Covid Variant Omicron (B.1.1.529)

[StevieTNZ]

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.

 

[Jarvis323]

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

 

[StevieTNZ]

My mum's friend reckons we're moving to red at midnight - https://www.nzherald.co.nz/nz/covid...equencing-results/7RMZATR73L5RYW4MWZBPEFLUTM/

Concerning.

 

[Ygggdrasil]

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:

https://covariants.org/

 

[StevieTNZ]

This link has just appeared - https://www.nzherald.co.nz/nz/covid...onference-at-11am/FPYXEZCL3IS2R3I5RPGAI4IFOA/

I wonder what she has in store for us?

 

[Oldman too]

https://www.nature.com/articles/d41586-022-00149-9

 

[StevieTNZ]

https://www.stuff.co.nz/national/he...o-red-traffic-light-setting-at-1159pm-tonight

* All of NZ will move to the red traffic light setting at 11.59pm tonight.
* Omicron is circulating in areas of Auckland and Nelson, and it is spreading in the community.

 

[Laroxe]

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. :)

 

[Ygggdrasil]

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 )?

 

[Jarvis323]

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.

 

[Laroxe]

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.

 

[StevieTNZ]

A sore throat seems the likely indication you've caught Omicron: https://www.nzherald.co.nz/world/co...ng-youre-infected/344GJ5YJL7LCWAGNWJGZ22VWAQ/

 

[Laroxe]

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.

 

[Laroxe]

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 )?

Your right, my mistake. should I delete the comment to avoid confusion.?

 

[Ygggdrasil]

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.

 

[bhobba]

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

 

[Astronuc]

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

 

[Astronuc]

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

 

[bhobba]

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

 

[StevieTNZ]

Prime Minister Jacinda Ardern and Governor General Dame Cindy Kiro are both now isolating after a flight attendant on their flight from Kerikeri to Auckland tested positive for Omicron.

All those on the flight are considered close contacts.

-- https://www.nzherald.co.nz/nz/covid...-every-three-days/I5FTRG4MBJUNXLUMKDVTVGQIYA/

 

[bhobba]

Queensland has turned the corner. We have recorded 7462 new Covid cases and three deaths.

Premier Annastacia Palaszczuk said “It’s very promising so fingers crossed it continues as case numbers are beginning to drop,"

Of the three deaths, one person was in their 60s, one in their 80s and one in their 90s.

Total deaths are still less than the 2019 flu season.

Thanks
Bill

 

[Tom.G]

In the Sunday Jan. 22, 2022 Los Angeles Times newspaper, page B1:

County virus cases fall 45%
The county recorded 21,700 new Coronavirus cases saturday, a 45% decline from a week ago, when there were 39,117, the public health department said in a news release...

The county population is 10 040 000.

And now the B.2 version is showing up.

 

[bhobba]

And now the B.2 version is showing up.

Yes, that is a worry. The best hope, of course, is the 3rd vaccination. But I am concerned that the Pfizer pill does not seem to be progressing fast enough.

Thanks
Bill

 

[Astronuc]

For New York State, as of January 31, 2021, the following numbers are reported (I did the fractions).

1/31/22     Cumul.  January   Fraction of
Age Group   Deaths   Deaths   Cumulative
90 and Over  8,376     812     0.0969
80 to 89    14,175   1,236     0.0872
70 to 79    13,680   1,131     0.0827
60 to 69     9,632     761     0.0790
50 to 59     4,604     399     0.0867
40 to 49     1,656     153     0.0924
30 to 39       688      63     0.0916
20 to 29       213      22     0.1033
10 to 19        28       6     0.2143
0 to 9          27       9     0.3333
Total       53,079   4,592

The cumulative deaths (from COVID-19) do not include 9 of unknown age. The cumulative deaths represent all deaths occurring during the pandemic starting March 1, 2020, so over 23 months. NY State has report 66319 deaths to the CDC. As previously mentioned, the lower number refers to those who died in a hospital, healthcare facility or elder care facility. The higher number includes probable cases, or those who died outside of a healthcare facility, e.g., at home, on the street, . . . , with the confirmed cases.

Note that 21% of death in 10-19 age group occurred in January, and one-third of deaths (33.3%) in the 0 to 9 age group. The 20-somethings (20-29) account for 22 deaths in January or 10% of the 213 deaths in that age group. The 30-somethings (30-39) account for 63 or 688 deaths, or 9.2%. The numbers obviously increase with age. The younger population were delayed in getting vaccinated, and some folks are still reluctant to get vaccinated.

The good news is that the daily death rate is decreasing in NY state from nearly 200/day to below 100/day. The daily new positive cases have fallen below 10,000/day for the last three days.

NY State has reported 4,791,065 positive cases (23.7% of population) from 97,061,178 tests, for a per capita testing rate of 4.8 per person. The mortality rate for SARS-Cov2 is approximately 1.1% of the positive cases. If one includes probable cases, the mortality rate increases to 1.37% of positive cases. What is not reported are the demographics of those reinfected or vaccinated/unvaccinated, although the fractions of unvaccinated and vaccinated hospitalizations are known and reported.

The test results data comes from a NYSDOH database that contains reported results from all the labs testing samples from New York State residents. Starting on September 20, 2020, this data also includes pooled/batch tests reported by institutions of higher education.

The Omicron variant dominates in NY; it represented 88.5% of COVID cases for the last two weeks of December (two weeds ending 1 Jan) and 97.9% of cases from 1 Jan to 15 Jan, 2022.

 

[bhobba]

Latest from the local paper where I live:

'Chief Health officer Dr John Gerrard said a study on the Gold Coast to “get a better idea of what is really happening” with Covid-19 revealed that on January 22, when the virus was peaking on the coast, 117 randomised households were visited and tests performed on an individual. Of those 117 people tested, 20 came back positive – one in six. Only four of the 20 reported having any symptoms, Dr Gerrard said. “There were people walking around the Gold Coast who had no idea they had Covid-19,” he said. Dr Gerrard said two among the 20 knew they were positive, meaning 18 did not know they were positive. “To recap, four out of five had no symptoms and nine out of 10 did not know they were positive,” he said. “It is quite extraordinary. There are people walking around the Gold Coast who had no idea they were infected. A lot of people that have been infected are completely unaware they were infected. That number is significant.” He said that cemented the reason masks were so important. Dr Gerrard said authorities were still “planning for the worst” in preparing for potential future waves, especially in winter. “Clearly the virus is much more widespread than the collected data has suggested,” he said.'

We already knew it would end like this from early on when it was reported most cases were picked up when people went to the hospital for other reasons.

Death rates of those they know had covid:
https://www1.racgp.org.au/newsgp/clinical/covid-19-chart-updated-with-omicron-risk-of-death

With the third booster it is .014% - the flu - about .016%. So the flu is slightly more deadly with the third vaccine - but Omicron is unbelievably contagious with most not even knowing it. That likely makes it, with the third dose, a good deal less deadly than the flu. But due to how contagious it is please, please, everyone GET THE THIRD DOSE. And we must protect the vulnerable - not lock them away in those Covid Petri dishes called aged care facilities. That is where most of the deaths are occurring. I thought we had already learned that - obviously not.

Thanks
Bill

 

[StevieTNZ]

https://abcnews.go.com/Health/us-co...1u5wmpNWQHAhWQH8KCkb8M4t1TBcmZnP7GwO2X2o6NYXo

US COVID-19 death toll tops 900,000, despite receding case rates

I hope someone is held accountable for this: https://www.newshub.co.nz/home/world/2022/02/coronavirus-world-leading-expert-says-catastrophic-failure-of-global-diplomacy-made-pandemic-far-worse.html

...
the situation could also mean that the origins of COVID-19 are never discovered.

Where, when and how the virus originated remains one of the central mysteries of COVID-19, which has killed more than six million people worldwide. The United States and other countries have criticised China for delaying sharing information when the virus emerged there in 2019.

In December, the World Health Organization (WHO) said Beijing had still not disclosed some early data that might help pinpoint the origins and called for a second phase of an investigation into it.

On Thursday, Farrar reiterated his position that the "overwhelming majority" of evidence points towards natural origins, although he said a lab leak still cannot be ruled out.

 

[Astronuc]

US COVID-19 death toll tops 900,000, despite receding case rates

Deaths will lag the positive cases. However, it appears that with the recent surge in the US, the number of deaths were not proportionally as high as was the case last January surge, which I believe was the Alpha variant. Another mitigating factor is the portion of the population who have been vaccinated, particularly those 65 and older who are much more vulnerable to the virus and its effects.

 

[bhobba]

Deaths will lag the positive cases.

That's is exactly what is happening here in Brisbane. The case peak has passed, but the death peak is now occurring. With the revelation that 90% of cases go unreported because they are asymptomatic or symptoms so mild, you ignore it - everybody has those slightly 'off' days. I certainly do, but I put it down to my autoimmune disease; the fatality rate seems way below the flu with the booster. The problem is how contagious it now is. Deaths in Queensland still has not exceeded the 2019 flu season (not our worst - but still bad) but is now inching closer - 216 from Omicron - 260 from flu. I think, unfortunately, it will eventually exceed it, but not by a large margin. Again, we know 100% for sure from data gathered here in Queensland; with the booster, you have a 24 times less chance of dying. Also, as we already know, it attacks the vulnerable and elderly worst of all. I am saddened that authorities have not learned the lessons from previous waves and are still locking people in Aged Care facilities. About 50% of deaths have occurred there. Now the advice, and I am doing it, is to open windows, doors, etc. This disease does not transmit readily in uncrowded open spaces.

I still am shaking my head at what NZ is doing. A gradual opening extending to October? They have no idea how contagious this is. It will fail. Much better to give as many as possible the third dose. Go house to house if necessary and try to reason with the recalcitrants. I know people I respect, such as Alan Dershowitz, advocate mandates. Still, the experience here in Aus, with states like the ACT getting 99% vaccination voluntarily, indicates it probably is not necessary if the rollout is done right. That is my real worry - doing the rollout correctly e.g. there are still aged care facilities whose residents do not have the booster:
https://www.abc.net.au/news/2022-02-02/qld-coronavirus-covid19-aged-care-booster-concerns/100793572

Thanks
Bill

 

[Ygggdrasil]

Some preliminary results from NIH's study of the Omicron-specific Moderna booster in animal tests:

mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron
https://www.biorxiv.org/content/10.1101/2022.02.03.479037v1?s=08

Abstract:

SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to antibody neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-specific vaccines would enhance immunity and protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing antibody titers against D614G were 4760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (pre-boost), respectively, and 320 and 110 for Omicron. Two weeks after boost, titers against D614G and Omicron increased to 5360 and 2980, respectively, for mRNA-1273 and 2670 and 1930 for mRNA-Omicron. Following either boost, 70-80% of spike-specific B cells were cross-reactive against both WA1 and Omicron. Significant and equivalent control of virus replication in lower airways was observed following either boost. Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine.

In other words, boosting primates with the original Moderna vaccine looks to be just as effective at inducing immunity as boosting with an Omicron-specific vaccine. This mirrors similar results in animal tests of the Beta-specific vaccine which observed similar efficacy against Beta for a boost with the original Moderna vaccine vs a Beta-specific version of the Moderna vaccine.

Here's a good popular press summary of the NIH pre-print:

We've had some interesting vaccine news in the last few days, and it's worth a closer look. A team from the NIAID, Emory, Moderna (and others) has reported results in a primate model for an Omicron-targeted mRNA booster shot that they've been working on, and the numbers are. . .a bit surprising. Macaque monkeys were dosed twice, four weeks apart, with the standard Moderna Coronavirus vaccine, and then 41 weeks later one group of them got a booster of the same shot, while another got a booster of the new one with an Omicron variant sequence. Subsequent tests for neutralizing antibody levels, B-cell expansion, and response to a challenge with the Omicron virus itself showed that there was no difference between the two treatments at all.

It's important to say right up front that both vaccine regimens did a strong job of protecting the test animals - strong enough that both groups of monkeys were pretty much completely protected in the lungs during the challenge study, which in its way makes comparison at that point a bit difficult (protection in the upper airway was strong, but less complete, as it is in humans). So I hope that people don't get confused as this news gets out into thinking that the Omicron-focused booster did nothing. It worked fine; it's just that it brought nothing extra compared to the regular booster.

[...]

The authors believe that this is most likely due to the phenomenon known (catchily) as "original antigenic sin", or less rousingly, antibody imprinting. That's been seen in many immune responses to many different antigens over the years. A person's first exposure to a type of virus, for example, can have a noticeable effect on their later responses to similar ones.

https://www.science.org/content/blog-post/omicron-boosters-and-original-antigenic-sin

The concept of "original antigenic sin" has been discussed before in a variety of other threads (including this one):
https://www.physicsforums.com/threa...o-endemic-coronaviruses.1005206/#post-6523013
https://www.physicsforums.com/threads/covid-delta-variant.1004265/page-13#post-6535624
https://www.physicsforums.com/threads/covid-delta-variant.1004265/page-14#post-6535822
https://www.physicsforums.com/threads/covid-variant-omicron-b-1-1-529.1009541/page-5#post-6569985

 

[StevieTNZ]

I still am shaking my head at what NZ is doing. A gradual opening extending to October? They have no idea how contagious this is. It will fail.

I'm not entirely sure what your objection to our gradual border re-opening is, considering in Australia they're re-opening in two weeks.