COVID Covid Variant Omicron (B.1.1.529)

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A new Covid-19 variant, B.1.1.529, has emerged in Botswana and South Africa, raising concerns due to its high number of mutations, particularly on the spike protein, which could affect vaccine efficacy. Scientists warn that this variant may evade monoclonal antibodies, potentially leading to new outbreaks as countries reopen borders. The UK has responded by banning flights from several African nations and reintroducing quarantine measures for travelers. The World Health Organization is set to evaluate the variant, which may be classified as a variant of concern, and could be named Omicron. The situation remains fluid as researchers continue to monitor the variant's spread and impact on public health.
  • #451
Rive said:
? o_O
As far as I know usually that works the other way around. With rapid tests, false negative is far more frequent than false positive. So if the rapid is positive it is accepted as positive: if it's negative, you may better to do a PCR.

I think you are right. But if you are negative and then get the test, it will not solve the issue it was introduced to address. Namely, the lines to get the PCR test was becoming so long as to be unworkable. If you test positive, they want to make sure you are, so the protocol for being Covid positive is required. That is under strain as well.

It is getting terrible in Brisbane. Things are moving fast. I will do a separate post about that. I think at the moment the PCR or rapid test is accepted as equally valid because the testing places are currently doing both.

Thanks
Bill
 
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  • #452
From today's local paper here in Brisbane, the Courier-Mail:

'Queensland has recorded seven new deaths – the highest single-day toll in the state since the pandemic began – and 15,122 new Covid-19 cases, with the Health Minister urging members of the public to come forward to get the booster shot as she revealed none of the latest fatalities had received it. Of the seven deaths, two were in their 80s and five were in their 90s. Two were unvaccinated and five had been double vaccinated. None had had their booster shot. Health Minister Yvette D’Ath said of the 29 deaths since December 13, only one person had received the booster shot. “It is not worth the risk, the vaccine is available,” she said. Chief Health Officer Dr John Gerrard issued a stark new statistic based on numbers coming from hospitals around the state, saying the unvaccinated are 24 times more likely to end up in intensive care than someone who has had all three shots. Ms D’Ath said there are 702 people in hospital including 42 in ICU. There are 15 people on ventilators. “We want the least amount of people needing to be hospitalised,” Ms D’Ath said. Dr Gerrard said he expected the Gold Coast would reach its peak ‘in the next week or so’ and Brisbane would follow a few days later.'

The moral is - get the third dose.

Thanks
Bill
 
  • #453
So, on Friday I started feeling a tingling at the back of my nasal area which has progressed steadily downward into my throat and now my lungs. I tested positive early Sunday with the rapid test. This feels just like a bad cold to me. Difficulty swallowing and a productive cough with a fever.

Double vaxxed and boosted. Treating with DayQuil and prescribed antibiotics (just to be sure).
 
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  • #454
  • #455
Thanks, I’m already much better than this am!
 
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  • #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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  • #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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  • #491
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?

I don’t believe that triple vaccinated folks are effectively protected 80% against getting Covid. Perhaps a relative risk is being reported?
I think a very real issue with all the reported levels of effectiveness is that they really reflect a snapshot in time, and this snapshot is often taken when the antibody levels are at their highest. It's certainly true that the booster dose results in significantly higher antibody levels and these can offer very high levels of protection, but really this level of protection is very short term.

We need to pay more attention to the longer term effects on serious disease and deaths and these will continue to vary based on age and co-morbidities, the percentages quoted give a false sense of precision. The vaccines are very effective, but the level of effectiveness is very different in people over 80 compared to a fit twenty-year-old and varies over time. Really, it's not easy to think of good ways to present data like this, and these difficulties are easily exploited by some anti vaccine groups.
 
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  • #493
Jarvis323 said:
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.
Apologies, both you and ygggdrasil are right, I got them mixed up.
 
  • #494
  • #495
Laroxe said:
Your right, my mistake. should I delete the comment to avoid confusion.?
It's probably ok to not delete the message, since the corrections come directly after your post (otherwise deleting the messages would make a few subsequent messages not make any sense). Maybe you could edit a message into the post to note the correction. It may also be worth preserving the message about the confusion because if you were confused about the two stories about new variants, it's likely that other may be as well.
 
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  • #496
Sydney is thought to be past its peak. Gold Coast has hit its peak, where I am at Redland Bay will hit the peak soon with all vulnerable people advised to stay at home as much as possible, Brisbane a couple of days later. The peak will not be the end - it will take several weeks to reduce slowly. There are 50 people in intensive care in Queensland hospitals, and about 40 per cent of them are unvaccinated. Considering that 90% are double vaccinated, double vaccination is still effective in preventing severe illness. Source: Todays Courier-Mail.

Thanks
Bill
 
  • #497
New Omicron Offshoot BA.2 Arrives In U.S. After Spreading In U.K., Denmark, India
https://deadline.com/2022/01/omicron-offshoot-ba2-in-us-1234918884/
Just as the Omicron wave may have broken across the U.S. comes word of another version of the more transmissible variant, dubbed BA.2. It’s been nicknamed by some “stealth Omicron” because it seems to evade identification better than its predecessor.

While other new variants that seemed worrisome — like Mu or Lambda — have had little impact, and details remain sketchy, early indications are that BA.2 seems to be spreading even in countries where the original Omicron lineage, BA.1, is dominant.

In Denmark, a country whose Covid policies are often contrasted with the U.S., BA.2 now accounts for nearly half of the test samples sequenced. In the final week of December, according to data from Statens Serum Institut under the auspices of the Danish Ministry of Health, the subvariant accounted for 20% of all Covid cases in Denmark. By the second week of January, its share had risen to about 45% of the total.
https://thehill.com/changing-americ...k-labels-new-omicron-subvariant-ba2-a-variant
 
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  • #498
Immunity developed from a previous infection fades over time. As the Coronavirus pandemic enters its third year, many people who once had natural immunity have lost it. Protection provided by vaccines also wanes, and even before that happens, infections are possible among vaccinated and boosted individuals.

The coronavirus, meanwhile, is mutating to more infectious forms such as the delta variant and, more recently, the highly transmissible omicron variant.

https://news.yahoo.com/had-covid-19-once-then-222659971.html

An unvaccinated man in Texas with underlying health conditions previously diagnosed with Covid-19 was the first omicron-related death identified in the United States. The Centers for Disease Control and Prevention in an August study found that "being unvaccinated was associated with 2.34 times the odds of reinfection compared with being fully vaccinated," using data from Kentucky for May and June 2021 - and that was before the delta or omicron variants had taken hold.

Oklahoma reported 148 reinfections in January 2021, a monthly total that grew to 1,213 in September. Washington state officials reported 4,404 reinfection cases from September to Dec. 26, of which 60% involved unvaccinated patients. Louisiana reports more than 47,000 reinfections out of more than 1 million cases since the start of the pandemic.

I'd like to know the number for all 50 states and the territories in the US. I would expect folks first got Alpha and Delta, and more recently were reinfected with Omicron. I wonder if there are any triple infections: Alpha/Delta/Omicron.

The seven-day average for newly reported Covid-19 deaths reached 2,191 a day by Monday, up about 1,000 from daily death counts two months ago, before Omicron was first detected, data from Johns Hopkins University show. While emerging evidence shows Omicron is less likely to kill the people it infects, because the variant spreads with unmatched speed the avalanche of cases can overwhelm any mitigating factors, epidemiologists say.
https://www.wsj.com/articles/covid-19-deaths-top-2-100-a-day-highest-in-nearly-a-year-11643135898

Covid-19 deaths, though still largely composed of older Americans, trended younger as the Delta variant tore through southern states this summer and then older again as it moved northward, recent death-certificate data show. It will take more time for these data to reflect demographic trends during the Omicron surge, Mr. Anderson said.

The new variant’s breakneck speed and its arrival during the winter holidays, when states slowed their data reporting, complicated efforts to closely track the impact and so have changes in the way the U.S. detects and counts infections.

https://www.latimes.com/california/story/2022-01-24/l-a-county-seeing-more-fatalities-from-omicron
Deaths from COVID-19 in Los Angeles County have soared over the last week, with officials saying most of the recent fatalities appear to be from the Omicron variant.

The spread of the latest Coronavirus variant has moved with unprecedented speed since December, although officials have said people who get infected with Omicron generally get less severe symptoms than with the earlier Delta variant. Even so, officials say it is fatal for some.

Of 102 deaths reported Thursday — the highest single-day tally since March 10 — 90% involved people who became ill with COVID-19 after Christmas, and 80% were among those who fell ill after New Year’s Day, indicating a high likelihood of Omicron infection, Los Angeles County Public Health Director Barbara Ferrer said.
BBC reports, "Two-thirds of people (in UK?) recently infected with the Omicron variant say they had already had Covid previously".
https://www.world-nuclear-news.org/Articles/Research-hope-for-shadow-corrosion-progress
 
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  • #499
Queensland passed its peak on the Gold Coast with half the hospital admissions than the week before. It is thought Brisbane is going through its peak right now. Total deaths 19 yesterday - but the Omicron total in Queensland is still below the flu deaths in 2019. We will see what it ends as.

Omicron specific vaccine on the way:
https://www.reuters.com/business/he...al-omicron-targeted-covid-vaccine-2022-01-25/

I would like greater availability of the Pfizer pill, which is 90% effective at parenting death. With that and the vaccine, I am hopeful.

Thanks
Bill
 

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