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Tags Coronavirus , vaccination , vaccines

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Old 12th December 2021, 11:51 PM   #681
dann
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Originally Posted by Dr.Sid View Post
Closely watching Norway, Denmark and other countries which flashed in the news with omicron.

Danish report in English: Status of the SARS-CoV-2 variant Omicron in Denmark (Dec 12, 2021)

Too early to say anything about hospitalizations and deaths.
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Last edited by dann; 12th December 2021 at 11:54 PM.
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Old 13th December 2021, 01:07 AM   #682
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Originally Posted by Puppycow View Post
Someone needs to tell Snopes and the WHO:

https://www.snopes.com/fact-check/omicron-deaths/
They are just like one forum I read. Everybody needs an opinion before enough facts are known.
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Old 13th December 2021, 07:21 AM   #683
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Originally Posted by Puppycow View Post
Someone needs to tell Snopes and the WHO:

https://www.snopes.com/fact-check/omicron-deaths/
Okey dokey.

https://www.bbc.co.uk/news/uk-59639007
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Old 13th December 2021, 07:26 AM   #684
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Originally Posted by Puppycow View Post
Someone needs to tell Snopes and the WHO:

https://www.snopes.com/fact-check/omicron-deaths/
That may have been true December 10th but it's now 13th.
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Old 13th December 2021, 07:31 AM   #685
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Originally Posted by The Atheist View Post
I'll see if Capsid can answer that, but my understanding is the vaccine creates production of antibodies that specifically attack the spike protein. When the spike changes, it doesn't work as well, and manufacturers are about to produce new vaccines to attack the new spikes.

And that process could well be never-ending.
Most vaccines are designed around a limited protein sequence. To overcome this, some vaccines are multivalent eg the HPV vaccine made by Merck is 9 valent. Fortunately, the immune response is amazing at producing a large antibody repertoire through somatic hypermutation that reacts with the limited protein sequence to varying degrees. This broad response can cross-react with different protein sequences as seen for the SARS-COV-2 variants of concern and why the focus is determining the reduction in antibody binding and neutralisation activity to a new variant. We could move to a flu scenario where there are distinct serotypes and the difference in antibody binding between flu strains is sufficient to warrant new vaccines eah year.
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Old 13th December 2021, 10:08 AM   #686
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Originally Posted by Capsid View Post
Most vaccines are designed around a limited protein sequence. To overcome this, some vaccines are multivalent eg the HPV vaccine made by Merck is 9 valent. Fortunately, the immune response is amazing at producing a large antibody repertoire through somatic hypermutation that reacts with the limited protein sequence to varying degrees. This broad response can cross-react with different protein sequences as seen for the SARS-COV-2 variants of concern and why the focus is determining the reduction in antibody binding and neutralisation activity to a new variant. We could move to a flu scenario where there are distinct serotypes and the difference in antibody binding between flu strains is sufficient to warrant new vaccines eah year.
Thanks yet again for the expert analysis!
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Old 13th December 2021, 10:52 AM   #687
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Originally Posted by dann View Post
Today 1,840 Omicron cases, so 560 new cases in 24 hours, 44% more: https://nyheder.tv2.dk/samfund/2021-...urealistisk-ud

Today:
966 nye tilfælde af omikron herhjemme siden i går: Varianten kan blive den dominerende coronavariant i denne uge (DR.dk, Dec 13, 2021 - 16:55)
966 new cases of Omicron in Denmark since yesterday: Omicron may become the dominant coronavirus variant this week
A total of 3.437 confirmed cases so far.
See graph of new cases per day in the article.

ETA: Another country that does extensive gene-sequencing analysis:
Omikron bliver dominerende i London inden for 48 timer (DR.dk, Dec 13, 2021 - 18:03)
Omicron will become dominant in London within the next 48 hours
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Old 13th December 2021, 03:07 PM   #688
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Originally Posted by marting View Post
Outstanding Omicron info in this UK technical briefing in such a short time. Best in class.

Nothing yet on severity. None hospitalized yet but some info on relative Ve. for mild infection and vacine types, boosters, and time since vax.

https://assets.publishing.service.go...riefing_31.pdf

Boosters bring Omicron Ve up from 35% with 2 doses to 70-75% Pfizer booster.

Severe disease Ve unknown but likely quite good for vaxxed with or without boosters.
Yes the UK (especially England) got its act together finally as far as publicly-available data is concerned

All the Variant of concern briefings here:

https://www.gov.uk/government/public...ical-briefings
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Old 13th December 2021, 03:21 PM   #689
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Some confusion today, Sajid Javid appeared to say that there were 200,000 new cases of omicron a day in the UK. A clarification was put out to say he meant there were an estimated 200,000 omicron cases in total in the UK.
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Old 13th December 2021, 04:24 PM   #690
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Hey guys, a fairly critical piece of data is what prior infection from Omicron produces. This will greatly affect the situation in Feb. 2022 and beyond. It may be more or less than the differential between Delta and Omicron and the amount will have a big effect going forward from there.

I expect Omicron to do a deep dive into the unvaccinated and a chunk of the vaccinated. With any luck we will, between vax immunity and prior infection immunity, see a good decline in cases from Jan->March. But it will depend a lot on the relative immunity of the different variants recovered from and the vaxxed.

Please post anything new along these lines. Early info may come out of SA.
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Old 13th December 2021, 04:32 PM   #691
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When delta became the dominant strain, it was clear that it was displacing previous strains. Is that necessarily the case with omicron; that is, is it possible that it could become the "dominant" strain, but rather than displace delta cases, add to them? If omicron can evade delta-induced immunity, then could not delta simultaneously evade omicron-induced immunity, such that we end up with a high prevalence of each strain?
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Old 13th December 2021, 04:50 PM   #692
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Originally Posted by marting View Post
I expect Omicron to do a deep dive into the unvaccinated and a chunk of the vaccinated. With any luck we will, between vax immunity and prior infection immunity, see a good decline in cases from Jan->March. But it will depend a lot on the relative immunity of the different variants recovered from and the vaxxed.
Good point, but as omicron has shown - and P1 in Manaus - prior infection isn't necessarily much use.

Plus, what the next variant is will be more important, and on that happy thought, I give you PNG.

We all need to shift to .jpg immediately.

Originally Posted by jt512 View Post
When delta became the dominant strain, it was clear that it was displacing previous strains. Is that necessarily the case with omicron; that is, is it possible that it could become the "dominant" strain, but rather than displace delta cases, add to them? If omicron can evade delta-induced immunity, then could not delta simultaneously evade omicron-induced immunity, such that we end up with a high prevalence of each strain?
When it's faster to infect, as omicron is, you'd expect it to displace the other strains, partly because most people who are sick will stay home, plus, everywhere outside of Europe and USA, delta is in decline and will be fairly easy to displace.

The omicron/delta war in America and Europe will be interesting, though.
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Old 13th December 2021, 10:19 PM   #693
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Originally Posted by Darat View Post
That may have been true December 10th but it's now 13th.
Yes, and I see that they have changed their ruling from true to false. But it's still very much lower than you would expect by this point in time.

I agree though that it's better to err on the side of caution until we know for certain.
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Old 13th December 2021, 10:49 PM   #694
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I found this BBC article informative.

Omicron: Why do boosters work if two doses struggle?
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Old 14th December 2021, 12:37 AM   #695
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Originally Posted by dann View Post
Danish report in English: Status of the SARS-CoV-2 variant Omicron in Denmark (Dec 12, 2021)

Omikron tager over (SSI, Dec 13, 2021)
Omicron is taking over

With a graph of:
Nuværende og estimeret vækst i Region Hovedstaden
Current and estimated growth of Omicron in the Copenhagen region - since Nov 29 with an estimate for the rest of this week.
Really scary!
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"Stupidity renders itself invisible by assuming very large proportions. Completely unreasonable claims are irrefutable. Ni-en-leh pointed out that a philosopher might get into trouble by claiming that two times two makes five, but he does not risk much by claiming that two times two makes shoe polish." B. Brecht
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Old 14th December 2021, 01:45 AM   #696
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Certainly one explanation for increased omicron transmission is if it has shifted a little in its primary site of infection from the lungs to the upper airways. This would potentially result in increased viral shedding and potentially less severe disease (less pneumonia).

This is just a hypothesis, there is limited evidence for this, but there is some evidence that omicron has more upper airways symptoms than alpha or delta.
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Old 14th December 2021, 08:25 AM   #697
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Originally Posted by Puppycow View Post
Yes, and I see that they have changed their ruling from true to false. But it's still very much lower than you would expect by this point in time.

I agree though that it's better to err on the side of caution until we know for certain.
Death vs cases is starting to get some usable amount of data, and it looks good !

https://ourworldindata.org/explorers...e&country=~ZAF
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Old 14th December 2021, 10:42 AM   #698
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cocktails versus adjuvants

The subject of designing antiviral compounds or mixtures of compounds is one that have have touched upon previously with respect to the effect that a possible inhibitor of nsp14 would have on molnupiravir or related compounds that interfere with polymerization of RNA. I thought a word or two more could be said. With respect to antibacterial compounds, the authors of a 2016 review stated, "By themselves, adjuvant compounds have little or no antimicrobial activity, but in combination with antibiotics they can overcome resistance, improve antibiotic efficacy or extend spectrum of activity (Figure 4a). The most effective antibiotic adjuvants identified thus far are inhibitors of beta-lactamases. The first such compound to find clinical use was clavulanic acid, now with over 30 years of clinical implementation in combination with amoxicillin (Augmentin) or ticarcillin (Timentin) [38]." In this example, the drug and the adjuvant are closely related: the inhibitor of beta-lactamase prevents the hydrolysis of the antibacterial compound.

The meaning of the term "drug cocktail" is different, although possibly it encompasses adjuvants such as clavulanic acid. An example from treatments for HIV might clarify this, namely the combination of a protease inhibitor and an inhibitor of reverse transcriptase. The two compounds inhibit enzymes that are not that closely related (this point might be arguable, the more I think about it). I am sure that there is some grey area in the terminology, but what I suggested regarding nsp14 inhibition was modeled after the adjuvant strategy.
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At In the Pipeline Derek Lowe wrote, "That leaves me pinning more hopes on Pfizer's protease inhibitor - and it also leaves me wondering why there hasn't been a trial started with these two drugs in combination. A lower dose of molnupiravir has the potential to add to the efficacy of the Pfizer drug and perhaps to extend its utility in the face of possible resistance. But it's not happening, and it should." I would be inclined to call the proposed mixture a cocktail, but I don't see a connection between the two targets; therefore, I don't see one compound as an adjuvant in the sense of how the word was used in my opening paragraph (a new term to replace adjuvant would be helpful). I admit that how close a metabolic connection is is difficult to quantify.
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Old 14th December 2021, 12:14 PM   #699
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Originally Posted by Dr.Sid View Post
Death vs cases is starting to get some usable amount of data, and it looks good !

https://ourworldindata.org/explorers...e&country=~ZAF
Indeed. The head of the South African Medical Association Dr. Coetzee has come straight out and said bluntly its been 4 weeks, we know what's going on, there is no reason that you cannot trust us when we say it gives a mild disease.

https://twitter.com/lbc/status/1469998211863621636
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Old 14th December 2021, 01:44 PM   #700
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Cambridge needle-free 'universal' coronavirus vaccine goes to trial.
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Old 14th December 2021, 01:48 PM   #701
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Still deaths are not the real issue with Covid, however sad they are. Full hospitals are the issue. And hospitalization admissions DO react on the omicron wave. Too soon to tell how it would compare with previous waves.
Also the speed of omicron alone is a problem, even if sick people will stay at home, it's likely paralyze public services.
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Old 14th December 2021, 02:32 PM   #702
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Originally Posted by Dr.Sid View Post
Still deaths are not the real issue with Covid, however sad they are. Full hospitals are the issue. And hospitalization admissions DO react on the omicron wave. Too soon to tell how it would compare with previous waves.
Also the speed of omicron alone is a problem, even if sick people will stay at home, it's likely paralyze public services.
And it will lead to more excess deaths, even if they are not directly due to omicron itself.
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Old 14th December 2021, 03:22 PM   #703
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Originally Posted by Chris_Halkides View Post
The subject of designing antiviral compounds or mixtures of compounds is one that have have touched upon previously with respect to the effect that a possible inhibitor of nsp14 would have on molnupiravir or related compounds that interfere with polymerization of RNA. I thought a word or two more could be said. With respect to antibacterial compounds, the authors of a 2016 review stated, "By themselves, adjuvant compounds have little or no antimicrobial activity, but in combination with antibiotics they can overcome resistance, improve antibiotic efficacy or extend spectrum of activity (Figure 4a). The most effective antibiotic adjuvants identified thus far are inhibitors of beta-lactamases. The first such compound to find clinical use was clavulanic acid, now with over 30 years of clinical implementation in combination with amoxicillin (Augmentin) or ticarcillin (Timentin) [38]." In this example, the drug and the adjuvant are closely related: the inhibitor of beta-lactamase prevents the hydrolysis of the antibacterial compound.

The meaning of the term "drug cocktail" is different, although possibly it encompasses adjuvants such as clavulanic acid. An example from treatments for HIV might clarify this, namely the combination of a protease inhibitor and an inhibitor of reverse transcriptase. The two compounds inhibit enzymes that are not that closely related (this point might be arguable, the more I think about it). I am sure that there is some grey area in the terminology, but what I suggested regarding nsp14 inhibition was modeled after the adjuvant strategy.
EDT
At In the Pipeline Derek Lowe wrote, "That leaves me pinning more hopes on Pfizer's protease inhibitor - and it also leaves me wondering why there hasn't been a trial started with these two drugs in combination. A lower dose of molnupiravir has the potential to add to the efficacy of the Pfizer drug and perhaps to extend its utility in the face of possible resistance. But it's not happening, and it should." I would be inclined to call the proposed mixture a cocktail, but I don't see a connection between the two targets; therefore, I don't see one compound as an adjuvant in the sense of how the word was used in my opening paragraph (a new term to replace adjuvant would be helpful). I admit that how close a metabolic connection is is difficult to quantify.
To expand on this you can have combinations of antibiotics that are synergistic, a good example is co-trimoxazole. This is a combination of sulphamethoxazole and trimethoprim. Both are effective antibiotics alone, but they both act at different sites in the bacterial synthesis of folic acid, so the combination has a magnified effect as compared with the effects of each agent separately.

Then there are combinations used to prevent resistance arising. The treatment of TB is a good example. If a single effective antibiotic is used, it is very likely that one of the tens of millions of bacteria causing an infection will develop a resistant mutation and the resistant mutations will then persist. If a mutation arises in one in a million bacteria, and you give two effective antibiotics then the chance of one bacteria getting two resistance mutations at the same time becomes very low. In fact one starts treatment for TB with four drugs, the combination is not more effective than any drug given alone, but the chance of resistance arising to all four is very small.

Modern anti-HIV treatment was primarily developed as a combination to prevent resistance arising, but combinations were also chosen that were synergistic. This may allow lower doses of drugs reducing side effects but maintaining efficacy. The problem with using two weak anti-virals in combination is, even if together they are strong, if resistance arises to one component then the combination becomes ineffective, and having two weak agents potentially doubles the risk of resistance.

A different combination is imipenem / cilastin. Imipenem is the antibiotic which is normally rapidly destroyed in the body, and cilastin is an enzyme inhibitor that stops the body destroying the antibiotic so it lasts long enough to work. This contrasts with the amoxicillin / clavulinic acid combination you mentioned where the bacteria produce beta lactamase to destroy penicillin type antibiotics and clavulinic acid stops the bacteria destroying the antibiotic before it can be effective. When penicillin was first invented one problem was that most penicillin was passed out in urine, so penicillin needed to be given very frequently and the urine was collected so the penicillin could be extracted from the urine and reused. Then probenecid was given with penicillin which blocked renal excretion of penicillin, so less penicillin needed to be given.
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Old 14th December 2021, 03:55 PM   #704
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Omicron's major trait, the substantially increased ability to infect both the vaccinated and previously recovered, will make the disease appear milder even if it is exactly as virulent to naive (unvaccinated and not previously recovered). This also is a major reason Omicron's growth is so darned fast.

But this is because vaccines and prior infection still provide high protection against serious disease. For Omicron, two doses of Pfizer is only 35% effective at preventing symptomatic infection, with booster 70%, and AZ even less effective. Previously Ve was 70% for 2 doses and 95% for 2 + booster.

This can be seen in the USA where 70 to 80% of new Delta cases are unvaccinated even though a good majority of the population is vaccinated. Fortunately, Ve against severe disease remains high against Omicron.

Omicron will shift that because breakthroughs are more likely. I expect most new cases of Omicron to be among the vaccinated and previously recovered. And they will suffer much milder disease than the smaller percentage that are unvaccinated.

The net effect is that even if Omicron is actually as virulent for naive patients, it will appear much less virulent because it will include a higher proportion of vaccinated and recovered.

The question extant is: Will Omicron prove to be even less virulent after factoring in these effects? Could well be and if so then that's great news to the large groups that remain unvaccinated.

Because it's coming for them.
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Old 14th December 2021, 04:37 PM   #705
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Originally Posted by marting View Post
The question extant is: Will Omicron prove to be even less virulent after factoring in these effects? Could well be and if so then that's great news to the large groups that remain unvaccinated.
Given the speed of growth, we'd better bloody well hope so.

The early signs are certainly encouraging, but I'll let you know when it gets established in a largely Covid-naive population. There are a couple of those countries about, so we won't have to wait long. I'll go check who the hell they are.
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Old 14th December 2021, 05:49 PM   #706
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Originally Posted by Elaedith View Post
Excellent!
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Old 15th December 2021, 02:33 AM   #707
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Originally Posted by The Atheist View Post
Given the speed of growth, we'd better bloody well hope so.

The early signs are certainly encouraging, but I'll let you know when it gets established in a largely Covid-naive population. There are a couple of those countries about, so we won't have to wait long. I'll go check who the hell they are.
South Africa is hardly Covid-naive, but at 26% fully vaccinated its a pretty good indicator of lower vaccination rates, and they are saying its not severe.

Agreed of course that the huge infection rate is going to put severe pressure on health services simply due to big numbers.

Good news from SA is that they are saying those who do go to hospital are discharged quicker, very different to Delta, so we can hope that faster turnaround will work against the bigger numbers.
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Old 15th December 2021, 02:38 AM   #708
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Originally Posted by GraculusTheGreenBird View Post
South Africa is hardly Covid-naive,...
Obviously, since it's already been established that they have a sero-positivity rate over 70%, which is why I specifically stated:

Quote:
I'll let you know when it gets established in a largely Covid-naive population
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Old 15th December 2021, 05:00 AM   #709
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Simpson's Paradox:

Quote:
Everybody is very optimistic about Omicron.
I HOPE they're right.
I FEAR they're prey to a statistical error, Simpson's Paradox
(...)
Simpson's Paradox says that you can see a trend because you're mixing two populations, but when you separate the populations, the trend is the opposite.
Simpson's Paradox (Wikipedia)
Thomas Pueyo on Twitter (Dec 14, 2021)
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Old 15th December 2021, 07:36 AM   #710
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Originally Posted by The Atheist View Post
Obviously, since it's already been established that they have a sero-positivity rate over 70%, which is why I specifically stated:
Sorry, I read Covid-naive = vaccination naive for some reason.
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Old 15th December 2021, 09:04 AM   #711
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Dann, given how fast it spreads, it would have to be FAR less severe than Delta



https://www.gov.uk/government/public...daily-overview December 14th version

51% in London

ETA: and it looks to me that Delta is still keeping steady in London

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Old 15th December 2021, 09:55 AM   #712
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Data to 12th December



ETA and London

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Every year since 1990 the US Public healthcare spending has been greater than the UK as a proportion of GDP. More US Tax goes to healthcare than the UK

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Old 15th December 2021, 10:20 AM   #713
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78,610 cases reported in the UK today, up 50% on last Wednesday, highest daily total recorded, by far, since the start of the pandemic.
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Old 15th December 2021, 11:51 AM   #714
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Originally Posted by jimbob View Post
Dann, given how fast it spreads, it would have to be FAR less severe than Delta
Yeah, we've been working on the basis that we're looking at delta x 2 in cases, when it looks more like a factor of 5 or more. Good on UK for keeping stats - the numbers from SA are all over the place.

Here's some news that suggests USA is going to follow the same trajectory in very short order: https://edition.cnn.com/2021/12/14/u...ses/index.html

Note a number of the kids had received the booster as well.
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Old 15th December 2021, 11:56 AM   #715
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Re: USA, here's a new piece suggesting it's well on the way to an explosion of omicron: https://www.usatoday.com/story/news/...ts/8898798002/

Quote:
Omicron has been moving “faster even than the most pessimistic among us thought that it was going to move," said Dr. Jacob Lemieux, an infectious disease expert at Massachusetts General Hospital.

While previous variants popped up in one country and then another, and "you could watch it unfold from place to place to place," Lemieux said, omicron "seems to be happening every place at once."
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Old 15th December 2021, 12:01 PM   #716
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Originally Posted by Planigale View Post
Certainly one explanation for increased omicron transmission is if it has shifted a little in its primary site of infection from the lungs to the upper airways. This would potentially result in increased viral shedding and potentially less severe disease (less pneumonia).

This is just a hypothesis, there is limited evidence for this, but there is some evidence that omicron has more upper airways symptoms than alpha or delta.
Of all the hypotheses so far this seems the most congruent with facts on the ground. If it pans out that's good news indeed.
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Old 15th December 2021, 02:05 PM   #717
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Originally Posted by Planigale View Post
Certainly one explanation for increased omicron transmission is if it has shifted a little in its primary site of infection from the lungs to the upper airways. This would potentially result in increased viral shedding and potentially less severe disease (less pneumonia).

This is just a hypothesis, there is limited evidence for this, but there is some evidence that omicron has more upper airways symptoms than alpha or delta.

Here's a reference to a study hopefully soon to come out:
https://www.med.hku.hk/en/news/press...ov-2-infection

The researchers found that Omicron SARS-CoV-2 infects and multiplies 70 times faster than the Delta variant and original SARS-CoV-2 in human bronchus, which may explain why Omicron may transmit faster between humans than previous variants. Their study also showed that the Omicron infection in the lung is significantly lower than the original SARS-CoV-2, which may be an indicator of lower disease severity.
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Old 15th December 2021, 02:25 PM   #718
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Originally Posted by marting View Post
Here's a reference to a study hopefully soon to come out:
https://www.med.hku.hk/en/news/press...ov-2-infection
Excellent stuff!

And man, do we need some good news on omicron. The world is going to set a new high for daily new cases in the next 7-8 days, and I'd say will break the million a day the week after.

It needs to be 90% lower in severity to make up for the massive spread.
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Old 15th December 2021, 02:28 PM   #719
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So far it seems stocking for 2 months still looks like good idea. But at least you don't need to buy coffins.
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Old 15th December 2021, 04:33 PM   #720
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Originally Posted by Elaedith View Post
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Developed by Professor Jonathan Heeney at the University of Cambridge and spin-out company DIOSynVax, this is a next generation coronavirus vaccine administered through a needle-free ‘injection’ – a blast of air that delivers it into the skin. This offers a possible future alternative to people who fear needle-based jabs.
That's not a new technology. I received shots like that back in the 1990s when I was in the Navy. In my experience it hurts more than a needle hurts.
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