Covid 44: The Sickening

[Fragile Bird]

I haven’t looked at stats this weekend but last week officials in Ontario were saying 50% of those who needed hospitalization were unvaccinated, and we have a very high rate of vaccination.

[Padraig]

5 hours ago, rotting sea cow said:

At the same time, Denmark outbreak is as old as UK's and they aren't seen any strain and they did have low levels of infections and the fraction of boosted population is not much higher than US.  I was reading some days ago they had around 50 persons in ICU with Delta and 5 with Omicron (they know) and epidemiologists do not consider Omicron worse than the flu but they are reluctant to easy the comparatively light restrictions. So uh?

I thought Denmark had the highest level of boosters in Europe?  

I'm actually a little less positive.  Europe hasn't been overrun (yet) but most metrics are negative at the moment (with a few weird exceptions).  Rising hospitalisations.  Rising fatalities.  Terrible case numbers.  Hospitalisations may not be as bad as last winter (although Canada/US are) but they are still going in the wrong direction.

Omicron is also moving into Central/Eastern Europe now, which could cause more havox.

There are some signs that cases in Denmark, UK, Malta have peaked at least.  Lets hope so.

[rotting sea cow]

1 hour ago, Padraig said:

I thought Denmark had the highest level of boosters in Europe?  

I misremembered this plot. It's UK that has a similar booster rate, not US. In fact, the US has a very low rate compared to other countries

 

 

1 hour ago, Padraig said:

I'm actually a little less positive.  Europe hasn't been overrun (yet) but most metrics are negative at the moment (with a few weird exceptions).  Rising hospitalisations.  Rising fatalities.  Terrible case numbers.  Hospitalisations may not be as bad as last winter (although Canada/US are) but they are still going in the wrong direction.

I'm not optimistic at all, but neither too pessimistic.  I think that there is too much recklessness in the face of an unknown and while Omicron dominates the numbers, many countries had significant Delta waves with the respective backlog of hospitalizations.

 

[Zorral]

"In much of the West, the walls are closing in on anti-vaxxers"  -- France, Italy, Germany, Belgium, Austria, Australia, Canada are mentioned in the piece.

https://www.washingtonpost.com/world/2022/01/10/european-unvaccinated-anti-mandate/

Not, of course, in the USA YAY!

[Padraig]

4 hours ago, rotting sea cow said:

I misremembered this plot. It's UK that has a similar booster rate, not US. In fact, the US has a very low rate compared to other countries

Right.  The US rate.  All those vaccines sitting on shelves.

4 hours ago, rotting sea cow said:

I'm not optimistic at all, but neither too pessimistic.  I think that there is too much recklessness in the face of an unknown and while Omicron dominates the numbers, many countries had significant Delta waves with the respective backlog of hospitalizations.

And all that sounds right.  I wouldn't be pessimistic either.  I suppose I was just a little hopeful that Omicron may not increase fatality rates too much.  And while we probably wouldn't get anywhere close to previous peaks, rates have definitely risen.  Although, as you say, Delta is probably behind a decent portion of that.

Moderna is talking about Autumn/Fall for its Omicron booster.  I suppose its lucky it isn't talking about earlier boosters!

Quote

 

Moderna is working on a booster shot that will target the omicron variant of Covid for this fall as nations around the world prepare to distribute annual vaccinations against the virus.

“We are discussing with public health leaders around the world to decide what we think is the best strategy for the potential booster for the fall of 2022. We believe it will contain omicron,” CEO Stephane Bancel told CNBC’s “Squawk Box” on Monday.

Bancel said the omicron-specific booster will enter clinical trials soon, and Moderna is discussing whether the shot needs to contain any other components to fight the virus.

“We need to be careful to try to stay ahead of a virus and not behind the virus,” he said.

 

https://www.cnbc.com/2022/01/10/covid-vaccine-moderna-ceo-says-fall-booster-shots-will-likely-target-omicron.html

And progress on another antiviral.  From Novartis this time.

https://www.europeanpharmaceuticalreview.com/news/167336/ensovibep-shows-promise-as-an-antiviral-for-covid-19/

I'll be curious to see about how the Merck/Pfizer drugs are working in practice.  Certainly been deliveries by now.

[rotting sea cow]

1 hour ago, Padraig said:

Moderna is talking about Autumn/Fall for its Omicron booster.  I suppose its lucky it isn't talking about earlier boosters!

I'm not that hopeful regarding variant specific boosters. Two potential problems

1.- Serotype replacement is occurring faster than vaccine deployment. Vaccines were designed around the ancestral strain. Since then few variants have come and go. In the Europe/US Alpha, Delta and Omicron have driven waves of infections. In other places you had Beta, Gamma, Lambda, Mu and few others. Fortunately until Omicron, there was more immune erosion rather than immune escape. But you see the problem. If Omicron follows that pattern, around mid year there should be another variant popping up that it's not necessarily a descendant of Omicron.

2. Immune imprinting (related to the Original Antigenic Sin). A variant specific vaccine would boost the immunity against conserved regions of the antigen instead of the mutated parts. As those parts in Omicron are also the most antigenic regions (like the RBD), the booster would not do necessarily better in comparison to what we have.  I believe that Moderna already ran into this problem with its Beta specific booster that didn't perform better than the original recipe. Of course, with Omicron being heavily mutated, it's possible that the immune system will able to "see" those mutated regions. I suppose that clinical studies will be out soon and tell us whether this is a real problem or not.

 

[The Anti-Targ]

45 minutes ago, rotting sea cow said:

I'm not that hopeful regarding variant specific boosters. Two potential problems

1.- Serotype replacement is occurring faster than vaccine deployment. Vaccines were designed around the ancestral strain. Since then few variants have come and go. In the Europe/US Alpha, Delta and Omicron have driven waves of infections. In other places you had Beta, Gamma, Lambda, Mu and few others. Fortunately until Omicron, there was more immune erosion rather than immune escape. But you see the problem. If Omicron follows that pattern, around mid year there should be another variant popping up that it's not necessarily a descendant of Omicron.

2. Immune imprinting (related to the Original Antigenic Sin). A variant specific vaccine would boost the immunity against conserved regions of the antigen instead of the mutated parts. As those parts in Omicron are also the most antigenic regions (like the RBD), the booster would not do necessarily better in comparison to what we have.  I believe that Moderna already ran into this problem with its Beta specific booster that didn't perform better than the original recipe. Of course, with Omicron being heavily mutated, it's possible that the immune system will able to "see" those mutated regions. I suppose that clinical studies will be out soon and tell us whether this is a real problem or not.

 

If Omicron becomes the ubiquitous strain globally one would expect the next strain to be a descendant of omicron, and so an omicron vaccine should be reasonably effective. Unless there is a variant brewing in another animal species that will jump back to humans and is as distinct from all existing strains as Omicron is from Delta.

I think it would be wise for a vaccine to be multi-variant, if they can do with with mRNA vaccines.

[Impmk2]

24 minutes ago, rotting sea cow said:

2. Immune imprinting (related to the Original Antigenic Sin). A variant specific vaccine would boost the immunity against conserved regions of the antigen instead of the mutated parts. As those parts in Omicron are also the most antigenic regions (like the RBD), the booster would not do necessarily better in comparison to what we have.  I believe that Moderna already ran into this problem with its Beta specific booster that didn't perform better than the original recipe. Of course, with Omicron being heavily mutated, it's possible that the immune system will able to "see" those mutated regions. I suppose that clinical studies will be out soon and tell us whether this is a real problem or not.

 

 

I think the problem is probably overstated for covid: See this recent data on immunity to a common cold coronavirus (229E) over time

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009453

Serum collected from people is always pretty good at neutralising the virus from around the years it was collected - as well as extremely good neutralisation of the virus they've encountered over their lifetimes - though dropping off pretty rapidly for future 229E. Ie they haven't had a problem 'updating' the new antibodies and they've been significantly backboosted for what they've already encountered, but the virus has continued to mutate to evade immunity.

Yes you may get a lower response to the new antigens, but that isn't no response, and that response can be boosted over time with repeat exposure. My first thought is this whole thing is probably a masking effect as weakly binding antibodies from prior infection block b-cell binding and proliferation (and so the development of new antibodies) - and that seems to be the dominant theory in the literature. It follows that the more antigenically distinct a new variant is (and omicron is pretty distinct) the less of a problem this will be.

However there are also ways around this if it turns out to be a big problem - you could (for example) conjugate the RBD and other epitopes to a different protein scaffold so this problem wouldn't occur.

[Padraig]

1 hour ago, The Anti-Targ said:

I think it would be wise for a vaccine to be multi-variant, if they can do with with mRNA vaccines.

This has definitely been done.  Moderna or Pfizer produced a combined original/Beta vaccine IIRC.  Something like that anyhow.  But as Rotting Sea Cow alluded to, it didn't get great results.

Omicron is so different, it may increase the need for this multivalent approach.  But I imagine it will take longer to approve.

They are similarly looking at a combined flu/COVID mRNA vaccine.  But it is a few years away.  First a flu mRNA vaccine.

[LongRider]

Fascinating article about Covin being spread by aerosol airborne transmissions, and why it has taken so long to understand this.  

Quote

Given the history of airborne spread that public health officials know well, it seems as though the notion of airborne spread has been characterized negatively because it had already been discarded. As we emerged from the era of folk science, “society neglected and forgot aerial health practices when germ theory promised better disease control,” writes Dr. Melanie Kiechle, a historian at Virginia Tech. 

The literature is right about contact with germs, but thanks to the urgency of this pandemic we have come to understand that germs themselves can travel readily through the air in ways we thought they generally didn’t. This is a really big deal.

This new aerosol understanding should be a true paradigm shift.

 

 

Why admitting Covid is Airborne is so hard. (substack.com)

[rotting sea cow]

11 hours ago, The Anti-Targ said:

If Omicron becomes the ubiquitous strain globally one would expect the next strain to be a descendant of omicron, and so an omicron vaccine should be reasonably effective. Unless there is a variant brewing in another animal species that will jump back to humans and is as distinct from all existing strains as Omicron is from Delta.

 

11 hours ago, Impmk2 said:

I think the problem is probably overstated for covid: See this recent data on immunity to a common cold coronavirus (229E) over time

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009453

Serum collected from people is always pretty good at neutralising the virus from around the years it was collected - as well as extremely good neutralisation of the virus they've encountered over their lifetimes - though dropping off pretty rapidly for future 229E. Ie they haven't had a problem 'updating' the new antibodies and they've been significantly backboosted for what they've already encountered, but the virus has continued to mutate to evade immunity.

I've seen that. But what they describe is the effect of antigenic drift which is not what we are observing with SARS-CoV-2

We all thought we would be battling Delta and its descendants forever. Instead we got Omicron which come from another direction, maybe even from a second spillover after reverse zoonosis (or from a second lab leak?). With SARS-CoV-2 being such a promiscuous virus, it is not warranted that next variants will come from Omicron. It can perfectly come from that deer variant. Now, Omicron definitively has such competitive advantage, that is really hard to imagine something that could replace it, so maybe?

11 hours ago, Impmk2 said:

However there are also ways around this if it turns out to be a big problem - you could (for example) conjugate the RBD and other epitopes to a different protein scaffold so this problem wouldn't occur.

 

One of the BionTech candidates was around that idea and one of the Cuban vaccines has the RBD attached to the tetanus toxoid. Of course there are advantages and disadvantages. If the virus mutates too much, you have basically zero protection. I read somewhere that another possibility is make a vaccine of conserved regions of the spike, but I guess you don't get such potent neutralizing antibodies.

Overall, I think that after 2020 groundbreaking development, there was little interest in looking for new ways to make vaccines, despite that the threat of variants started to become more obvious.

 

 

 

 

[rotting sea cow]

9 hours ago, LongRider said:

Fascinating article about Covin being spread by aerosol airborne transmissions, and why it has taken so long to understand this.  

Don't let me started with this. Probably the second greatest mistake during the pandemic. Many warned about this very early on and it was considered a scientific fact in mid 2020. Instead, we have been disinfecting every surface with dangerous chemicals and washing our hands into oblivion. Good quality masks and air filtration should have been a priority, at least in developed countries that can afford that.

 

[Heartofice]

46 minutes ago, rotting sea cow said:

Don't let me started with this. Probably the second greatest mistake during the pandemic. Many warned about this very early on and it was considered a scientific fact in mid 2020. Instead, we have been disinfecting every surface with dangerous chemicals and washing our hands into oblivion. Good quality masks and air filtration should have been a priority, at least in developed countries that can afford that.

 

We are still doing it. So many people I know have become obsessed with hand sanitiser, even now, wiping down all of the shopping after you've bought it, washing hands after touching anything. It doesn't matter that the science has changed, because its become an obsession.

[A wilding]

Agreed that we got transmission wrong initially. However it is still important to wash your hands regularly, especially after touching items touched by many other people. And not to touch you own face before doing so.

[butterbumps!]

I'm struggling to see the value in shutting down schools in certain contexts, and want to know if I'm overlooking something.

Basically, in an early education/ Pre K program, where all of the staff and anyone entering the building must be fully vaxxed, does it make sense to shut down class whenever someone tests positive?  The kids at the school are 1-5, and anyone over 5 needs to be vaccinated in order to attend.  However, all of the positive cases at the school have been asymptomatic and at worst, like a very mild cold (as in, a runny nose), for both kids and staff.  These positives are only being detected because of a mandatory testing policy, otherwise no one would have known.  Are kids in the 1-5 age range (and the fully vaccinated, boosted staff) truly in that much danger if they contract it to the point where it's worth shutting down?  

I guess it's a little frustrating because it feels at this point like we're totally shutting things down over what seems to be affecting these cohorts like a mild cold at worst or not at all (at least in this very local context of very young kids + fully boosted adults).  It's a bit of a disaster to lose an outlet like school for toddlers in the dead of winter when the weather isn't as conducive to running around outside all day to compensate for the lack of programming.  It's starting to feel like a bureaucratic and logistical hassle more than a genuine health concern in this one particular context.  So is this kind of shut down necessary?

[The Anti-Targ]

I mean, washing any fruit or vegetable that you will eat without cooking or peeling and that is sitting out in the open in the shop has probably always been a pretty good idea. Washing hands regularly (at least before putting your hands on food you are about to eat, or putting our fingers in your mouth or up your nose) is also not a bad idea. But there are people who are OCD about it, and I think COVID has exacerbated the OCD germophobe. Most people I know have pretty much gone back to BAU with hand and surface hygiene.

1 hour ago, rotting sea cow said:

 

I've seen that. But what they describe is the effect of antigenic drift which is not what we are observing with SARS-CoV-2

We all thought we would be battling Delta and its descendants forever. Instead we got Omicron which come from another direction, maybe even from a second spillover after reverse zoonosis (or from a second lab leak?). With SARS-CoV-2 being such a promiscuous virus, it is not warranted that next variants will come from Omicron. It can perfectly come from that deer variant. Now, Omicron definitively has such competitive advantage, that is really hard to imagine something that could replace it, so maybe?

As I said in my post you quoted, unless it comes from another animal intermediary like Omicron probably has. I have my doubts a [wild] deer variant will pass back to people, there is just not enough contact. Mice are everywhere people are, so there's more proximate contact. Aerial spread helps with explaining the jump, since most people don't typically let mice breather or sneeze in close proximity.

10 hours ago, LongRider said:

Fascinating article about Covin being spread by aerosol airborne transmissions, and why it has taken so long to understand this.  

 

Why admitting Covid is Airborne is so hard. (substack.com)

This denial or reluctance to admit airborne spread doesn't track with me. Perhaps it's because learning about animal diseases, some of the severe ones that countries put a lot of effort keeping out (like Foot and Mouth disease) are well known to spread aerially over quite long distances. FMD can spread up to 10km (6-ish miles?) on the wind, with at least one instance of 60km (~38mi) spread. Bird flu has also spread between poultry farms separated by up to 13km (8-ish miles?). So it's kind of surprising to hear that there is reluctance to acknowledge / disbelief in aerial spread of viruses. We're pretty fortunate COVID-19 doesn't spread on the wind like that, even just 1 or 2km would have made life exceedingly difficult. OTOH, it probably would have prevented political division about what to do, because there's really not much to do if you could catch COVID simply by walking out your front door 2 minutes after someone 500m up wind from you sneezed. There's only one way to control these sorts of diseases in animals, and that's depopulation, which is not an option for people...right?...RIGHT?

[Deadlines? What Deadlines?]

The positivity rate here is now at 38%. ICU and non-ICU hospital are definitely trending up, though not as quickly as they did in the previous wave. Maybe Omicron is less likely to have a severe outcome; possibly as a consequence of the vaccination rate, which is about 15 percentage points higher than it was at the beginning of our last wave. It may just be early and we'll get swamped next week. We'll see.  

I reported that just before the new year my niece had a contact who tested positive. She learned this the same day she had to miss her booster because she came down with flu-like symptoms. She is double vaccinated and never goes out without a mask; even outdoors. She got herself tested and sure enough,  she had Covid-19. She's fine now. She was under the weather for a few days but has largely recovered.

However, she is reporting an interesting after effect. She can't eat meat. It's like her sense of taste has been effected but in the opposite way that has been commonly reported. 

Most of the time, she finds chicken agreeable enough; but red meat is completely out of the question. She says the flavor is super gamey and not pleasant at all. Who knows how long this will last.

She may need to buy herself a vegan cook book. 

[Fragile Bird]

The headline in Toronto’s Globe and Mail this morning: How Australia turned Djokivic into the world’s richest working-class hero.

[DireWolfSpirit]

2 hours ago, The Anti-Targ said:

There's only one way to control these sorts of diseases in animals, and that's depopulation, which is not an option for people...right?...RIGHT?

Well off the table for depopulating blue states. Red states are still on the table if they don't stop acting up.

[DireWolfSpirit]

2 hours ago, butterbumps! said:

I'm struggling to see the value in shutting down schools in certain contexts, and want to know if I'm overlooking something.

Basically, in an early education/ Pre K program, where all of the staff and anyone entering the building must be fully vaxxed, does it make sense to shut down class whenever someone tests positive?  The kids at the school are 1-5, and anyone over 5 needs to be vaccinated in order to attend.  However, all of the positive cases at the school have been asymptomatic and at worst, like a very mild cold (as in, a runny nose), for both kids and staff.  These positives are only being detected because of a mandatory testing policy, otherwise no one would have known.  Are kids in the 1-5 age range (and the fully vaccinated, boosted staff) truly in that much danger if they contract it to the point where it's worth shutting down?  

I guess it's a little frustrating because it feels at this point like we're totally shutting things down over what seems to be affecting these cohorts like a mild cold at worst or not at all (at least in this very local context of very young kids + fully boosted adults).  It's a bit of a disaster to lose an outlet like school for toddlers in the dead of winter when the weather isn't as conducive to running around outside all day to compensate for the lack of programming.  It's starting to feel like a bureaucratic and logistical hassle more than a genuine health concern in this one particular context.  So is this kind of shut down necessary?

The kiddies being asymptomatic isn't the issue, they can still bring it home and spread to it to the more vulnerable population.