster.

Thanks
Bill
Yes indeed. That is why early this year people who had their second dose four months ago are now eligible for the booster, rather than the original six month period. So far we have very limited spread of Omicron - some people have it who have been out in the community. But at this stage it is under control - but it could be tomorrow, next week or next month where its just bang and we're back in red. It is only a matter of time.
 
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  • #482
I am reading a sublineage called BA.2, dubbed stealth omicron, is on the rise now.

https://www.forbes.com/video/629292...ant-gaining-ground-in-europe/?sh=68c512424a17

BA.2 was first identified in India and South Africa in late December 2021. It is a sub-variant, believed to have emerged from a mutation of Omicron (officially known as BA.1). Omicron itself was born from a mutation of Delta. Other sub-lineages have already been referenced, such as BA.3 or BB.2, but they have attracted less attention from epidemiologists because of the dramatic increase in cases of people who have contracted BA.2.

BA.2 has more than 20 mutations, about half of them in the spike protein. This is the famous protein that interacts with human cells and is the key to the virus entering the body.

https://www.france24.com/en/france/...tics-of-new-covid-19-omicron-sub-variant-ba-2
 
  • #484
Jarvis323 said:
Omicron itself was born from a mutation of Delta.
This is not correct. Omicron is quite evolutionarily distant from Delta based on current phylogenetic data for SARS-CoV-2:
1642882428990.png

https://covariants.org/
 
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  • #488
Jarvis323 said:
I am reading a sublineage called BA.2, dubbed stealth omicron, is on the rise now.

https://www.forbes.com/video/629292...ant-gaining-ground-in-europe/?sh=68c512424a17
https://www.france24.com/en/france/...tics-of-new-covid-19-omicron-sub-variant-ba-2
The team of Virology researchers on TWiV (this week in virology) are fairly sure that this finding resulted from lab contamination of the sample.
Sorry, please ignore this, I mistook the variant being discussed, I'm furiously working on a credible excuse. :)
 
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  • #489
Laroxe said:
The team of Virology researchers on TWiV (this week in virology) are fairly sure that this finding resulted from lab contamination of the sample.
Are you sure they were talking about BA.2 and not the "Deltacron" news (e.g. https://www.nature.com/articles/d41586-022-00149-9 )?
 
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  • #490
Laroxe said:
The team of Virology researchers on TWiV (this week in virology) are fairly sure that this finding resulted from lab contamination of the sample.
I think you're thinking of deltacron, which is different from "stealth omicron"/BA.2. BA.2 is also called 21L, which is shown on ygggdrasil's phylogenic tree.
 
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