Covid-19 #42 Nu Tsunami Incoming

[Luzifer's right hand]

25 minutes ago, RhaenysBee said:

We seem to be peaking as well. At least in terms of daily new cases. No decrease but no increase either and sewer samples indicate stagnation too. I suppose we’ll see if we start slowing down or there’s another upward jump in store for us in the upcoming weeks. 

A lot depends on how Omicron behaves and Xmas gatherings I guess. 

[Padraig]

5 hours ago, Luzifer's right hand said:

A lot depends on how Omicron behaves and Xmas gatherings I guess. 

Yes.  There is a lot of uncertainty still.   Of the countries with a lot of cases, Austria is improving.  Netherlands is now improving.  Ireland, Germany, Hungary all flat now.  Belgium and Czech are the few country with a lot of cases that are still getting worse.   But there is a danger that there could be another surge given the time of year.

Interestingly, Romania now has one of the lowest case rates in Europe.  That's after it rampaged through there for a few months.  That seems to be COVID's style in places with limited vaccination.  Big waves.  Romania still has a very high death rate.

We are benefiting from boosters, as the older age groups are seeing improved metrics, with it is good too.  Hopefully most people will get the vaccine again.  Booster uptake is misleading if lots of older people opt-out.

In other words, Scientists believe they may have found the "trigger" behind the extremely rare blood clot complications stemming from the J&J/AstraZeneca vaccines.  Nice.

https://www.euronews.com/next/2021/12/02/scientists-may-have-solved-the-mystery-linking-rare-blood-clots-to-astra-zeneca-j-j-covid-

[Deadlines? What Deadlines?]

On 12/1/2021 at 8:11 PM, The Anti-Targ said:

On the other side of the vaccination coin. One of our recent deaths was of a (locally in his region) well known retired journalist / editor in his 80s. He was not only an outspoken anti-vaxxer, but also a general pandemic denier. He got the COVID by being at a gathering attended by infected people, and even while he was getting some significant symptoms he was unrepentant about being anti-vax and made the comment "I have an immune system, you ever heard of that?". A few days later he was in hospital, not long after that he was dead.

I'm glad those types represent a tiny minority there.

Two recent developments from Alberta:

I got an email today from the province indicating that booster shots are beginning to open up. I'll probably be eligible to get one early next year. I'm not in a vulnerable population so I can wait.

Vaccinations have opened up to 5-11 year olds and it looks like some parents aren't messing around with getting their kids jabbed. 40,000 1st doses in six days; representing just over 10% of that age cohort. 

[rotting sea cow]

Things are getting more and more worrisome with Omicron as data start to pour in

This really looks like an immune evading variant. S. Africa is reporting the largest uptick of reinfections from all waves

https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2.full.pdf

we can see in Fig 1. reinfections amounted to a ~1% percent of the reported cases in previous waves and now it's shooting through the roof even as the cases are not yet that high.

Despite the claims of infections being "mild" hospitalizations are increasing. https://twitter.com/jburnmurdoch/status/1466480120215048199/photo/1

Although I haven't found a word regarding of age breakdown, vaccine breakdown or previous infections. It is still possible that's generally "mild" and having lots of hospitalizations due to a very large underreported outbreak. The high positivity rate may indicate that.

Omicron cases are being reported everywhere, in many cases without a travel link so we have cryptic spread around countries that evaded surveillance. Weirdly enough UK is reporting an uptick of S-gene failures (landmark of Alpha, Omicron and few other variants) and despite having the best sequencing capabilities, somehow it wasn't noticed (it can still be something else, ofc).

Scientists are scratching their heads regarding the origin of this variant:

https://www.science.org/content/article/where-did-weird-omicron-come

https://www.npr.org/sections/goatsandsoda/2021/12/01/1055803031/the-mystery-of-where-omicron-came-from-and-why-it-matters

The first retrospective cases were detected in four diplomats who entered Botswana early November. They tested positive before departure and posterior sequencing showed it was Omicron. The government statement does not state the country of origin. Some sources say they were fully vaccinated.

At this point I'm not ruling out anything, even a 12 Monkeys scenario.

 

[williamjm]

50 minutes ago, rotting sea cow said:

Despite the claims of infections being "mild" hospitalizations are increasing. https://twitter.com/jburnmurdoch/status/1466480120215048199/photo/1

Although I haven't found a word regarding of age breakdown, vaccine breakdown or previous infections. It is still possible that's generally "mild" and having lots of hospitalizations due to a very large underreported outbreak. The high positivity rate may indicate that.

One thing I was wondering about was if there are more reinfections whether those infections might tend to be milder if the immunity from the original infection isn't enough to stop the reinfection but still provides some protection against serious illness. So the Omicron wave could appear to have a higher proportion of mild infections despite Omicron not intrinsically being any less severe.

Of course, it's also too early to tell whether really there is any difference in severity of cases in the first place.

[rotting sea cow]

1 hour ago, williamjm said:

One thing I was wondering about was if there are more reinfections whether those infections might tend to be milder if the immunity from the original infection isn't enough to stop the reinfection but still provides some protection against serious illness. So the Omicron wave could appear to have a higher proportion of mild infections despite Omicron not intrinsically being any less severe.

I'd think that it's the case (or better say I'm hoping for this), same with the vaccination. As pointed out, there is more than antibodies in the protection against disease, but from what we have learn from Delta, antibodies are the ones that protect you against infection.

S. Africa seems to have a prevalence of antibodies between 70-90% (I've seen both values) and vaccination rate of 35-50% (I've also seen both values), the later skewed towards older people I'd guess.

My take of the numbers is there has been a lot of missed infections in the previous days and weeks, mostly because people are experiencing few symptoms. So the outbreak is more advanced than numbers suggest. Is because Omicron is intrinsically milder or because previous infection/vaccination is protecting people? Hopefully we will have more clarity soon, BUT if Omicron is not milder, we will have a problem regardless in places with low vaccination/infection rates and with older vulnerable populations.

There is a practical problem because if vaccines do not protect against infection, the whole idea of the vaccination passports can be thrown in the garbage bin. I've been already hearing the 2G+ rule (vaccinated/recovered + negative tested), which will create a whole set of problems too.

[JoannaL]

On 12/2/2021 at 4:11 AM, The Anti-Targ said:

We just crossed 93% actual first dose today. We could well get 95% as a Christmas present.

While I live in a fairly low population region with the population spread over quite a large area (for the size of the population - population density 0.4/km², 0.7/mi² ), just reading our local vaccination stats today there are only 3000 eligible people in my region who have not yet received their first vaccination dose. Percentage-wise we're at 93/84.

 

Is that percantage for adults or over 60 years old? I am a bit confused, because "our world in data" has New Zealand at 71,2 (full vac)/76,3 (first vac).  That is only 3 % more full vaccinated population than here in Germany (68,2) but with these numbers we here  are totally unhappy and now even think to make vaccination mandatory.

[Padraig]

5 hours ago, rotting sea cow said:

This really looks like an immune evading variant. S. Africa is reporting the largest uptick of reinfections from all waves

Interesting. On face value, you'd expect more re-infections because if you got infected in wave one or even the Beta wave, then its 12-18 months later, and your immunity might be falling naturally?

Now Omicron might indeed make it more likely to get re-infected but perhaps South Africa was on the cusp of another wave anyhow, because of that declining immunity?  So its a combination of both?  Just wondering, I could easily be wrong.

Especially since, as mentioned, South Africa had very high prior infection rates.  That was protecting them until now.

[JoannaL]

5 hours ago, rotting sea cow said:

Scientists are scratching their heads regarding the origin of this variant:

https://www.science.org/content/article/where-did-weird-omicron-come

https://www.npr.org/sections/goatsandsoda/2021/12/01/1055803031/the-mystery-of-where-omicron-came-from-and-why-it-matters

Thank you, very interesting! Before I read that article I though omicron was a mutant of beta, which also came from south africa and has some immunescape features. But it is something totally differnt! How strange. It will be interesting to see how this puzzle will be solved.

[Week]

Not feeling super boosted, but hopefully my immune system is! About to boost myself out of my work chair and onto the couch.

Hat-trick for the Pfizer-pfam over here.

[Larry of the Lawn]

9 minutes ago, Week said:

Not feeling super boosted, but hopefully my immune system is! About to boost myself out of my work chair and onto the couch.

Hat-trick for the Pfizer-pfam over here.

Nice.  I'm getting my booster on Monday, had Pfizer the first two times, couldn't get moderns this time, so going with Pfizer again.  JJ is also available.  I didn't do any research on which one I should get but I figure I can ask them?

[Zorral]

Here is a summary by Derek Lowe of what we know currently of Omicron, dated yesterday, 12/02/2021 -- concluding paragraphs:

https://www.science.org/content/blog-post/omicron-time

Quote

 

.... But the greater immune evasion is, of course, still not good news. Again, that does not mean that vaccine protection (or protection via prior infection) is suddenly useless, just that it may have been eroded to some degree that isn't clear yet. Just as before, you really, really need to get vaccinated, and you really, really need to get a booster if you can do that as well. That's a far better option than facing either Delta or Omicron with a naive immune system -  and if the latter really is a bit better at evading the human immune response, it's even more desirable to tune that up as much as possible before you get exposed at all. I get a lot of email from people who are worried about vaccine safety, and although I don't share most of their concerns, I can at least understand them. But the people who refuse to get vaccinated because they apparently think they can fight off the virus better without it, those are the folks that I'm completely baffled by.

What Now?

We gather as much reliable data as we can, as quickly as we can. We carefully monitor the spread of this variant and we try to figure out how many people each new patient has infected. We sequence cases as much as we can to make sure that Omicron isn't drifting into something even more concerning. Once people have recovered from it, we take blood samples from them and characterize what their immune response looks like and compare it to post-Delta cases and others. And (in experiments that are going on right now) we take blood samples from people who've had Delta, others who've had two shots of vaccine, and others who've had those plus a booster and we see how well their antibodies can neutralize Omicron in vitro. Those experiments will give us the earliest read on what we might expect in all these populations if this variant does really take off in the world, and we'll be watching the real-world data to make sure that things follow in the way we expect. We don't know nearly enough today - but we're going to know a lot more very soon.

 

 

[maarsen]

The evolutionary pressure on a virus is to replicate better than other viruses. Killing or incapacitating the host tends to limit the spread while keeping the host active and mobile greatly enhances the rate of replication. I suspect that omicron will spread rapidly but be much like a flu or cold in severity, helping it to replicate quickly and replace nastier strains. If there was a way for the virus to make us all anti maskers,  that would easily make it the dominant strain.

[Mlle. Zabzie]

55 minutes ago, maarsen said:

The evolutionary pressure on a virus is to replicate better than other viruses. Killing or incapacitating the host tends to limit the spread while keeping the host active and mobile greatly enhances the rate of replication. I suspect that omicron will spread rapidly but be much like a flu or cold in severity, helping it to replicate quickly and replace nastier strains. If there was a way for the virus to make us all anti maskers,  that would easily make it the dominant strain.

Feel like parts of the US already had that variant.....

Anyhow, had dinner last night with a group of moms from my son's grade.  It was interesting.  Though everyone was vaccinated, not everyone was boosted, though the non-boosted suggested that they would boost ASAP.  They were much more hesitant about vaccinating their children.  I was the only "early adopter."  There were other people who had reluctantly gotten their kids the first shot already because of a desire/need to travel internationally to see family members (it's a pretty international group), and others who were getting it solely because the school is requiring it.  In the last group, they are more or less waiting until the last minute to meet the school's deadline.  These are 7-8 year olds.  Whatever, I was clear that it was a no-brainer in my view.  And I'm pretty persuasive usually.  But also, it really shows that clear requirements WORK.

[Impmk2]

Latest data from South Africa - omicron wave increasing much faster than either previous beta or delta waves, test positivity >20%. Hospitalizations now increasing in Gauteng (epicenter) on a steeper trajectory than previous waves too. Worryingly admissions of <5 year olds are way up on previous waves. Hopefully that's an early artifact of the numbers and isn't a trend which continues.

Evidence of community transmission now occurring across multiple countries. I'm usually a pretty optimistic person but this all looks extremely grim. Hoping the vaccines hold up better than prior infection. Still early days.

Edit: This thread is probably the most complete current summation.

 

[felice]

4 hours ago, JoannaL said:

Is that percantage for adults or over 60 years old? I am a bit confused, because "our world in data" has New Zealand at 71,2 (full vac)/76,3 (first vac).  That is only 3 % more full vaccinated population than here in Germany (68,2) but with these numbers we here  are totally unhappy and now even think to make vaccination mandatory.

93% is first dose for eligible population (currently people 12 years and over), while it looks like ourworldindata.org is showing percentage of total population. New Zealand started much later than Germany, so the trend is more encouraging even if the raw numbers aren't that different. Also, Germany has a smaller percentage of under 12s, so percentage of eligible population vaccinated would be lower.

[Deadlines? What Deadlines?]

4 hours ago, JoannaL said:

Is that percantage for adults or over 60 years old? I am a bit confused, because "our world in data" has New Zealand at 71,2 (full vac)/76,3 (first vac).  That is only 3 % more full vaccinated population than here in Germany (68,2) but with these numbers we here  are totally unhappy and now even think to make vaccination mandatory.

NZ didn't start jabbing significant numbers until May/June; about 3 months after Germany. They've done a better job of keeping infection rates low through lockdowns, masks, etc. Though Germany hasn't done a bad job of this overall.

3% might not sound like much but it makes a big difference in transmission rates at the top of the scale and therefore reduces the strain on the healthcare system. This is why NZ changed their vaccination target from 85% to 90%. Their modeling (post delta) showed that at 85% they get swamped.

Our World in Data is a good resource but it isn't always completely up to date.

https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-vaccine-data

[felice]

1 hour ago, maarsen said:

The evolutionary pressure on a virus is to replicate better than other viruses. Killing or incapacitating the host tends to limit the spread while keeping the host active and mobile greatly enhances the rate of replication.

Killing or incapacitating quickly limits the spread; it makes no difference to the virus whether the host ceases to spread it due to death or recovery. But yes, a long transmission period with minimal symptoms is probably most easily achieved by being relatively harmless in general.

[Impmk2]

UK technical briefing today showed a marked increase in S-gene target failure (SGTF) in the UK - the PCR marker being used as an early indicator for Omicron (also shows up in Beta, Alpha and Gamma). Now accounts for 0.2% of positive PCR tests in the UK. Some of this is due to Delta which sometimes has (~0.06% recently) SGTF. Largest increases seen in areas with known (sequenced) Omicron.

There's a lag on sequencing so will know for sure in the next day or 2.

(source on the technical breakdown)

 

[The Anti-Targ]

19 hours ago, JoannaL said:

Is that percantage for adults or over 60 years old? I am a bit confused, because "our world in data" has New Zealand at 71,2 (full vac)/76,3 (first vac).  That is only 3 % more full vaccinated population than here in Germany (68,2) but with these numbers we here  are totally unhappy and now even think to make vaccination mandatory.

Our official stats are:

[Edit] I don't know what happened to the official stats that I copy pasted from the health ministry website. Anyway, they are 93 (1st)/86(2nd) for the 12+ population 78/72 for the total population. [/edit]

			Our aim is at least 90% of the eligible population fully vaccinated. Right now we don't have COVID throughout the country, maybe when it is spreading everywhere we'll decide that 90% of the eligible population is not enough because that's not proving to be enough to keep the demand on hospitals and the death rate low enough. Canada right now is approx what our minimum vaccination goal is. Its daily case and death rates adjusted for population may be tolerable. Germany's not so much. Transmission rates have to at least partly be a function of population density. Ours is 18/km2, Germany's is 235/km2 Canada's is 4/km2. So we're closer to Canada, and hopefully our stats at a high vaccination rate will be more like Canada's and less like Europe's. COVID is really going to start spreading in about 2 weeks when Aucklanders can start traveling the country. That won't be such a great Christmas present. Lucky it's summer.