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Tags Coronavirus , vaccination , vaccines

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Old 24th November 2021, 09:32 PM   #401
marting
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Originally Posted by Chris_Halkides View Post
In the spring I used Israel as a real-world example of the effectiveness of the vaccines. Do you have a link handy that discusses the downside (as suggested above)? I found this from the NIH director's blog. Thanks.
Just published:

Elapsed time since BNT162b2 vaccine and risk of SARS-CoV-2 infection: test negative design study
https://www.bmj.com/content/375/bmj-2021-067873
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Old 25th November 2021, 02:32 AM   #402
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Originally Posted by Chris_Halkides View Post
In the spring I used Israel as a real-world example of the effectiveness of the vaccines. Do you have a link handy that discusses the downside (as suggested above)?
The numbers speak for themselves: https://www.worldometers.info/corona...ountry/israel/

Massive post-vaccination wave, dwarfing the previous ones, although deaths were a fair bit lower.

That seems to be a fairly universal result, with Europe going through it right now. Germany's numbers are appalling.
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Old 25th November 2021, 03:00 AM   #403
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Could not come at a better time

https://www.nzherald.co.nz/nz/opinio...3ZDYJAS5LZU6I/
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Old 25th November 2021, 03:06 AM   #404
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Originally Posted by macdoc View Post
I know Leo well and he's in the middle of campaigning to be Auckland's mayor right now, so he has lots of reasons to talk positive. He may well be right, but I'll wait for more evidence before I declare victory.

His scientific experience is that he's a vet, so while he understands a lot of the science, he's no authority.
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Old 25th November 2021, 03:09 AM   #405
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On the subject of ivermectin and other existing drugs as possible Covid treatments, the Together trial is ongoing. They've stopped looking at hydroxychloroquine and ivermectin, among others, as they found no effect at all. Fluvoxamine Maleate showed a positive benefit, others are still being trialled.
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Old 25th November 2021, 08:37 AM   #406
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Originally Posted by macdoc View Post

Originally Posted by The Atheist View Post
I know Leo well and he's in the middle of campaigning to be Auckland's mayor right now, so he has lots of reasons to talk positive. He may well be right, but I'll wait for more evidence before I declare victory.

His scientific experience is that he's a vet, so while he understands a lot of the science, he's no authority.
After reading that, my opinion is that... it would be nice, but I think that there are a number of points made in the article that make me doubt how reliable the opinion expressed is. Still, I will agree with one major premise - the worst part of this pandemic seems to be over, especially with an increasing array of actually effective tools at our disposal to prevent and treat.
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Old 25th November 2021, 09:54 AM   #407
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Originally Posted by angrysoba View Post
Sounds like bollocks to me.

My best guess is that the state of emergency + masking + vaccination campaign which started late but which has reached almost 80% of the whole population (whole population, mind you, not this "eligible population" crap!) has driven down the virus and prevented it spreading.

Why is it sky rocketing elsewhere? Because people are acting like the pandemic is over in much of Europe. Or they were until it came back with a vengeance in the last few weeks.
It is bollocks.

You do get a selective pressure against producing fewer reproducing offspring.

If they said "more benign" that might be conceptually possible. But not to die out.
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Old 25th November 2021, 11:53 AM   #408
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Originally Posted by The Atheist View Post
New variant to watch very closely: https://www.theguardian.com/world/20...r-of-mutations



Very few cases so far - let's hope it stays that way.
It's showing exceptionally rapid spread quickly becoming the dominant strain overtaking Delta.
See this tweet:

https://twitter.com/Tuliodna/status/1463911571176968194
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Old 25th November 2021, 12:05 PM   #409
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Originally Posted by marting View Post
It's showing exceptionally rapid spread quickly becoming the dominant strain overtaking Delta.
See this tweet:

https://twitter.com/Tuliodna/status/1463911571176968194
So they're saying, although I note that officially there are still only 22 cases.

If the Gauteng numbers are right and it's responsible for 90% of infections there, then it might well trouble - there can't be many people in RSA who haven't been vaccinated or infected.

I hope the Krauts are checking what's driving their enormous wave right now.
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Old 25th November 2021, 12:40 PM   #410
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Originally Posted by The Atheist View Post
So they're saying, although I note that officially there are still only 22 cases.
The 22 knowns are samples with full genomic decode. Would be nice to know what proportion of all the cases it was and when each of those 22 samples were taken.

Absolutely huge growth rate but overall Covid-19 incidence is low so might be a statistical anomoly. I'm tending toward it not being an anomoly. But this doesn't look good. Growth rate is not mostly an escape from vaccines or prior infection though that may be a factor. Haven't yet seen history data on priors of vax status of those 22. Would be valuable.
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Old 25th November 2021, 04:57 PM   #411
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Apparently Dr John Campbell is promoting more pseudoscience.

https://www.youtube.com/watch?v=LEBGl8MVE-c

Mark my words, he is going down the quack rabbit hole and promoting anti-vax.

I think his title is an attempt to hide from the You Tube algorithm.
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Old 26th November 2021, 01:10 AM   #412
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UK stops flights from Southern Africa because of new heavily mutated variant.
https://www.bbc.co.uk/news/health-59418127

https://www.nature.com/articles/d41586-021-03552-w
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Old 26th November 2021, 03:03 AM   #413
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Originally Posted by Planigale View Post
UK stops flights from Southern Africa because of new heavily mutated variant.
https://www.bbc.co.uk/news/health-59418127

https://www.nature.com/articles/d41586-021-03552-w
And you're not the only one. The experts are clearly ******** themselves over it. The next few days are going to be very interesting.
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Old 26th November 2021, 06:29 AM   #414
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Originally Posted by Planigale View Post
UK stops flights from Southern Africa because of new heavily mutated variant.
https://www.bbc.co.uk/news/health-59418127

https://www.nature.com/articles/d41586-021-03552-w
Can you measure this risk?
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Old 26th November 2021, 07:23 AM   #415
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Originally Posted by Samson View Post
Can you measure this risk?
Rapid epidemiological analysis of surge in South Africa with sequencing of isolates and look at protective effect of vaccination. But first look is R is currently high.

In vitro work looking at efficacy of neutralising antibodies generated by current vaccines. Porton down is planning on doing some animal work with live virus. Develop probes to pick up this isolate on multiplex PCR. Current PCR can pick up this variant by s drop out, but this may also occur with delta so is non-specific. Increased sequencing across southern Africa.

Start developing vaccines that express the spike protein from this new variant.
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Old 26th November 2021, 09:37 AM   #416
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Originally Posted by marting View Post
Just published:

Elapsed time since BNT162b2 vaccine and risk of SARS-CoV-2 infection: test negative design study
https://www.bmj.com/content/375/bmj-2021-067873
On first pass, no problems.

Looks good for vaccination. When even some 180 days after second dose only 20% get infected and likely by delta, that's better than was hoped. (Not ideal, but booster against delta/ny might correct it)

There's anomaly, where younger population has increased risk of infection, which might be pointing at missing variables (like amount of risky behavior).

Reminder: Main target/endpoint was 50%+ against hospitalization.

As always keep following disclaimer from paper on mind:
Quote:
The study had several limitations. With an
observational study design, the potential for
unmeasured confounding factors exists. In particular,
we included vaccinated individuals who chose to
request an RT-PCR test for SARS-CoV-2 during the study
period. Individuals might have variable thresholds for
requesting a test and might request a test for reasons
unrelated to symptoms of the infection. In most cases,
positive RT-PCR tests were not followed by full serology
testing. Throughout the study period, the prevalence
of covid-19 increased substantially in the study
population.
====

I tried and failed to find any study that would investigate amount of antibodies (A, G and M) after vaccination over time. (Respectively, there are few, but they use indexes or other similar incomparable values and I can't use them to compare it with my own lab results after Covid)

Does anybody know about such study?
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Old 26th November 2021, 11:24 AM   #417
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The new variant is called "Omicron". I would not have been surprised if they'd called it "Omigod!"
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Old 26th November 2021, 12:12 PM   #418
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Originally Posted by alfaniner View Post
The new variant is called "Omicron". I would not have been surprised if they'd called it "Omigod!"
From never before seen to a Variant of Concern (highest level) in just over 2 weeks. Boggling. The Director of CERI (Centre for Epidemic Response & innovation, South Africa) states over 1,000 cases a day of Omicron are occurring there.

Quote:
Because this variant (B.1.1.529) can be detected by a normal qPCR due to deletion at Spike position 69-70 (like Alpha), it will make it easy for the world to track it. We estimate that 90% of the cases in Gauteng (at least 1000 a day are this variant, due to qPCR proxy testing)
https://twitter.com/Tuliodna/status/...011780/photo/1
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Old 26th November 2021, 01:27 PM   #419
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Originally Posted by Planigale View Post
Rapid epidemiological analysis of surge in South Africa with sequencing of isolates and look at protective effect of vaccination. But first look is R is currently high.

In vitro work looking at efficacy of neutralising antibodies generated by current vaccines. Porton down is planning on doing some animal work with live virus. Develop probes to pick up this isolate on multiplex PCR. Current PCR can pick up this variant by s drop out, but this may also occur with delta so is non-specific. Increased sequencing across southern Africa.

Start developing vaccines that express the spike protein from this new variant.
Yes! This strain apparently has >30 mutations in the spike protein gene (though it occurs to me I don't know which strain they are using as the reference sequence - presumably the first SARS-CoV2 genome)
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Old 26th November 2021, 01:30 PM   #420
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Word is that it's also hit Israel and Hong Kong, among other locations. If it's in Hong Kong, it's everywhere. This may be the one that does us in.

I like "end of the world!" stories, but not real ones. I'm not embarrassed to be pessimistic or paranoid about this. I can even imagine unvaxxed mobs doing smash & grabs for vaccines when it gets really bad. (I know... it's already really bad.)
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Old 26th November 2021, 01:33 PM   #421
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For anyone who (like me) was wondering what's going on with the quick adjustability of the vaccines, Reuters reports that Pfizer/Biontech (a) would be able to redesign their vaccine for Omicron within about 6 weeks, and ship initial batches in around 100 days, and (b) do have versions specifically for both Alpha and Delta, undergoing clinical trials, but "Those efforts are not meant to yield commercial products; the exercise is carried out to establish a routine with regulators that will help speed up any future vaccine relaunch."

[I'd been a bit surprised that a new version for Delta wasn't out already, but I suppose the current ones seem to be good enough in that context. I'm also aware that (as I understand it) it's often best to boost with the same antigen, to get a stronger response even if it's not precisely targeted. Obviously doesn't apply if a new variant completely escapes the existing vaccine.]
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Old 26th November 2021, 01:54 PM   #422
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Originally Posted by Meridian View Post
For anyone who (like me) was wondering what's going on with the quick adjustability of the vaccines, Reuters reports that Pfizer/Biontech (a) would be able to redesign their vaccine for Omicron within about 6 weeks, and ship initial batches in around 100 days, and (b) do have versions specifically for both Alpha and Delta, undergoing clinical trials, but "Those efforts are not meant to yield commercial products; the exercise is carried out to establish a routine with regulators that will help speed up any future vaccine relaunch."
Not bad. I mean, designing the mRNA is easy, but I'm impressed they can scale it up that fast.
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Old 26th November 2021, 02:20 PM   #423
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Originally Posted by alfaniner View Post
Word is that it's also hit Israel and Hong Kong, among other locations. If it's in Hong Kong, it's everywhere. This may be the one that does us in.
Hong Kong quarantines arrivals in addition to requiring vaccination certs and negative tests on arrival.

Omicron showed up on day 4 for an arrival from SA. Another traveler, in a room across the hall, tested positive on day 8 apparently catching it from the first. Both were fully Pfizer vaxxed. Both with low CTs (under 20) on the first positive tests.

With luck they have contained it. Problem is that most countries don't quarantine. It's likely out and about most everywhere.

Not looking good.
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Old 26th November 2021, 03:35 PM   #424
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Originally Posted by marting View Post
Hong Kong quarantines arrivals in addition to requiring vaccination certs and negative tests on arrival.

Omicron showed up on day 4 for an arrival from SA. Another traveler, in a room across the hall, tested positive on day 8 apparently catching it from the first. Both were fully Pfizer vaxxed. Both with low CTs (under 20) on the first positive tests.

With luck they have contained it. Problem is that most countries don't quarantine. It's likely out and about most everywhere.

Not looking good.
Surely the response to this is to continue vaccinating, and increase the rate at which people are vaccinated, and get vaccines to as many people around the world as possible.

The rich world cannot just seal up the borders indefinitely while new variants are spawned throughout the unvaccinated world.
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Old 26th November 2021, 05:19 PM   #425
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Originally Posted by marting View Post
With luck they have contained it.
I think you'd need divine intervention rather than luck.
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Old 26th November 2021, 06:10 PM   #426
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Originally Posted by angrysoba View Post
Surely the response to this is to continue vaccinating, and increase the rate at which people are vaccinated, and get vaccines to as many people around the world as possible.

The rich world cannot just seal up the borders indefinitely while new variants are spawned throughout the unvaccinated world.
Right. Sealing up borders is not a long term solution. Vaccination is. The current unknown is the efficacy of vaccines agsinst hospitalization/death for Omicron. Limited evidence at this point is that vaccines don't do much to prevent infection hence spread once it's loose in a country. Current vaccines may or may not be good at controlling more serious consequences. If they don't we have technology that can adapt vaccines to Omicron or anything else. Optimal approach will depend on what the data shows about the above. Depending on what that evidence turns out to be short term lockdowns and/or border controls may be needed. Until that data comes, which is in a few weeks, strict border controls for those that currently impliment them may need to be continued on the precautionary principle. . Once it's loose in a country border controls are counterproductive. The decision is state by state.
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Old 26th November 2021, 06:17 PM   #427
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Originally Posted by The Atheist View Post
I think you'd need divine intervention rather than luck.
Divine intervention is probably needed for those countries that don't quarantine travelers like Hong Kong. Sadly, that's the large majority like USA/UK/Europe and many others. Hong Kong may well get by on luck.

There's speculation R0 is in measles range but without measles lower IFR. If so it's going to be a race with vaccine dev.

This has the makings of a real black swan event.

Meanwhile, 1 in 6 passengers from SA to Amsterdam in 2 flghts today are testing positive for Covid-19. Unreal percentage! Not known what proportion are Omicron but, given SA's realtively low case rate until maybe a week ago, I'd say the fraction is way over 50%.

Holy crap.

https://www.reuters.com/world/europe...am-2021-11-26/
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Old 26th November 2021, 08:31 PM   #428
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Originally Posted by marting View Post
If so it's going to be a race with vaccine dev.
If it escapes vaccines I'm off to the bush for a couple of years.
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Old 26th November 2021, 11:45 PM   #429
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Originally Posted by Klimax View Post
On first pass, no problems.
There's anomaly, where younger population has increased risk of infection, which might be pointing at missing variables (like amount of risky behavior).

That has shown up consistently across studies. Presumably it is due to lifestyle.
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Old 27th November 2021, 09:44 AM   #430
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Originally Posted by marting View Post
Meanwhile, 1 in 6 passengers from SA to Amsterdam in 2 flghts today are testing positive for Covid-19. Unreal percentage! Not known what proportion are Omicron but, given SA's realtively low case rate until maybe a week ago, I'd say the fraction is way over 50%.
Numbers are in and it's not quite as bad. 61 out of 600 passengers tested positive or just over 10%. All were required to have a negative rapid flow test prior to departure.

What's quite odd is that SA has a very low Covid-19 incidence. Order of magnitude lower than most EU countries. Even in the peaks of the epidemic prevalence rarely went over 2% and SA prevalence is supposidly under .1%. What's special about these travelers? Stayed at the same hotel?

Also flights landed in the UK. Passengers were not tested but told to go home and self isolate. Meanwhile 2 people in the UK have tested positive and are linked to SA travel.
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Old 27th November 2021, 09:50 AM   #431
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South African medical association says Omicron variant causes 'mild disease'
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Old 27th November 2021, 10:51 AM   #432
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Originally Posted by Pixel42 View Post
Sounded good until I got to this part:

The official noted that hospitals have not been overburdened by Omicron patients and that the new strain is [sic] not been detected in vaccinated persons.

The passengers from SA were vaccinated and 10% of them tested positive. So I find this extremely unlikely.


Added:
Looks like the prevalence is up. 2.8k cases yesterday and cases tripling every 6 days over the last 2 weeks. Prevalence probably around .5% now adding in all the cases detected in the last 14 days and applying a factor of 4 or so for cases not detected. Still a large distance from the plane passengers.

Another update:
The same person was quoted differently in a Telegraph piece:

https://www.telegraph.co.uk/global-h...says-symptoms/
She said, in total, about two dozen of her patients have tested positive for Covid-19 with symptoms of the new variant. They were mostly healthy men who turned up “feeling so tired”. About half of them were unvaccinated

Also symptoms quite different. No loss of smell for instance. If, in fact, this turns out to be mild that would be great. But it's a bit early to know.

Also, turns out that the UK keeps records of PCR test details and there was a uptick in S gene dropout (Omicron trait) in the last week. Small numbers and statistically noisy.
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Old 27th November 2021, 11:57 AM   #433
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It looks to me like fairly premature comment. Covid in all the forms to date has been mostly mild in younger people, so it's no surprise - although probably good news - that omicron is acting the same way.
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Old 27th November 2021, 12:07 PM   #434
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Originally Posted by The Atheist View Post
It looks to me like fairly premature comment. Covid in all the forms to date has been mostly mild in younger people, so it's no surprise - although probably good news - that omicron is acting the same way.
Yeah. My guess is the good doctor, who also chairs the SA Med. Assoc., is under pressure to mitigate the economic consequences of countries closing borders with SA.

Probably won't know for a few weeks. Would be nice if it wasn't as serious. Seems unlikely but possible. There would be a transmission advantage if it produced more asymptomatic disease or was asymptomatic for longer after infection.
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Old 27th November 2021, 12:57 PM   #435
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Originally Posted by marting View Post
Yeah. My guess is the good doctor, who also chairs the SA Med. Assoc., is under pressure to mitigate the economic consequences of countries closing borders with SA.
That was my first thought, immediately after Ramaphosa had had a cry about countries cutting them off.

Also, I'm completely pissed off at blaming the west for holding up vaccines. South Africa is 100% the architect of its own position regarding vaccines, and blaming the west is a sly political ploy. Note the date of this piece:

https://theconversation.com/south-af...one-now-163784

Originally Posted by marting View Post
Probably won't know for a few weeks. Would be nice if it wasn't as serious. Seems unlikely but possible. There would be a transmission advantage if it produced more asymptomatic disease or was asymptomatic for longer after infection.
Interesting point, and probably impossible to gauge the answer with vaccine sin play, but it looks to me as though none of the variants are actually more deadly, they just transmit more readily.

And yes, the next 3-4 weeks will be interesting, because it's clear, with cases seeded across the world, that it's well and truly out of the bag.
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Old 27th November 2021, 01:02 PM   #436
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Am I the only person who noticed WHO skipped straight past "xi" in the Greek alphabet?

I can understand them skipping "nu" due to potential confusion, but I don't see a problem with Xi.
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Old 27th November 2021, 01:24 PM   #437
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Originally Posted by The Atheist View Post
Am I the only person who noticed WHO skipped straight past "xi" in the Greek alphabet?

I can understand them skipping "nu" due to potential confusion, but I don't see a problem with Xi.
The problem is Xi Jinping
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Old 27th November 2021, 01:47 PM   #438
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Originally Posted by The Atheist View Post
Am I the only person who noticed WHO skipped straight past "xi" in the Greek alphabet?

I can understand them skipping "nu" due to potential confusion, but I don't see a problem with Xi.
Lol. I rather like Omicron. I shorten it to just OhMy!
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Old 27th November 2021, 03:25 PM   #439
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Originally Posted by The Atheist View Post
Am I the only person who noticed WHO skipped straight past "xi" in the Greek alphabet?
No, there's lots of comments on Twitter about it.
Quote:
I can understand them skipping "nu" due to potential confusion, but I don't see a problem with Xi.
As already pointed out, it's almost certainly to avoid any confusion/embarrassment with Xi Jinping.
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Old 27th November 2021, 04:31 PM   #440
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Originally Posted by Dr.Sid View Post
The problem is Xi Jinping
Sorry mate, I thought it was so obvious I was being sarcastic that I didn't think anyone would respond.

I actually mentioned it a month or so back when I was looking at the upcoming letters of the Greek alphabet.

It might already be in Australia: https://www.stuff.co.nz/world/austra...-test-positive
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