COVID Covid Variant Omicron (B.1.1.529)

[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.

 

[Astronuc]

Infectious disease doctors say it is still mainly unvaccinated people, most of whom are in their 30s and 40s with no underlying health issues, who are dying.

https://www.yahoo.com/gma/dying-covid-still-mainly-unvaccinated-090546286.html

 

[morrobay]

While the above graph is factual . The percent of Covid deaths in unvaccinated: 9/100000 , 009% Have different perceptions.

 

[StevieTNZ]

The case numbers in NZ today -- https://www.newshub.co.nz/home/new-...R8Kuo8wgh1Vtlslowc7-fByDgHnctd4R-_K1yHrT2d3gs -- now Omicron has taken hold, as well as updates on the rather unruly protest happening at Parliament grounds.

 

[atyy]

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: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.

I'm hoping immunity will be progressively more variant resistant, at least immunity against severe illness. Hybrid immunity even shows some poor but detectable neutralization against SARS1. RNA vaccination of people who've had SARS1 shows pretty decent neutralization against both SARS1 and SARS2 and a pretty wide range of coronaviruses. https://www.nejm.org/doi/full/10.1056/NEJMoa2108453

 

[Ygggdrasil]

I'm hoping immunity will be progressively more variant resistant, at least immunity against severe illness. Hybrid immunity even shows some poor but detectable neutralization against SARS1. RNA vaccination of people who've had SARS1 shows pretty decent neutralization against both SARS1 and SARS2 and a pretty wide range of coronaviruses. https://www.nejm.org/doi/full/10.1056/NEJMoa2108453

T-cell immunity, which is likely a major factor providing protection against severe illness, does not seem to be affected much by the variants. For example, see the following article:

SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron
https://www.cell.com/cell/fulltext/S0092-8674(22)00073-3

While the initial two dose immunization with the mRNA vaccines does not provide good protection against infection by some of the newer variants like Delta or Omega (while still providing protection against hospitalization and death), the booster dose (> 6 months after the initial series) does seem to expand the breadth of antibodies produced to be able to neutralize the newer variants:

Omicron’s message on vaccines: Boosting begets breadth
https://www.cell.com/cell/fulltext/S0092-8674(22)00006-X

This data is in line with what we know about somatic hypermutation and other processes during B-cell maturation that help to refine antibody affinity over time. Of course, it still remains to be seen how long protection from the booster shot lasts and whether the breadth of the neutralizing antibody response will be sufficient to protect against the next major variant that arises.

 

[Astronuc]

New York state just passed 4.9 million cases. They have been collecting data on reinfections, and the state started reporting the trend recently. Some earlier reinfections, last year, were probably Delta on top of Alpha, but more recently, it seems the reinfections were Omicron at a high rate.

Cumulative, 4885066 first infections, 195058 reinfections.
https://coronavirus.health.ny.gov/covid-19-reinfection-data

 

[StevieTNZ]

Cases in NZ continue to grow:
* 14,633 new community cases
* 344 people in hospital; 5 in intensive care or high dependency care unit

Most are likely Omicron, though I'm sure Delta will still be spreading.

 

[bhobba]

now Omicron has taken hold, as well as updates on the rather unruly protest happening at Parliament grounds.

I do not know if they were 'peaceful' or not (i.e. in what way they were unruly), but here in Aus, what we eventually figured out is if the police work with the protesters, you get better results. How feasible it is in NZ, I have no idea. Of course, Australia went through precisely the same issues - we had to learn it the hard way.

Thanks
Bill

 

[bhobba]

Most are likely Omicron, though I'm sure Delta will still be spreading.

Just like Aus. What concerns me most is the demographic of the deaths; 50% are aged-care residents. We knew from the Melbourne outbreak it would happen. Authorities should have done something to protect them sooner. Due to the floods on the east coast, nurses with Covid had to be pulled from isolation; staff shortages are that bad.

Thanks
Bill

 

[bhobba]

Cumulative, 4885066 first infections, 195058 reinfections.
https://coronavirus.health.ny.gov/covid-19-reinfection-data

The experience here in Brisbane is 90% seem to be asymptomatic, or experience symptoms so mild they hardly notice it. The numbers could be much much higher. That is the hypothesis our new Chief Medical Officer is using. People are getting worried if that group get long Covid. It could be a long term health tsunami, but I don't think anyone knows for sure.

Thanks
Bill

 

[StevieTNZ]

There are 19,566 new community cases in New Zealand on Tuesday, the Ministry of Health has confirmed.

There are also 373 people in hospital with the virus, nine of whom are in intensive care.

In total, there are just under 100,000 active cases across New Zealand currently.

-- https://www.stuff.co.nz/national/he...-conferences-with-dr-ashley-bloomfield-return

 

[StevieTNZ]

I do not know if they were 'peaceful' or not (i.e. in what way they were unruly), but here in Aus, what we eventually figured out is if the police work with the protesters, you get better results. How feasible it is in NZ, I have no idea. Of course, Australia went through precisely the same issues - we had to learn it the hard way.

Thanks
Bill

https://www.stuff.co.nz/national/he...sters-in-dramatic-confrontation-at-parliament

Some action finally done to remove the illegal occupation of Parliament grounds (the Speaker trespassed them many weeks ago).

 

[pinball1970]

-- https://www.stuff.co.nz/national/he...-conferences-with-dr-ashley-bloomfield-return

UK has seen decreasing numbers cases/deaths through FEB with all restriction ceased by March 1st. We are at July numbers now.

 

[pinball1970]

Yes. They are reporting the numbers in a different way prior to March 2022 in the UK technical briefings. We are officially 'out' of the pandemic. From March 1st
https://www.worldometers.info/coronavirus/country/uk/

A lot of people died last week. I'll post the technical link tomorrow. No access now, apologies

 

[pinball1970]

A little bit late...

https://www.ons.gov.uk/peoplepopula...soccurringbetween1january2021and31january2022

Also https://www.worldometers.info/coronavirus/country/uk/

Considering high rates of vaccination and Omicron less virulent strain quite high deaths. 250 per day on a 7 day average.

Trend is now coming down again though.