SARS CoV-2 coronavirus / Covid-19 (No tin foil hat silliness please)

ha_rooney

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Big jump in cases in the UK today (+16,000), and deaths doubled from last Wednesday.

Things seem to be accelerating over the last couple of days it seems.
Ffs… do they breakdown the data to show where the numbers are increasing? I’d be hopeful if the older/double vaccinated groups aren’t seeing a large increase & the jump is in younger/unvaccinated groups.
 

groovyalbert

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Ffs… do they breakdown the data to show where the numbers are increasing? I’d be hopeful if the older/double vaccinated groups aren’t seeing a large increase & the jump is in younger/unvaccinated groups.
It looks like it's being driven regionally - Scotland rising, whilst England's hospital admissions appear down. Either way, it's hardly promising.
 

lynchie

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Ffs… do they breakdown the data to show where the numbers are increasing? I’d be hopeful if the older/double vaccinated groups aren’t seeing a large increase & the jump is in younger/unvaccinated groups.

Big rises in young males over the last week.

Hmmm... I wonder what a lot of young men are getting together for at the moment.

Anyway, at least with Scotland being knocked out, that might bring their numbers back down again.
 

Mb194dc

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Need to see the excess deaths numbers to see if anything to be bothered about. The latest ones I can see from the beginning of June for England are negative, e.g less people died than you would normally expect in total.

That really isn't the problem though. The problem is that because there are infections you're going to get recombination / mutation of new clades / variants which will ultimately defeat the present vaccines. The big problem, is that even if you fully vaccinate 100% of the population, you will still get a lot of infections as they are seeing in the US. Even if they're asymptomatic or very mild.

Without sterilising vaccines, you're going to get seasonal evolution of new variants indefinitely. There is likely very little we can do about that, other than live with it and create seasonal vaccines adjusted to whatever nature is evolving at us.
 

Pogue Mahone

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Need to see the excess deaths numbers to see if anything to be bothered about. The latest ones I can see from the beginning of June for England are negative, e.g less people died than you would normally expect in total.

That really isn't the problem though. The problem is that because there are infections you're going to get recombination / mutation of new clades / variants which will ultimately defeat the present vaccines. The big problem, is that even if you fully vaccinate 100% of the population, you will still get a lot of infections as they are seeing in the US. Even if they're asymptomatic or very mild.

Without sterilising vaccines, you're going to get seasonal evolution of new variants indefinitely. There is likely very little we can do about that, other than live with it and create seasonal vaccines adjusted to whatever nature is evolving at us.
Excess deaths are only useful in retrospect. They’re useless when it comes to predicting the future, which is what’s most important now. Hospitals can end up in deep deep shit long before we’ll get any useful insights from excess deaths data.

Agree with the rest of your post. Although I’m optimistic that vaccines will be a great help against all future variants, especially when it comes to taking the pressure off hospitals.
 

Mb194dc

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Excess deaths are only useful in retrospect. They’re useless when it comes to predicting the future, which is what’s most important now. Hospitals can end up in deep deep shit long before we’ll get any useful insights from excess deaths data.

Agree with the rest of your post. Although I’m optimistic that vaccines will be a great help against all future variants, especially when it comes to taking the pressure off hospitals.
Are we really worried about hospitals being overwhelmed in the middle of summer with the vulnerable groups vaccinated as best they can be? That's ridiculous surely? If anyone is really concerned about that, what about this winter?

Lots of cases, quite a lot which must be asymptomatic in younger age groups should be of little concern in mid summer other than from an evolutionary perspective.
 

Pogue Mahone

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Are we really worried about hospitals being overwhelmed in the middle of summer with the vulnerable groups vaccinated as best they can be? That's ridiculous surely? If anyone is really concerned about that, what about this winter?

Lots of cases, quite a lot which must be asymptomatic in younger age groups should be of little concern in mid summer other than from an evolutionary perspective.
Yes we are worried and no it’s not ridiculous. Based on this variant being definitely more transmissible, probably causing more serious illness and probably vaccine resistant the experts that model these things are predicting hospitals getting at least as busy as they were during spring if this current surge really gets going. Warm weather won’t be enough to stop it in its tracks in the same way that didn’t help in India.

Winter’s a whole new ball game but, on the plus side, there will be many millions more people fully vaccinated then there are right now.
 

jojojo

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Are we really worried about hospitals being overwhelmed in the middle of summer with the vulnerable groups vaccinated as best they can be? That's ridiculous surely? If anyone is really concerned about that, what about this winter?

Lots of cases, quite a lot which must be asymptomatic in younger age groups should be of little concern in mid summer other than from an evolutionary perspective.
The trouble is that we don't know how many cases will turn into hospitalisations and that ratio is massively dependant on vaccination status. In the last wave cases to hospitalisation ran at something like 8% (hospitalisation 10 to 12 days behind test). Currently the rate looks like it's around 4% and falling. In fact (like the rate of growth in cases) there's some early evidence that over the last month as vaccinations increased that hospitalisation rate may now be heading towards 3%. Time in hospital seems to be falling as well, reflecting the fact that the hospitalised are mostly younger and recover faster.

For 10,000 cases per day that's currently best guess 300 hospital admissions (and a lot more A&E visits) and roughly 2000 in hospital. For 40,000 cases (expected in July) 1200/8000 and that's worse than the winter hospitalisation peak we see in a bad flu year and it's back where we were in March this yea. That means A&E is a covid triage zone and the hospitals are stopping non urgent surgery and outpatient visits. Not overwhelmed in the "no oxygen in the tanks" sense, just an unsustainable burden on the system. The only obvious way for us to stop that happening (without another round of restrictions) is with vaccinations - which will hopefully be simultaneously reducing the case growth and the rate of hospitalisation amongst the cases.

So no, it's not of little concern. It should be of enough concern that it encourages people to get vaccinated.
 

Dan_F

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Ffs… do they breakdown the data to show where the numbers are increasing? I’d be hopeful if the older/double vaccinated groups aren’t seeing a large increase & the jump is in younger/unvaccinated groups.
I was watching local news for Bristol/Bath yesterday and I’m pretty sure it said about 60% of new cases in this area were 20-29 year olds. Im not sure what the time frame was, maybe for last week.
 

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Ffs… do they breakdown the data to show where the numbers are increasing? I’d be hopeful if the older/double vaccinated groups aren’t seeing a large increase & the jump is in younger/unvaccinated groups.
The dominant age group is in the 20-29 age range, then the 10-19 age range, and then 30-39. It tallies well with those that have only had vaccinations opened up to them.

https://assets.publishing.service.g...994577/Weekly_Flu_and_COVID-19_report_w24.pdf
 

berbatrick

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That’s a very impressive review in a short space of time on not much sleep! Thanks.
He has a twitter thread up which seems to explain why the number of sequences analysed are different, it does have to do with stringency.
He was more stringent with one criteria (reconstructing the full sequence), they with the other (getting a lot of depth for the available sequence, they chose 10, he chose 3X coverage).
So they ended up with 50 sequences and he with 13.


I do not do nanopore sequencing, which was used for this, but I'm vaguely familiar with it. Compared to typical modern sequencing, it sequences longer and continuous fragments at the expense of sequencing depth. I don't know if one set of criteria is better than the other for nanopore. For my sequencing we are generally happier with better depth.

And I still feel too stupid to figure out what it means when you get opposite conclusions by using different cutoffs for your data quality.
 

Pogue Mahone

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The trouble is that we don't know how many cases will turn into hospitalisations and that ratio is massively dependant on vaccination status. In the last wave cases to hospitalisation ran at something like 8% (hospitalisation 10 to 12 days behind test). Currently the rate looks like it's around 4% and falling. In fact (like the rate of growth in cases) there's some early evidence that over the last month as vaccinations increased that hospitalisation rate may now be heading towards 3%. Time in hospital seems to be falling as well, reflecting the fact that the hospitalised are mostly younger and recover faster.

For 10,000 cases per day that's currently best guess 300 hospital admissions (and a lot more A&E visits) and roughly 2000 in hospital. For 40,000 cases (expected in July) 1200/8000 and that's worse than the winter hospitalisation peak we see in a bad flu year and it's back where we were in March this yea. That means A&E is a covid triage zone and the hospitals are stopping non urgent surgery and outpatient visits. Not overwhelmed in the "no oxygen in the tanks" sense, just an unsustainable burden on the system. The only obvious way for us to stop that happening (without another round of restrictions) is with vaccinations - which will hopefully be simultaneously reducing the case growth and the rate of hospitalisation amongst the cases.

So no, it's not of little concern. It should be of enough concern that it encourages people to get vaccinated.
Plus in a “normal” year the summer is a chance to work through elective waiting lists while the seasonal illness burden is relatively low. And those lists are longer than ever, after the shit show of the last 18 months. This was supposed to be a summer where the health services could get back on an even keel and right now that is looking very much in the balance (to put it mildly!).
 

Brwned

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A Covid cases gender gap has opened up as the total number testing positive in the past 24 hours hit nearly 3,000. On Wednesday five new deaths were reported, and 2,969 cases recorded - the highest daily number since the start of mass testing. In recent days about two thirds of cases in the 15 to 44 age range have been male.

Behaviour expert Prof Stephen Reicher has suggested that men meeting up to watch Euro 2020 is behind the rise. National Clinical Director Prof Jason Leitch said he believed indoor socialising was the main factor, though not necessarily linked to football. Public health expert Prof Linda Bauld said it was too early to link the spike in male cases to one particular activity - but she said the trend was "striking" and should be investigated further.
https://www.bbc.co.uk/news/uk-scotland-57580118

You can understand why some people dismiss experts when this is how they're presented in fairness
 

Pogue Mahone

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Brwned

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Not sure what you mean by last sentence? With a surge of cases in young men the idea that watching the Euros together might be a factor isn’t the craziest hypothesis, surely?
I don’t think we need a “behaviour expert” to draw that conclusion! Of course it’s what we’re all thinking. There is no concrete evidence of it, but it’s the common sense assessment.

So they have an expert saying what most people are thinking, but in the interest of appearing balanced, they bring in another expert that says it might be that, but it also could be this, and then another expert that says it’s too early to say anything, but it is something to keep an eye on. If you assign equal weight to all experts there then you come out knowing less than what you came in with!

That amalgamated view of expertise is such a caricature of what actual expert analysis is that when people roll their eyes at experts, really they’re rolling their eyes at that caricature. I don’t agree with a lot of criticisms of mainstream media but that’s among their biggest failings!
 

Pogue Mahone

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I don’t think we need a “behaviour expert” to draw that conclusion! Of course it’s what we’re all thinking. There is no concrete evidence of it, but it’s the common sense assessment.

So they have an expert saying what most people are thinking, but in the interest of appearing balanced, they bring in another expert that says it might be that, but it also could be this, and then another expert that says it’s too early to say anything, but it is something to keep an eye on. If you assign equal weight to all experts there then you come out knowing less than what you came in with!

That amalgamated view of expertise is such a caricature of what actual expert analysis is that when people roll their eyes at experts, really they’re rolling their eyes at that caricature. I don’t agree with a lot of criticisms of mainstream media but that’s among their biggest failings!
Ah. Ok. Sure. I still prefer that sort of attempt at balance than the fringe media’s preference for trumpeting the most hysterical, click-generating single opinion possible.
 

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I don’t think we need a “behaviour expert” to draw that conclusion! Of course it’s what we’re all thinking. There is no concrete evidence of it, but it’s the common sense assessment.

So they have an expert saying what most people are thinking, but in the interest of appearing balanced, they bring in another expert that says it might be that, but it also could be this, and then another expert that says it’s too early to say anything, but it is something to keep an eye on. If you assign equal weight to all experts there then you come out knowing less than what you came in with!

That amalgamated view of expertise is such a caricature of what actual expert analysis is that when people roll their eyes at experts, really they’re rolling their eyes at that caricature. I don’t agree with a lot of criticisms of mainstream media but that’s among their biggest failings!
Reminds me of the way the BBC treated the MMR debate for years, they gave equal air time to the anti-vax loons in the interests of balance, ignoring the weight of argument of just about every scientific and health institution in the world.
 

Brwned

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Ah. Ok. Sure. I still prefer that sort of attempt at balance than the fringe media’s preference for trumpeting the most hysterical, click-generating single opinion possible.
Oh yeah me too. I just don’t think it’s too idealistic to expect something beyond those two choices!

Reminds me of the way the BBC treated the MMR debate for years, they gave equal air time to the anti-vax loons in the interests of balance, ignoring the weight of argument of just about every scientific and health institution in the world.
Yeah exactly! I understand the intention but it has obvious dangers to it. The gradual breakdown in expert trust at least partly lies there.
 

Balljy

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Silverstone is going to be allowed to have the full 140,000 people for the Silverstone GP on July 18th. That feels like a weird decision to me with the current rise in cases and the Delta variant. I guess they're hoping vaccinations will be at such a high level by then it won't matter. There is a quote in the article which suggests there are conditions for entry which might mean fully vaccinated only.

It will be an interesting test at the very least with that number of people in one location.

British Grand Prix: Silverstone at full capacity crowd for next month's race - BBC Sport
 

Pogue Mahone

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He has a twitter thread up which seems to explain why the number of sequences analysed are different, it does have to do with stringency.
He was more stringent with one criteria (reconstructing the full sequence), they with the other (getting a lot of depth for the available sequence, they chose 10, he chose 3X coverage).
So they ended up with 50 sequences and he with 13.


I do not do nanopore sequencing, which was used for this, but I'm vaguely familiar with it. Compared to typical modern sequencing, it sequences longer and continuous fragments at the expense of sequencing depth. I don't know if one set of criteria is better than the other for nanopore. For my sequencing we are generally happier with better depth.

And I still feel too stupid to figure out what it means when you get opposite conclusions by using different cutoffs for your data quality.
Here’s the first explanation I’ve found that’s dumbed down enough for my feeble brain to understand.

 

berbatrick

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Here’s the first explanation I’ve found that’s dumbed down enough for my feeble brain to understand.

ya i think as an explanation of what the paper says, this thread is good.
the implications are just very vague for me:

maybe the deleted ones change the relative frequencies of lineage a or b?

if the original study authors are uncooperative, i think NCBI should release the email request for deletion they were sent, at the very least.
 
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stw2022

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Last time cases were this high I think was around early December and deaths were around 600 a day

There is going to be an ‘acceptable’ number of dead each day.
 

Stack

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Last time cases were this high I think was around early December and deaths were around 600 a day

There is going to be an ‘acceptable’ number of dead each day.
That is exactly the type of thinking that resulted in the carnage of the last year or so.
 

jojojo

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https://www.bbc.co.uk/news/uk-scotland-57580118

You can understand why some people dismiss experts when this is how they're presented in fairness


The trouble is that science and scientists in general are like that. Probabilities, statistics, likelihoods over certainty. They're experts because they know the limits of their knowledge as well as their capability.

It's one of the things that the extremes score well on - they "know" they're 100% right, however weak their evidence base, and what's more they know that morality, emotion and/or common sense is on their side. Science gets stuck with a lot of trends, percentages and hypotheses instead.
 

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This could be major plot twist on SARS-CoV-2 origin story. I wish I knew enough about genetics to understand it better :(

@berbatrick?
As I understand it, there is no data that supports zoonotic origin, and what we see doesn't follow what we expect to see on those cases. It's a long story though, there is a group called Project Evidence that has done incredible work, the news recently that supports lab release in the media has come from their work.

https://project-evidence.github.io

Found out about them here :

"Exclusive: How Amateur Sleuths Broke the Wuhan Lab Story and Embarrassed the Media"

https://www.newsweek.com/exclusive-...oke-wuhan-lab-story-embarrassed-media-1596958
 
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stw2022

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That is exactly the type of thinking that resulted in the carnage of the last year or so.
Not really. Zero covid is probably not achievable and restrictions cannot go on forever.

We already have an acceptable number of deaths for all types of infectious diseases and viruses and other types of environmentally influenced/caused deaths

Of course COVID ISN’T the flu but due to vaccines if we eventually get to a point where the number of deaths each year is within a comparable range then that’s when the acceptable level of deaths will be achieved.
 

bsCallout

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Are Robert Malone, Bret Weinstein & Steve Kirsch credible in any way? They all seem like anti-vaxxers and clever blokes.
 

Mickeza

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The case to hospitalisation rate is about 3% now (13% in winter wave which still blows my mind tbh) and falling as more get vaccinated - length of stay is also reduced due to it primarily being younger patients/at least partially vaccinated - so I think we’re looking as good as could be expected considering what a twat this new variant is and schools breaking up in a few weeks. Other parts of the world won’t be so lucky though unfortunately due to far lower vaccination rates.
 

Pogue Mahone

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The case to hospitalisation rate is about 3% now (13% in winter wave which still blows my mind tbh) and falling as more get vaccinated - length of stay is also reduced due to it primarily being younger patients/at least partially vaccinated - so I think we’re looking as good as could be expected considering what a twat this new variant is and schools breaking up in a few weeks. Other parts of the world won’t be so lucky though unfortunately due to far lower vaccination rates.
Yeah, I’m really worried about Africa. Something like 1% vaccinated. There’s a lot of AZ knocking around in countries who aren’t sure what to do with it. Time to shit or get off the pot.
 

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Yeah, I’m really worried about Africa. Something like 1% vaccinated. There’s a lot of AZ knocking around in countries who aren’t sure what to do with it. Time to shit or get off the pot.
We will phase out AZ use within 6 months yet can make 1 million doses a week. You would hope that we would move to help vaccinate the pacific region. But with #scottyfrommarketing and Peter Dutton in the mix I doubt it somehow.
 

Pogue Mahone

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https://www.thejournal.ie/taoiseach-virgin-media-interview-5476881-Jun2021/

What are your thoughts @Pogue Mahone ? Scaremongering or real threat? Cases, hospitalisations, ICU beds all still going down and vaccinations moving at a faster pace than ever, from the outside it seems a bit nuts to stop the July 5th reopening but after seeing what's happening in the UK I'm unsure.
All seems very reasonable to me. Delta variant is a curve ball and the way our vaccine roll-out panned out we’ve ended up giving almost exclusively AZ to 60-69 year olds, who are a few weeks away from getting their second dose and, hence, remain vulnerable (vaccination stats overall are very encouraging though).


I’m fully in agreement with him about “not going back”. Much better to delay the next stage of reopening then crack on and end up with a surge that forces us to roll back. Sick people aside it would be a devastating blow to the morale of the nation if we went down that path. Absolutely shite state of affairs for people in the hospitality industry but it is what it is.