Corona Virus Updates Part 6

COVID-19 tracker: Japan reports 15 new omicron cases

Japan on Wednesday reported 15 new cases of the omicron variant of the coronavirus detected at airport screening sites. It seems the cases are coming in from the airports. 32 cases so far.

Japan has not detected any community transmissions, so I wonder how all the transmissions are happening around the world?


The health ministry said Wednesday the nationwide number of seriously ill COVID-19 patients was unchanged from Tuesday at 27.

On Tuesday, Japan confirmed 144 new COVID-19 cases and one death linked to the virus.

Might not have access to the paper, but here is the link.

www.japantimes.co.jp...

Dec. 17 Friday Tokyo no new deaths today in Japan from the corona virus.

originally posted by: puzzled2
So between Xmas and New year no-one will die without a positive result for a sars-cov-2 infection therefore they will claim Millions are dying and will be justified in forcing the jabs they already have the laws, goons and public opinion to do so.

Sadly, that's all too plausible! Let's hope it doesn't go that way.

I suspect Boris is gambling that omicron isn't all that severe, so he can dodge a lockdown, meanwhile using omicron to scare everyone into booster jabbing, simply because there's a lot of money in it and promises have probably been made.

It's the only explanation imo that gives the mixed messages a rational. Alternatively he's just an idiot!

a reply to: McGinty

Saw him on tv today. Did he get the booster?

a reply to: musicismagic

He apparently got it Dec 2nd! But that could be anything being injected into his arm - proves nothing. Probably viagra, knowing him.

UK PM Johnson receives COVID-19 booster shot

a reply to: McGinty

It is still an experimental drug. No way would a PM get that, there might be some law in a dusty obscure place preventing him from partaking in medical trials. It would be too great a way to assassinate a head of state.

a reply to: anonentity

Our Head of State is the Queen.
The PM's a figurehead of the Conservative party.
He is entirely replaceable.
You vote for the Party, not the person.
That's why they can be replaced without having a General Election.

He has to show he has had the vaccine, though not necessarily which one, as an example to the population to get vaccinated.
If it was ever found out or leaked that he had faked having the vaccine, it would ruin the country.

I would suspect he had Astrazenica, or Pfizer.

On a different note, here in France the Govt has just announced our "Sanitary Pass" (Passe Sanitaire) is to be replaced/renamed "Vaccine Pass" (Passe Vaccinale) in January.
Basically it removes the possibility of using PCR or lateral flow tests as an option.
They have admitted it's basically obliging people to get vaccinated if they want to do things, but say it would be accepted better than an obligation to get vaccinated.

Over at The Guardian, there's an article entitled Kamala Harris concedes White House ‘didn’t see’ Delta and Omicron coming

“We didn’t see Delta coming. I think most scientists did not – upon whose advice and direction we have relied – didn’t see Delta coming,” Harris said.

“We didn’t see Omicron coming. And that’s the nature of what this awful virus has been, which as it turns out, has mutations and variants.”

Delta was already highly prevalent in Europe before it got to the US, and the Scientists were telling everyone they could it was worse than Alpha.
From the second statement in the above quote, it would seem that they have just discovered that the virus can mutate and create variants.
I'd like to know where the hell they have been, and what they have been watching for the last couple of years, as it was obvious to almost everyone else that it mutates and creates variants...
But the Scientists are the ones to blame, they didn't tell them about it (which i'm pretty damn sure they did).

London is having trouble with it's Services, as Police and Fire brigades, as well as Hospitals, are seeing a lot of employees off sick, or isolating. They are running out of personnel to run the services.

This could end up being one of the major problems over the next few weeks/months everywhere.
Especially since a lot of countries seem to be relying on massive Vaccination, whereas Omicron, and Delta to some extent, do not seem to be affected. The vaccinated can catch and transmit Delta/Omicron pretty well, so it's not going to do anything to slow down, or stop the spread.

All of the Brits that wanted to get to France to go on Hols that managed to get through before the tightening of rules last night, I hope they weren't bringing Omicron with them.
We'll see what happens in the ski stations this year, probably a lot like last year.

I'm on Hols for the next two weeks, so i'll just be observing from the sidelines.
No Family here this year, and I didn't fancy going to the UK, as I suspected that the poo was about to hit the fan.
Going to be keeping very much to myself, have lots of TV and Films to catch up on

a reply to: MonkeyBalls2

Enjoy your down time MB

Btw, i only just noticed your signature! I've always been a huge Carpenter

a reply to: McGinty

Yeah, Great film
Watched it Thursday.
I think my favorite J.Carpenter film has to be Christine, but i'm a car guy.

Almost watched the X-files film, the first one, which was about an alien virus trying to wipe out the Human race iirc.
Didn't want anything that close to reality

On a Covid note, The Forbes Guy has upped a couple of new articles :

The 3rd part in the Series about Omicron, How Omicron Evades Natural Immunity, Vaccination, And Monoclonal Antibody Treatments (Pt 3)

and

Non-Spike Proteins Contribute To Transmission And Virulence Of Sars-Cov-2

Not read them yet, going to make another cup of tea and prepare to have my brain hurt a bit with the 2nd one lol

..................................BREAKING!!!..................................

House Committee Report Reveals Trump's Efforts To "Undermine" COVID Response

a reply to: TheAMEDDDoc

Hi Doc,
The Forbes Guy's latest article has a bit of a scary section about "Epistasis" which is freaking me out a bit.
It's the Non-Spike Proteins Contribute To Transmission And Virulence Of Sars-Cov-2 a couple of posts above.

The success of a SARS-CoV-2 variant depends on many factors, but there are three elements that are particularly crucial: transmissibility, immune evasion, and virulence. Any mutation that productively impacts one of these three factors is a dangerous one. Any variant with higher transmissibility, a better capacity to evade our natural (innate) immunity, or heightened virulence is one to keep a vigilant eye on.

More often than not, however, this vigilant eye is reserved for what happens within the spike (S) protein of SARS-CoV-2. Understandable, since the S protein plays a major role in allowing the virus to enter and infect our cells, but perhaps slightly misguided.

A new report, led by researchers with the Oak Ridge National Laboratory, prompts us to shift our focus towards the entirety of the viral genome, rather than just the S protein. Applying tools from the field of human genetics, Garvin et al. suggest that mutations outside of SARS-CoV-2’s spike protein may be just as significant as those within. The reason for this? Epistasis.

Many traits are polygenic, meaning a variety of different genes all affect the way that trait is eventually expressed. When multiple genes affect the same trait, they can end up interacting with one another in different ways. Epistasis is a kind of polygenic interaction. At its simplest, it’s when the expression of one gene or genetic mutation is modified by the presence of another.

Bolding is mine.
The definition of Epistasis from a google search is

the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another.

The simple definition is

Epistasis refers to the behavioral effect of interaction among gene alleles at multiple locations. Epistasis is observable when phenotypic differences among individuals with the same genotype at one locus depend on their genotypes at another locus.

Reminds me of "Event Horizon" : "Laymans terms ? Do you speak English ?"

From what i've understood of the text, if we keep targeting, or focusing on, the Spike protein for our vaccines, we're doomed to failure.

Can you please enlighten us, and allay the fears that we might still have a way to get out of this, without going all "Gung Ho" as China has done (and which seems to be working) ?

Is our best option to just lock people up until we stop the spread ?
By the time we come up with any new vaccines, it will have possibly (probably) have moved on.

I'm just worried that our Vaccine scientists may all be barking up the wrong tree en masse, and might miss, or ignore, other methods to fight the Virus.
Officially super-pessimistically freaked out right now.

Cheers.

edit : I'm happy that the ORNL is researching this, and it does alleviate some concern, but the cat would be "Out of the Bag" as it would seem to targeting the Spike Protein only.
Can they target the Non-Spike parts at the same time, in the same vaccine ? Has this been done, or even tried before ?

edit2 : While freaking out, I decided to do a searchs for "How do T-cells attack Covid ?" and "Do T-Cells only attack the Spike protein ?" and got two interesting articles :

This one from John Hopkins medicine (Dated 1§th Nov 2021) entitled Study Shows Immune Cells Against Covid-19 Stay High in Number Six Months After Vaccinatio That goes on about how CD4+ T lymphocytes (aka "Helper T-Cells") help B Cells :

CD4+ T lymphocytes get their nickname of helper T cells because they assist another type of immune system cell, the B lymphocyte (B cell), to respond to surface proteins — antigens — on viruses such as SARS-CoV-2. Activated by the CD4+ T cells, immature B cells become either plasma cells that produce antibodies to mark infected cells for disposal from the body or memory cells that “remember” the antigen’s biochemical structure for a faster response to future infections. Therefore, a CD4+ T cell response can serve as a measure of how well the immune system responds to a vaccine and yields humoral immunity.

but this article from the American Society for Microbiology (July 21st 2021) entitled T Cell Response Not Critical for Immune Memory to SARS-CoV-2 or Recovery from COVID-19 seems to indicate that there are other things at work, that possibly increase our Antibody response to Covid, and that T-Cells might only be part of the immune response :

The researchers found that the monkeys were able to mount a good memory response against the virus regardless of T cell depletion. "We found we got really good memory responses regardless of whether we depleted T cells or not. Basically, we found very strong virus neutralizing antibodies, and they are the most important antibodies in controlling the infection. That was unexpected by most immunologists, virologists and vaccinologists," said Hasenkrug.

"The other thing that happens during a memory response is that antibodies mature, becoming, stronger and more potent at binding the viral pathogen. We saw indications of this through what’s called 'class switching.'" said Hasenkrug. "Class switching" was also unexpected in these monkeys with depleted T cells. "We don’t have a firm explanation as to why that happened, but we think it involves some sort of compensatory response, which you can see in our study. For example, when we depleted CD8+ T cells, we saw stronger CD4+ T cell or B cells responses in some animals. When the animals are missing something, they will try to make up for it by making more of something else."

Hasenkrug doesn’t know why the T cells didn’t turn out to be more important, but it is probably a good thing that they are not required, because then, people who fail to mount sufficient T cell responses still have opportunities to recover.

"This implies that the innate immune response is critical for initial control of the virus, rather than the adaptive immune responses we studied," said Hasenkrug.

Also found these two articles from Science Daily, first one (27th Jan 2021) entitled T cells can mount attacks against many SARS-CoV-2 targets -- even on new virus variant New research gives detailed look at vulnerable sites on the novel coronavirus -- beyond the receptor binding domain

The new study shows that while the immune system often mounts a strong response against a particular site on the virus's "spike" protein called the receptor binding domain, this region is actually not as good at inducing a strong response from CD4+ helper T cells.

Without a strong CD4+ T cell response, however, people may be slow to mount the kind of neutralizing immune response that quickly wipes out the virus. Luckily, the broad immune response comes in handy, and most people have immune cells that can recognize sites other than the receptor binding domain.

Among the many epitopes they uncovered, the researchers identified several additional epitopes on the SARS-CoV-2 spike protein. Grifoni says this is good news. By targeting many vulnerable sites on the spike protein, the immune system would still be able to fight infection, even if some sites on the virus change due to mutations.

"The immune response is broad enough to compensate for that," Grifoni says.

Since the announcement of the fast-spreading UK variant of SARS-CoV-2 (called SARS-CoV-2 VUI 202012/01), the researchers have compared the mutated sites on that virus to the epitopes they found. Sette notes that the mutations described in the UK variant for the spike protein affect only 8% of the epitopes recognized by CD4+ T cells in this study, while 92% of the responses is conserved.

and this second one (16th Nov 2021) entitled Immune cells against COVID-19 stay high in number six months after vaccination, study shows Findings also show that vaccine-elicited fighters recognize and help attack coronavirus delta variant

CD4+ T lymphocytes get their nickname of helper T cells because they assist another type of immune system cell, the B lymphocyte (B cell), to respond to surface proteins -- antigens -- on viruses such as SARS-CoV-2. Activated by the CD4+ T cells, immature B cells become either plasma cells that produce antibodies to mark infected cells for disposal from the body or memory cells that "remember" the antigen's biochemical structure for a faster response to future infections. Therefore, a CD4+ T cell response can serve as a measure of how well the immune system responds to a vaccine and yields humoral immunity.

In their study, Blankson and colleagues found that the number of helper T cells recognizing SARS-CoV-2 spike proteins was extremely low prior to vaccination -- with a median of 2.7 spot-forming units (SFUs, the level of which is a measure of T cell frequency) per million peripheral blood mononuclear cells (PBMCs, identified as any blood cell with a round nucleus, including lymphocytes). Between 7 and 14 days after vaccination, the T cell frequency rose to a median of 237 SFUs per million PBMCs. At six months after vaccination, the level dropped slightly to a median of 122 SFUs per million PBMCs -- a T cell frequency still significantly higher than before vaccination.

The researchers also looked six months after vaccination at the ability of CD4+ T cells to recognize spike proteins atop the SARS-CoV-2 delta variant. They discovered the number of T cells recognizing the delta variant spike protein was not significantly different from that of T cells attuned to the original virus strain's protein.

Although the study was limited because of the small number of participants, Blankson feels it pinpoints areas that merit further research.

"The robust expansion of T cells in response to stimulation with spike proteins is certainly indicated, supporting the need for more study to show booster shots do successfully increase the frequency of SARS-CoV-2-specific T cells circulating in the blood," says Blankson. "The added bonus is finding that this response also is likely strong for the delta variant."

This article from the NIH seems positive Latest on Omicron Variant and COVID-19 Vaccine Protection

In lab studies working with live Omicron virus, the researchers showed that this variant still relies on the ACE2 receptor to infect human lung cells. That’s really good news. It means that the therapeutic tools already developed, including vaccines, should generally remain useful for combatting this new variant.

Once again, these data show that boosting the immune system after a pause produces enhanced immunity against new viral variants, even though the booster was designed from the original virus. Your immune system is awfully clever. You get both quantitative and qualitative benefits.

It’s also worth noting that the Omicron variant mostly doesn’t have mutations in portions of its genome that are the targets of other aspects of vaccine-induced immunity, including T cells. These cells are part of the body’s second line of defense and are generally harder for viruses to escape. While T cells can’t prevent infection, they help protect against more severe illness and death.

One last one from biorxiv.org (9th December 2021) entitled Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals

abstract :

There is a growing concern that ongoing evolution of SARS-CoV-2 could lead to variants of concern (VOC) that are capable of avoiding some or all of the multi-faceted immune response generated by both prior infection or vaccination, with the recently described B.1.1.529 (Omicron) VOC being of particular interest. Peripheral blood mononuclear cell samples from PCR-confirmed, recovered COVID-19 convalescent patients (n=30) infected with SARS-CoV-2 in the United States collected in April and May 2020 who possessed at least one or more of six different HLA haplotypes were selected for examination of their anti-SARS-CoV-2 CD8+ T-cell responses using a multiplexed peptide-MHC tetramer staining approach. This analysis examined if the previously identified viral epitopes targeted by CD8+ T-cells in these individuals (n=52 distinct epitopes) are mutated in the newly described Omicron VOC (n=50 mutations). Within this population, only one low-prevalence epitope from the Spike protein restricted to two HLA alleles and found in 2/30 (7%) individuals contained a single amino acid change associated with the Omicron VOC. These data suggest that virtually all individuals with existing anti-SARS-CoV-2 CD8+ T-cell responses should recognize the Omicron VOC, and that SARS-CoV-2 has not evolved extensive T-cell escape mutations at this time.

Bolding mine.

a reply to: MonkeyBalls2

Great work! I look forward to the Doc's reply when he gets the chance, not that i'll understand too much of it, but will hopefully glean whether Caesar's generally giving us the thumbs up, or down at this point in the journey. That at least seemed a vaguely positive note in the bolding you ended on.


.....Btw, off topic, watched Mouth of Madness myself recently - what a great movie! Was intending to get around to Christine soon, as i haven't seen it since in over 3 decades. My favourite JC works are The Thing and They Live, the latter seeming more prescient with every viewing. His movies age extremely well.

a reply to: McGinty

Yeah, I seemed to get a bit carried away last night, one article feeding another, lol.
May have gone a bit overboard, but there is some interesting info there.

In any case, Omicron might eventually get to be dominant in every country/continent, whereas Delta didn't, nor did Beta.
Beta was more prevalent in South Africa, delta barely made a dent iirc. Same with South America, they had a different prevalent strain to the European and North Americans.

Also, Full on lockdown in the Netherlands. I wasn't expecting that, but we'll at least be able to see if it does anything or not compared to say Belgium, and France...


The Thing was a really good film, but have you seen the original, The Thing from Another World ?
It's actually very, very good, especially since it's from 1951 !

a reply to: MonkeyBalls2

Let's hope that Omicron being milder means Covid doing as some seemed to predict a while back with more transmissible, yet milder strains winning the evolutionary battle. I recall in 2020 people saying that this was the common fate of viruses, but then again 2020 seems like an awful long time ago.

I've only seen the finale of The Thing From Another World as part of a documentary, but will seek it out

Ah for F`cks sake, just got pinged with our "Tousanticovid" app here.
Apparently was in contact with a now positive person on the 13th.
Wasn't planning to go out or see anyone over the next two weeks, but now I have to get tested.
Bugger.

Will let you know how it goes.

The 13th was last monday. I remember I had night sweats for 3 days in a row, monday to wednesday, if i remember correctly.
Didn't think anything of it, as it happens quite often when I eat and drink just before going to bed.
Been pigging out on a big pack of dry roasted peanuts this last week, so thought it was that.
Didn't have any sweats thursday and friday though, or since, even though I have also been pigging out a bit, especially since friday as i'm on hols.

Just went out to see if the local testing places are open, and they are not.
Going to have to get up at crack of dawn, and get tested from 7am tomorrow.
Should have the result by lunchtime, so i can let my colleagues at work know.

All my colleagues have been forewarned, as we all share an office, which is pretty well ventilated, but many of them eat in the office, and are therefore without masks during lunch.

We'll see what tomorrow brings crossed fingers.
I've only had 2 Pfizer jabs, 4 months since 2nd jab.

a reply to: MonkeyBalls2

Good luck - hoping its negative

a reply to: MonkeyBalls2

Well you do know that The distinctive new Omicron symptom that appears during the night

Doctors in South Africa, where the variant was first detected, have said patients are reporting experiencing night sweats.

a reply to: puzzled2

Yeah, found that out on Friday.
I've had them before though, so didn't think anything of it.
It was only when i got pinged today that it came back.
We'll see tomorrow if it was Covid or not.

An article in the New York Times has just been published about the efficacy of the Vaccines.
"Most of the World’s Vaccines Likely Won’t Prevent Infection From Omicron"

I don't think any of them will fully prevent infection, but some might protect from severe illness better than others.