Covid Variant Omicron (B.1.1.529)

[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.

 

[Astronuc]

MIS-C is a rare condition that sometimes occurs in children who have had COVID-19 infection. Symptoms of MIS-C typically develop two or more weeks following infection with COVID-19 and involves inflammation of different parts of the body, such as the heart, lungs, kidneys, brain, skin, eyes, or gastrointestinal system. What causes some children to develop MIS-C is not known. MIS-C can be serious or even deadly, but most children recover with medical care.

As of January 31, 2022, the New York State Department of Health has investigated and confirmed 654 cases of MIS-C and 3 deaths attributed to MIS-C in New York children (under 21 years old).

Of the children confirmed as MIS-C cases, 94 percent tested positive for COVID-19 either by diagnostic tests (PCR or antigen), antibody tests or both.

As of 10/15/21, only confirmed MIS-C cases are being reported.

https://coronavirus.health.ny.gov/multisystem-inflammatory-syndrome-children-mis-c
On January 3, the number of MIS-C cases in children in New York State was 610, so 44 new cases during January.

 

[bhobba]

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.

The objection is Omicron is so transmissible a gradual reopening likely will not work. Western Australia tried to keep it out:
https://7news.com.au/news/wa/wa-rec...wing-concerns-over-undetected-cases-c-5633111

“But what we’ve seen with Omicron internationally and interstate is that it tracks along fairly low and then spikes very quickly, so we are expecting any day a very steep spike.”

I can understand giving it go to buy time so as many as possible can get a third dose - but I doubt it is enough for it not to be widely spread before October. Anyway, we will see.

Thanks
Bill

 

[bhobba]

Latest from the local paper where I am:

'Chief health officer John Gerrard said he expected up to half of the state's population would have been infected by the end of February, and residents had established a 'wall of immunity through vaccinations, boosters and infection which would help see them through further waves. He said the winter months would be critical, stressing "we don't know" how further variants will play out and again urged the population to get vaccinated and boosted. "What we are seeing is the establishment of a wall of immunity, and we are seeing immunity through vaccination, bolstering and through natural infection, and those three arms are creating a wall of immunity in the Queensland community," he said. However, he said the 'unknown' would happen going forward because the world had experienced Omicron simultaneously. Australia would be the first to go into winter with the strain prevalent. "We don't know whether the amount of immunity we've established through natural infection and vaccination is enough to protect us from another wave ... and if there is another wave, how big that will be," he said. "It's obvious the virus is not going to go away. "It will circulate ... and it will find you." He said of the eight people who died, three of them were unvaccinated - while only one had received a booster.'

The excellent news is hospitalisations are falling rapidly. Still not at the 2019 flu deaths, but inching closer. The big discussion issue is should people be allowed in without the third dose. I can see both sides of that one. I feel more optimistic now that the military has been called into manage where 50% of deaths occur - aged care facilities.

Thanks
Bill

 

[bhobba]

Sad news from Australia overall. In Queensland, things are looking good with the peak passed and still not yet reaching 2019 flu deaths. But the Actuarial Institute has been looking at all of Australia and for the first time, overall deaths may have increased.

'Deaths from all causes may have increased in January for the first time during the pandemic, spiking by about 10 per cent as the Omicron variant infected millions of Australians. Modelling by the Actuaries Institute’s COVID-19 working group shows the 1582 COVID-19 fatalities recorded in January – more than the whole of either 2021 or 2020 – drove up the number of overall deaths without any expected offset from fewer influenza deaths. COVID-19 deaths during the Omicron wave appears to have driven up the number of overall deaths in Australia. “Until the Omicron surge in cases, overall mortality in Australia has been lower than previous years, as the increase in deaths from COVID-19 has been more than offset by the reduction in deaths from other respiratory illnesses,” actuary Jennifer Lang, the working group’s convenor, said. As the nation began to open up over summer, the highly transmissible variant pushed up COVID-19 deaths, but there was no significant drop in flu or pneumonia deaths. “If COVID-19 deaths are near the peak of this current wave, and we do not have another significant wave, total COVID-19 deaths in 2022 may not result in a material net increase in total mortality given the gains in other areas, most notably respiratory disease,” the modelling said. “However, if COVID-19 deaths continue at this level for several months, or we have another wave later this year, Australia could be expected to record excess mortality in 2022, the first such year during the pandemic.” Without a pandemic, Ms Lang said, between 13,500 and 14,000 deaths would be expected in January, meaning the 1582 COVID-19 deaths will have increased mortality in Australia by about 10 per cent that month, factoring in minimal change to flu and pneumonia deaths. “We expect to see excess mortality of around 10 per cent once the complete death data is available,” she said. The outlook seeks to predict official data yet to be released by the Australian Bureau of Statistics. “There is unlikely to have been a corresponding reduction in deaths from lockdowns, social distancing, border closures or other measures as we have observed very little reduction in overall mortality during the summer months of 2020 and 2021 from these measures.”

Added Later, and with equal sadness, from today's paper:
'About 75 per cent of patients in intensive care at the peak of the Gold Coast’s Omicron wave were unvaccinated, and “pretty much all of them” regretted their decision, a medical specialist says. Dr Jon Field, an intensive care specialist at the Gold Coast University Hospital, said staff did not delve too deeply into why patients were not immunised, but he said “misinformation and misunderstanding” were the main reasons.'

With Sadness
Bill

 

[atyy]

The objection is Omicron is so transmissible a gradual reopening likely will not work. Western Australia tried to keep it out:
https://7news.com.au/news/wa/wa-rec...wing-concerns-over-undetected-cases-c-5633111

“But what we’ve seen with Omicron internationally and interstate is that it tracks along fairly low and then spikes very quickly, so we are expecting any day a very steep spike.”

I can understand giving it go to buy time so as many as possible can get a third dose - but I doubt it is enough for it not to be widely spread before October. Anyway, we will see.

Thanks
Bill

A mixture of partial restrictions, isolation during the most infectious days, early boosters might buy some time. In Singapore, it looks like the doubling time of Omicron is about 5 days, compared to 2-3 days in many places. But it's still enough to stress the emergency department, even though the case fatality rate seems now to be in the range of flu (0.05%).
https://www.channelnewsasia.com/sin...ood-emergency-rooms-amid-omicron-wave-2492571

 

[bhobba]

Latest sad news from Brisbane (taken from today's Courier-Mail). We had 39 deaths yesterday.

'Dr Gerrard said of the 39 deaths; one was in their 50s, five in their 60s, 10 in their 70s, 12 in their 80s, 10 in their 90s and one over 100. He said 21 of the deaths occurred in aged care facilities.'

I do not understand why the aged care occupants are not protected more. Since the beginning of the pandemic, we have known they are the most vulnerable. So sad

Thanks
Bill

 

[morrobay]

Latest sad news from Brisbane (taken from today's Courier-Mail). We had 39 deaths yesterday.
Thanks
Bill

But the 39 is a total going back to mid January.
https://www.brisbanetimes.com.au/na...-many-are-from-weeks-ago-20220217-p59x8y.html

 

[bhobba]

But the 39 is a total going back to mid January.
https://www.brisbanetimes.com.au/na...-many-are-from-weeks-ago-20220217-p59x8y.html

Wonder why the Courier Mail didn't make that clear? Regardless the percentage from aged care facilities is both sad and worrying. I am watching the news at the moment. The same blame game. The regulator says it is the owners of the facilities responsibility; others complain the regulator is not doing their job.

Thanks
Bill

 

[Ygggdrasil]

Here's a nice opinion piece in STAT news speculating about possible scenarios for evolution of the SARS-CoV-2 virus going forward, laying out four different possible scenarios that have been observed in the evolution of other viruses. Here's a good summary from later in the article:

I’m not confident about how the pandemic endgame will play out. While I do think the most likely future scenario for SARS-CoV-2 is that it will become endemic, the other more worrisome scenarios I describe here are within the realm of possibility: a mutant that produces a different disease, a new recombinant virus, or a variant that exploits immunity. And these scenarios are not mutually exclusive. A new SARS-CoV-2 recombinant virus containing animal Coronavirus genes might well cause altered disease.

Some other scenarios I haven’t discussed are also worth thinking about, like ongoing back-and-forth spillover from humans to animals and back to humans, or increased transmissibility from chronically infected people with “long Covid.”

None of these epidemic scenarios is a fantasy. All are variations of the known evolution of real-world coronaviruses. A new viral variant can emerge anywhere on Earth to cover the globe in a matter of weeks, as SAR-CoV-2 did.

Coronaviruses are ‘clever’: Evolutionary scenarios for the future of SARS-CoV-2
https://www.statnews.com/2022/02/16...onary-scenarios-for-the-future-of-sars-cov-2/

The article emphasizes the importance of ongoing surveillance to catch new variants as they arrive as well as ensuring global distribution of effective vaccines to limit the opportunities for new variants to evolve.

 

[bhobba]

The article emphasizes the importance of ongoing surveillance to catch new variants as they arrive as well as ensuring global distribution of effective vaccines to limit the opportunities for new variants to evolve.

I noticed one person gave a worried up-vote. Please be assured with the new mRNA vaccines, how quickly they can be developed, and what we have learned; we can manage all the possibilities. They are now trialling an Omicron specific vaccine that, if required, can be distributed in March. It is not sure if it will produce better results than the third regular shot or even a fourth in the vulnerable population. As Pogo said - we have met the enemy - and he is us. Nothing during the pandemic captured it more than the picture of the heroes crossing the river to get the vaccine to people in Nepal. In contrast, conspiracy theorists (and I know highly educated, scientifically literate ones) protested against the vaccine (as is their right in a free country). We will keep the faith and inform those that come here of the actual science on this forum. And not hide, like all science, what we know can change over time. And we must pressure the bureaucracy to protect those in aged care facilities. At least in Aus that is where 50% of the deaths are from.

The Actuarial Insitute has produced a paper on the increase in mortality. Only recently has it increased over normal. 10% in January:
https://www.actuaries.digital/2022/...y-remains-steady-but-january-increase-likely/

For comparison, in 2019, a bad but not Australias worse flu season, 808 in total died. That is just to keep things in perspective.

We must investigate further where this is occurring and take appropriate precautions. My guess is it is the aged care facilities. That IMHO needs urgent attention .

Thanks
Bill

 

[Ygggdrasil]

I noticed one person gave a worried up-vote. Please be assured with the new mRNA vaccines, how quickly they can be developed, and what we have learned; we can manage all the possibilities. They are now trialling an Omicron specific vaccine that, if required, can be distributed in March. It is not sure if it will produce better results than the third regular shot or even a fourth in the vulnerable population.

Preliminary data from animal experiments suggest that boosting with the Omicron-specific vaccine is not any more effective than boosting with the original mRNA vaccine:

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.

This mirrors result 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.

For more discussion see:
https://www.physicsforums.com/threads/covid-variant-omicron-b-1-1-529.1009541/post-6597185
https://www.science.org/content/blog-post/omicron-boosters-and-original-antigenic-sin

 

[jim mcnamara]

https://pubmed.ncbi.nlm.nih.gov/35169598/ BA.2 sub-variant of Omicron
Shows increased transmissability over the parent BA.1 Some other comments are worth reading.

The link above is an abstract of observational data - which limited. Basically I would consider this report to be more of a heads up note at this point in time 17:23 MST 2/18/22, rather than a 'here we go again' lament.

-- @Ygggdrasil thanks for the correction. (in red above NOT observational data)

But:

If you want an in depth consideration, which shows how we basically shot ourselves in the foot with our handling of the pandemic, and what to expect see: Dr Gregory Poland Mayo Clinic -

 

[bhobba]

If you want an in depth consideration, which shows how we basically shot ourselves in the foot with our handling of the pandemic, and what to expect see: Dr Gregory Poland Mayo Clinic -

God, this guy is GOOD. He is not whistling dixie when he says people are, at least as far as basic probability goes, illiterate and innumerate. It's a BIG problem. Most don't even get if you have 95% vaccination and the vaccine was ineffective, then 95% in ICU would be vaccinated. This, of course, is NOT what we see - it seems to be about 60% to 70%. They instead conclude vaccination is not only useless but increases your risk. I want to bang my head against the wall.

Thanks
Bill

 

[Astronuc]

CNN — The BA.2 virus – a subvariant of the Omicron Coronavirus variant – isn’t just spreading faster than its distant cousin, it may also cause more severe disease and appears capable of thwarting some of the key weapons we have against Covid-19, new research suggests.

New lab experiments from Japan show that BA.2 may have features that make it as capable of causing serious illness as older variants of Covid-19, including Delta.

And like Omicron, it appears to largely escape the immunity created by vaccines. A booster shot restores protection, making illness after infection about 74% less likely.

https://www.cnn.com/2022/02/17/health/ba-2-covid-severity/index.html

https://www.cdc.gov/coronavirus/201...-briefs/scientific-brief-omicron-variant.html

The BA.2 omicron subvariant evolved from the same lineage as the BA.1 omicron strain that quickly has become dominant around the world. But BA.2 has 28 unique spike protein mutations, so it's like a cousin in the family of four currently identified omicron subvariants.

https://www.freep.com/story/news/he...variant-michigan-covid-19-stealth/9283576002/

 

[Ygggdrasil]

https://pubmed.ncbi.nlm.nih.gov/35169598/ BA.2 sub-variant of Omicron
Shows increased transmissability over the parent BA.1 Some other comments are worth reading.

The link above is an abstract of observational data - which limited. Basically I would consider this report to be more of a heads up note at this point in time 17:23 MST 2/18/22, rather than a 'here we go again' lament.

Are you sure that the abstract is of observational data? Here's the text of the abstract that you link to:

The Omicron variant of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2 variant because of natural selection, which favors the variant with higher infectivity and stronger vaccine breakthrough ability. Omicron has three lineages or subvariants, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3). Among them, BA.1 is the currently prevailing subvariant. BA.2 shares 32 mutations with BA.1 but has 28 distinct ones. BA.3 shares most of its mutations with BA.1 and BA.2 except for one. BA.2 is found to be able to alarmingly reinfect patients originally infected by Omicron BA.1. An important question is whether BA.2 or BA.3 will become a new dominating "variant of concern". Currently, no experimental data has been reported about BA.2 and BA.3. We construct a novel algebraic topology-based deep learning model trained with tens of thousands of mutational and deep mutational data to systematically evaluate BA.2's and BA.3's infectivity, vaccine breakthrough capability, and antibody resistance. Our comparative analysis of all main variants namely, Alpha, Beta, Gamma, Delta, Lambda, Mu, BA.1, BA.2, and BA.3, unveils that BA.2 is about 1.5 and 4.2 times as contagious as BA.1 and Delta, respectively. It is also 30% and 17-fold more capable than BA.1 and Delta, respectively, to escape current vaccines. Therefore, we project that Omicron BA.2 is on its path to becoming the next dominating variant. We forecast that like Omicron BA.1, BA.2 will also seriously compromise most existing mAbs, except for sotrovimab developed by GlaxoSmithKline.

Seems like to me, the authors are building a machine learning model based on experimental data on other variants to infer the properties of Omicron BA.2 (without including any experimental or observational data on BA.2 itself). However, the estimates that they do come up with seem to be roughly in line with preliminary experimental data on BA.2. For example, see this pre-print posted by @Tom.G in another thread about BA.2:

Virological characteristics of SARS-CoV-2 BA.2 variant
https://www.biorxiv.org/content/10.1101/2022.02.14.480335v1

Soon after the emergence and global spread of a new severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Omicron lineage, BA.1 (ref1, 2), another Omicron lineage, BA.2, has initiated outcompeting BA.1. Statistical analysis shows that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralisation experiments show that the vaccine-induced humoral immunity fails to function against BA.2 like BA.1, and notably, the antigenicity of BA.2 is different from BA.1. Cell culture experiments show that BA.2 is more replicative in human nasal epithelial cells and more fusogenic than BA.1. Furthermore, infection experiments using hamsters show that BA.2 is more pathogenic than BA.1. Our multiscale investigations suggest that the risk of BA.2 for global health is potentially higher than that of BA.1.

This paper includes analysis of actual epidemiological data of BA.2 as well as experiments with the BA.2 virus in cultured cells and in animals.