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

[jojojo]

I don't have a crystal ball.

I just say statistics without details and information about the context and the employed methodology have a limited meaning.

Unfortunately, an increase in the number of cases is the price to pay for an easing of the restrictions.

If there is a high increase in the number of deaths and hospitalisations, then we will have another lockdown.

Otherwise, the debate should be open.

Context and methodology of the ONS survey.
https://www.ons.gov.uk/peoplepopula...onaviruscovid19infectionsurveypilot/2july2021
A national statistically weighted weekly sampling that balances regions, gender, age, ethnic background and relative deprivation. They test around 15,000 people per day to create the survey.

It is not directly related to the national testing system, but because it has followed a consistent model it's used to see national trends over time.

The headline data from the national system is here:
https://coronavirus.data.gov.uk/
Most of the raw data is also available for download in csv format.
They also publish detailed reports on the statistical analysis going on behind the headline numbers, those are here:
https://www.gov.uk/government/publi...ars-cov-2-variant-variant-of-concern-20201201

If you want to look at the current day by day modelling, you can work from the raw numbers oy you can go with the current best fit on the data which is case:hospitalisation ratio around 2% (with a delay of 10 days). However that's a massive fall in case:hospitalisation ratio compared to the end of the winter wave (when it was 8%) and is mostly down to vaccination in older adults and case growth amongst young adults. However that suggests that hospitalisations will hit 1000/day before case rates fall (which we're hoping they will do due to vaccination and school holidays). It's changing by the day though and the calculations of vaccine v virus are not straightforward.

Sometimes, information overload isn't particularly useful in a tweet or a post.

 

[Ecstatic]

@jojojo

Very great post. Thanks, greatly appreciated. Will have a look now

 

[fergies coat]

I've got 2 kids as well. They've had to isolate a few times too. It's a massive inconvenience, but I don't have any better ideas. If your child tests negative they still have to isolate because there is an incubation period to consider. Same goes for adults.

But say kids were treated differently and you were able to send them in after a negative test, who's going to teach them? Because the teachers are often having to isolate too when the class they teach gets sent home. I have friends who teach so I know this to be true. I also know how much grief they've been getting from parents who blame them for what is government policy.

Something better needs to be done. They can't go back in September and have another year like this. It will be a massive disadvantage for them in the future.

 

[neverdie]

It’s basically the same thing. If you have 100 individuals, each 95% protected against severe illness, then you would expect 5% of them to get severe illness assuming they’re all exposed to the virus.

It’s that last bit where his logic falls apart but he doesn’t say that 25000 will get sick. Just that they’ll be vulnerable. A lot of the time you get people jumping all over “errors” from experts on twitter when all that’s happened is that they’ve tried to dumb tricky concepts down to make them easier to digest for the majority of readers.

At the end of the day, his point is essentially correct. Despite vaccinating (almost) all of our elderly, thousands of them can still get sick and die if case numbers get extremely high. Which is something that’s glossed over by people who like to think all our most vulnerable are definitely protected. There’s a big movement right now to try and claim we should ignore case numbers altogether with the elderly vaccinated. That’s an important point to argue against.

Doesn't the calculation require a more complex form of algebraic reasoning? Almost akin to compound interest?

If 100 people each has a 5% level of risk (950/1000) that doesn't equate to 50% "group risk" (as you would get if you multiplied the decimal value by the principal/number of people present) or even necessarily 5% personal risk. In other words, surely it moves exponentially in the inverse direction? We don't just multiply personal risk by the number of persons in a group to arrive at an answer or probability. Maybe someone better at math can help here.


https://www.wikihow.com/Calculate-Relative-Risk

Or just use above ^

 

[Droid_Repairs]

My dad is 73, smokes, and doesn't really take care of himself. He has been double-dosed with Astrazeneca.

4 days ago he came down with what seemed to be a heavy flu, accompanied by a chest/lung infection. He has these awful coughing fits every few minutes.

He has taken two lateral flow tests, 2 days apart. Both came back negative.

He went to the doctor who said that there is infection in his lungs, prescribed antibiotics and advised a PCR test for covid.

When my dad said he'd already taken two lateral flow tests, the doctor 'gritted his teeth' and said he really needed a PCR.

Just wondering if anybody can advise about this, are the lateral flow tests not reliable enough? Is there a possibility that despite having two negative results with LF, he's actually positive for Covid-19?

 

[F-Red]

Just wondering if anybody can advise about this, are the lateral flow tests not reliable enough? Is there a possibility that despite having two negative results with LF, he's actually positive for Covid-19?

Could be, the turnaround is quick (12-24hrs) so I'd suggest getting one booked for him to put your mind at ease.

 

[Droid_Repairs]

Could be, the turnaround is quick (12-24hrs) so I'd suggest getting one booked for him to put your mind at ease.

Thank you, he actually took the PCR test this morning. Hopefully we'll hear something back before long.

I'm also concerned if it's not covid, that his infernal cough is the start of some other nasty like lung cancer or COPD from a lifetime of smoking. Then again, I guess the doctor would likely have flagged that when listening to his lungs.

 

[jojojo]

Just wondering if anybody can advise about this, are the lateral flow tests not reliable enough? Is there a possibility that despite having two negative results with LF, he's actually positive for Covid-19?

Yep. LFTs are really for people who don't think they're ill, your dad is ill. PCRs are more sensitive to the virus, so can spot it earlier and later and can usually spot it even when the sample taking technique hasn't been that great.

 

[Droid_Repairs]

Yep. LFTs are really for people who don't think they're ill, your dad is ill. PCRs are more sensitive to the virus, so can spot it earlier and later and can usually spot it even when the sample taking technique hasn't been that great.

That's great, thanks. I did read that one of the biggest issues with LFTs is untrained users not doing a very good job of obtaining the sample.

 

[oneniltothearsenal]

@Pogue Mahone and other doctors

Is there a counterargument to people posting this: https://journals.lww.com/americanth...in_for_prevention_and_treatment_of.98040.aspx supporting the Joe Rogan argument about Ivermectin?

 

[Ludens the Red]

On the plus side you can always get work on the bin lorries

Haha. When it comes to bad smells, bin lorries would be an upgrade on my current job.

fecking bizarre, its been 2+ months since I tested positive and I still can't smell shit smells, not with the previous intensity anyways. Its a bit alarming because that's an important safety mechanism.

Bloody hell. It is a weird one. Good to not have to smell shit but then like you said it’s quite important in general to be able to smell shit. Have you tried retraining your sense of smell? Apparently that’s what you have to do.

 

[Baxter]

I’m now in my last day of the 10 in isolation. Have zero taste or smell. I do hope this isn’t long term. Meant to be going for a pint or three tomorrow and not sure what the point is

 

[Penna]

Sorry to read about all you folks who either have Covid or still have symptoms. Get well soon. x

 

[hp88]

My dad is 73, smokes, and doesn't really take care of himself. He has been double-dosed with Astrazeneca.

4 days ago he came down with what seemed to be a heavy flu, accompanied by a chest/lung infection. He has these awful coughing fits every few minutes.

He has taken two lateral flow tests, 2 days apart. Both came back negative.

He went to the doctor who said that there is infection in his lungs, prescribed antibiotics and advised a PCR test for covid.

When my dad said he'd already taken two lateral flow tests, the doctor 'gritted his teeth' and said he really needed a PCR.

Just wondering if anybody can advise about this, are the lateral flow tests not reliable enough? Is there a possibility that despite having two negative results with LF, he's actually positive for Covid-19?

I have been taking LFT every few days for a while now and I’m yet to get a positive result. I’m either doing it wrong, really lucky or got a box of duff kits.

I’m now in my last day of the 10 in isolation. Have zero taste or smell. I do hope this isn’t long term. Meant to be going for a pint or three tomorrow and not sure what the point is

Guy at work had Covid just after Christmas and the poor fecker still can’t taste anything.

 

[Droid_Repairs]

I have been taking LFT every few days for a while now and I’m yet to get a positive result. I’m either doing it wrong, really lucky or got a box of duff kits.

Hmm, do you have any reason to expect a positive result?

 

[Baxter]

I have been taking LFT every few days for a while now and I’m yet to get a positive result. I’m either doing it wrong, really lucky or got a box of duff kits.

Guy at work had Covid just after Christmas and the poor fecker still can’t taste anything.

I am quite worried about it. Such a normal thing to take for granted, can’t imagine what your man feels like.

 

[Beans]

@Pogue Mahone and other doctors

Is there a counterargument to people posting this: https://journals.lww.com/americanth...in_for_prevention_and_treatment_of.98040.aspx supporting the Joe Rogan argument about Ivermectin?

Is a prophylactic so it definitely won't work if you're already in the ICU. This is in line with all the early data I saw over a year ago.

 

[Droid_Repairs]

There was a suggestion a couple of months ago, I believe from PHE, that the Delta variant may be more severe and carry an increased risk of hospitalisation. Has there been any data to back this up?

 

[hp88]

Hmm, do you have any reason to expect a positive result?

I have been going into the office a fair bit and as much as you try and follow the guidance it just ain’t happening in an office environment especially when you have over a thousand people onsite.

I was away for a few days earlier this week at a wedding so that will be the real test, I have
given out some of the test kits to a few of the families who were at the wedding as well so it will be interesting to see what the outcome is.

 

[Pogue Mahone]

There was a suggestion a couple of months ago, I believe from PHE, that the Delta variant may be more severe and carry an increased risk of hospitalisation. Has there been any data to back this up?

That PHE data is the only I’ve seen. Think they worked it out as 50% more likely to hospitalise someone than alpha.

 

[The Firestarter]

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

Feck

 

[McGrathsipan]

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

Feck

I'll need that translated

 

[The Firestarter]

I'll need that translated

According to the paper Epsilon variant is showing higher resistance to vaccines due to mutations in the spike protein. However, according to this , it actually is deescalated in concern, and vaccines seem to work against it.

This is not my field, I had a microbiologist summarise the paper for me.

@WI_Red can probably pitch in here as well.

 

[Droid_Repairs]

That PHE data is the only I’ve seen. Think they worked it out as 50% more likely to hospitalise someone than alpha.

Thank you.

In my dad's case (still awaiting PCR result) - he has a bad cough, but his SATs are currently fine, so praying it's not Covid, and especially not Delta. In his age, condition, and with a lifetime of smoking, he's ill prepared for it.

 

[WI_Red]

According to the paper Epsilon variant is showing higher resistance to vaccines due to mutations in the spike protein. However, according to this , it actually is deescalated in concern, and vaccines seem to work against it.

This is not my field, I had a microbiologist summarise the paper for me.

@WI_Red can probably pitch in here as well.

@WI_Red is a bottle and a half of wine in with the missus and will need to read the papers tomorrow.

 

[The Firestarter]

@WI_Red is a bottle and a half of wine in with the missus and will need to read the papers tomorrow.

Dude why you even replying

 

[WI_Red]

Dude why you even replying

We were heading outside to finish bottle 2 when I saw the message.

she is also a microbiologist and we were just discussing the delta variant (I know, we have amazing sexy talk) so replying was on topic.

 

[McGrathsipan]

According to the paper Epsilon variant is showing higher resistance to vaccines due to mutations in the spike protein. However, according to this , it actually is deescalated in concern, and vaccines seem to work against it.

This is not my field, I had a microbiologist summarise the paper for me.

@WI_Red can probably pitch in here as well.

Thanks. Mere mortals like me have no idea

 

[jojojo]

Interesting update from someone who's usually a good source of balanced but up to date information, a London ICU consultant and research professor.

Tweet

— Twitter API (@user) date

Broadly as anticipated, hospitalisations rising. ICUs are getting busy, but mostly supporting people with additional oxygen rather than ventilators. They're currently expecting patient numbers to peak in August, and are hoping that they won't all arrive at once.

 

[jojojo]

Covid too tough for Tough Mudder. This year's race has been cancelled.
https://www.theguardian.com/uk-news...cotland-cancelled-at-last-minute-due-to-covid

Understandably the organisers aren't impressed by the late cancellation especially given:
“The irony is not lost on us that just this past weekend, almost 16,000 rugby fans gathered together in Murrayfield, just 10 minutes up the road."

And the big crowds at Wimbledon and Wembley this week.

 

[golden_blunder]

Covid too tough for Tough Mudder. This year's race has been cancelled.
https://www.theguardian.com/uk-news...cotland-cancelled-at-last-minute-due-to-covid

Understandably the organisers aren't impressed by the late cancellation especially given:
“The irony is not lost on us that just this past weekend, almost 16,000 rugby fans gathered together in Murrayfield, just 10 minutes up the road."

And the big crowds at Wimbledon and Wembley this week.

Yeah that’s something I don’t get, small gatherings banned but for example Ascot was allowed. Lots of toffs dressed up. Hmmm

 

[WI_Red]

According to the paper Epsilon variant is showing higher resistance to vaccines due to mutations in the spike protein. However, according to this , it actually is deescalated in concern, and vaccines seem to work against it.

This is not my field, I had a microbiologist summarise the paper for me.

@WI_Red can probably pitch in here as well.

ok, so after giving the paper a read I think I understand. The epsilon variant is more resistant to both vaccination induced antibodies and infection generated antibodies. Interestingly, the vaccine antibodies are still more potent. My guess is because they are monoclonals targeted at specific, highly conserved, regions of the S protein. However, I do not think that these mutations confer any significant increase in transmissibility.

essentially this variant is starting the “infect the humans race” late and does not have an advantage in transmission to give it a boost. It does have an advantage in overcoming an antibody mediated defense, but that appears to not be great great enough to be able to make a dent in the vaccinated population, and more established variants still dominate the unvaccinated population. While the percent of the infections for epsilon variant remains low the CDC will keep tracking it, but will likely keep it deescalated. However, should it begin to increase in prevalence compared to other variants they will like escalate it.

does this help?

 

[The Firestarter]

ok, so after giving the paper a read I think I understand. The epsilon variant is more resistant to both vaccination induced antibodies and infection generated antibodies. Interestingly, the vaccine antibodies are still more potent. My guess is because they are monoclonals targeted at specific, highly conserved, regions of the S protein. However, I do not think that these mutations confer any significant increase in transmissibility.

essentially this variant is starting the “infect the humans race” late and does not have an advantage in transmission to give it a boost. It does have an advantage in overcoming an antibody mediated defense, but that appears to not be great great enough to be able to make a dent in the vaccinated population, and more established variants still dominate the unvaccinated population. While the percent of the infections for epsilon variant remains low the CDC will keep tracking it, but will likely keep it deescalated. However, should it begin to increase in prevalence compared to other variants they will like escalate it.

does this help?

Thanks. So it's less transmissible than delta? I'd also guess that the data is still very limited (<1000cases).

 

[WI_Red]

Thanks. So it's less transmissible than delta? I'd also guess that the data is still very limited (<1000cases).

That would be my guess. I took a look at the WHO's variant tracking site and it looks like epsilon may have been around longer than most other variants. If this is true then that would double suggest that it is not as highly transmissible as other variants and maybe even wild type. Do we have an epidemiologist on the caf?

 

[Stanley Road]

2 weeks after easing restrictions cases are rising quickly in NL, who'd have thunk

 

[Sandikan]

2 weeks after easing restrictions cases are rising quickly in NL, who'd have thunk

What percentages of adults have had their jabs?

 

[Stanley Road]

What percentages of adults have had their jabs?

I'm looking for that figure. 16m jabs have been given, population 17m. 12-17 year old can get jab. Nearly all the new cases are people that have not been vaxxed or have had 1 jab only.

 

[stw2022]

I'm looking for that figure. 16m jabs have been given, population 17m. 12-17 year old can get jab. Nearly all the new cases are people that have not been vaxxed or have had 1 jab only.

If that’s true the effectiveness of the vaccines is insane

 

[Ecstatic]

I'm looking for that figure. 16m jabs have been given, population 17m. 12-17 year old can get jab. Nearly all the new cases are people that have not been vaxxed or have had 1 jab only.

If it's true, why do we have some people who expect another wave and lockdown in the UK given the success of the vaccine campaign?

 

[11101]

I'm looking for that figure. 16m jabs have been given, population 17m. 12-17 year old can get jab. Nearly all the new cases are people that have not been vaxxed or have had 1 jab only.

73% 1 dose 44% both. So still plenty of room for it to spread.