Coronavirus outbreak

[Ajax Bay]

I will beware of your credentials when you tell me what they are.
So you just cut and paste then?

Cummon, Craig, this is CycleChat, not ITMAT or the Old Road Campus common rooms.
If you think people are making it up, ignore it or say so.

I would very much encourage you to beware of my credentials. Or those of anyone else, even Nobel Prize winners.
I have some experience and skills relevant to help me, which I would rather not go into, but there is nothing I've posted that cannot be readily researched by anyone with good numeracy, basic science knowledge, and an ability to judge the reliability of sources . . .
I am absolutely not an original researcher into COVID, not by a very long distance.

Same here. Superbly put, @rt, but I infer you have a firmer knowledge base foundation.

 

[Deleted User]

I'm amazed why you all care so much?

The easing of lockdown will happen as and when Bozzer says so, in England anyway, whatever anyone on here thinks or the stats of various Internet sources is immaterial, why you're ars*d to quote/post all this is beyond me.

 

[Craig the cyclist]

@Pale Rider

I wanted to explain the different tests before going to herd immunity.

[2] The R number defines, on average how many people each infected person will infect.
3. But if some are immune, that number reduces.
4. If R=4 for current COVID strain, then on average every infected person will infect for others.
5. So let's imagine 5 people.
6. One catches COVID.
7. R=4, so they infect all four others, and the virus expands exponentially.
8. But now imagine three of those are immune. Whether through vaccination or previous infection.
9. Now, the one person only infects that one other person. And R=1.
10. We don't have a definitive test for immunity, but the serology test is the closest we have.
11. Once that 15% becomes 75% we have herd immunity.

[There are many caveats and details to this, but that's the gist of it]

It's posts like this that prompted me to ask your experience in the area. You see, it is conflating things, making things too simple, and is generally not accurate.
Line by line, from line 2.......

2. Correct
3. If some are immune and not infectable, they will not change the R as they won't become infected
4. There are several Covid strains out and about at the moment, this makes it sound like there is just one
5. ok
6. ok
7. Hmmm, possibly, but of the 5 people we are imagining, 3 may be immune or not susceptible. It is not a given that the other 4 will all become infected
8. So what was the point of 7?
9. But that doesn't mean the R has become 1, it just means only one person of those 5 has become infected, 32 others may have become infected on the train on the way in to work
10. No, the test is for antibodies, not immunity
11. Absolutely not! The level for herd immunity is nowhere near to be understood for Covid. 75% is not a Golden Figure for herd immunity, for example Measles needs around 95%, Polio nearer 80%, some flu strains as low as 13%!

 

[the snail]

It's posts like this that prompted me to ask your experience in the area. You see, it is conflating things, making things too simple, and is generally not accurate.
Line by line, from line 2.......

2. Correct
3. If some are immune and not infectable, they will not change the R as they won't become infected
4. There are several Covid strains out and about at the moment, this makes it sound like there is just one
5. ok
6. ok
7. Hmmm, possibly, but of the 5 people we are imagining, 3 may be immune or not susceptible. It is not a given that the other 4 will all become infected
8. So what was the point of 7?
9. But that doesn't mean the R has become 1, it just means only one person of those 5 has become infected, 32 others may have become infected on the train on the way in to work
10. No, the test is for antibodies, not immunity
11. Absolutely not! The level for herd immunity is nowhere near to be understood for Covid. 75% is not a Golden Figure for herd immunity, for example Measles needs around 95%, Polio nearer 80%, some flu strains as low as 13%!

facepalm. By definition, if vaccination prevents infection, it reduces the r number

 

[roubaixtuesday]

Line by line, from line 2.......

You'll have noted

[There are many caveats and details to this, but that's the gist of it]

Or perhaps not.

 

[Craig the cyclist]

facepalm. By definition, if vaccination prevents infection, it reduces the r number

Maybe go and have a re-read of the quoted post and of my reply?

 

[Craig the cyclist]

You'll have noted

[There are many caveats and details to this, but that's the gist of it]

Or perhaps not.

Maybe you should have written

[Most of this is factually incorrect, so not really the gist of it at all]

Or perhaps not.

Writing things that are wrong isn't particularly helpful for anyone. I understand that you were trying to explain things in a simple way, but too much of it was simply wrong, especially point 11. If someone reads this, the obvious conclusion is that when the immunisation rate reaches 75% then we are all suddenly safe as herd immunity is reached and lockdown becomes irrelevant. Too many people do not understand the complexity of this, over-simplicity doesn't help.

There is soooooo much data around C19, that you can produce a number or a graph for absolutely any aspect of the outbreak you could possibly wish. My question around the professional backgrounds of those quoting all the stats is just a genuine query to get an idea of the level of understanding of those using the data. Especially in this pandemic, data is massively useful, but also hugely problematic if used incorrectly.

 

[roubaixtuesday]

Most of this is factually incorrect

Please identify the incorrect parts.

Thank you.

 

[mjr]

3. If some are immune and not infectable, they will not change the R as they won't become infected

I suspect the above is confused, possibly confusing R (the observed reproduction rate) with R0 (the theoretical reproduction rate of the uncontrolled virus in a fresh population).

And seeing as you care, I'm a graduate statistician who did post-grad in it but has been working in IT for 15+ years, so literally "out of practice" and not completely up-to-date with latest thinking.

4. There are several Covid strains out and about at the moment, this makes it sound like there is just one

Arguably it was missing a "dominant" but this seems minor to me.

9. But that doesn't mean the R has become 1, it just means only one person of those 5 has become infected, 32 others may have become infected on the train on the way in to work

I think you've changed @roubaixtuesday's simplified example scenario there by adding a train.

11. Absolutely not! The level for herd immunity is nowhere near to be understood for Covid. 75% is not a Golden Figure for herd immunity, [...]

This much is correct, but some virology experts are estimating 75% based on experience with other coronaviruses. What's your expertise in virology?

 

[Ajax Bay]

Herd immunity calculation
'R' Number For an infectious disease, such as COVID-19,

is the basic reproduction number of the disease: the average number of people an infected person goes on to infect, given that everyone in the population is susceptible to the disease with no restrictions. For COVID-19 B1.1.7 variant estimates vary: let's go for

=3.
NPIs (restrictions on behaviour etc) can reduce the 'R' - so for any time and dominant variant R = Rt. NB This Rt (as I shall use it) does not account for the number of people who are no longer susceptible to the disease: that's accounted for by the other calculations qv.
Only a proportion of 1-1/Rt of the population need to be immune to achieve herd immunity.

Effectiveness If a vaccine has an effectiveness of x%, then this means that x% of people who receive it are immune: not susceptible to the disease.
But let's take care to be clear what we mean by effectiveness.
#1) Immune so the virus does not cause illness: of course this means the subject does not transmit virus.
#2) Immune from serious illness. Catches C19 but asymptomatic or slight illness but the subject CAN transmit virus (transmissability will vary with subject, and this matters - I've treated it as factored into the 80% figure below).
Aiui the quoted efficacy figures from the RCT (Ph3) trials were for #2: Pfizer 94% and 70% for Ox-Az. Since these trials far more data are available and aiui effectiveness averages 89% (#2 version).
For herd immunity considerations, the severity of the illness 'doesn't matter'. So (leap of faith) let's assume for 'type #1 immunity' (which takes those people out of the transmission chain) x = 80% effectiveness. 20% of those vaccinated can still catch C19 and if they do they will be able to transmit the virus (assumed still at Rt). Note that effectiveness will be less until 7 days after the second dose, but I'm ignoring that for now - by mid-summer 32M will have had their second dose.

To achieve herd immunity we therefore require that P% (the proportion) of people who are vaccinated times the effectiveness (x%) is at least 1-1/Rt of the population. In other words,
Substituting Rt = 2.5 (slight restrictions) gives P needs to be greater than 0.6/x
For a vaccine that is 80% effective (#1) with no restrictions we therefore need to vaccinate (first dose) at least 75% of the population (51M) to achieve herd immunity (see Note below).
I estimate we will achieve that (4M a week) by 21 June.

Recall at its maximum in UK since May, Rt was at 1.6 on 2 Oct (90% confidence, upper bound) - this was a time when a few areas were in Tier 3, but for most, restrictions were 'light'. We might assume that by July the restrictions will be lighter still.
If we used Rt = 2 then the numbers needed to be vaccinated for herd immunity is 42M (63%).

the context for Covid is that we don't know the figure

Note: There is uncertainty about several (all?) of the figures I've chosen above, but to make some sense I have tried to choose 'reasonable ones'. Choosing Rt = 2.5 is certainly pessimistic but allows for a more transmissible dominant variant. Choosing 80% effectiveness is optimistic (but as the data come in we'll be able to narrow the uncertainty on that).
Conclusion: With these figures, to get to herd immunity in the summer we may need to retain some restrictions or Rt will push the herd immunity percentage up to a figure we (UK) can't reach.
@matticus - think you need to review your use of the expression "exponential", let alone "pretty".

 

[mjr]

Effectiveness If a vaccine has an effectiveness of x%, then this means that x% of people who receive it are immune: not susceptible to the disease.
But let's take care to be clear what we mean by effectiveness.

Please do. The above incorrect definition contradicts the following correct definition:

#1) Immune so the virus does not cause illness: of course this means the subject does not transmit virus.
#2) Immune from serious illness. Catches C19 but asymptomatic or slight illness but the subject CAN transmit virus (transmissability will vary with subject, and this matters - I've treated it as factored into the 80% figure below).

Aiui the quoted efficacy figures from the RCT (Ph3) trials were for #2: Pfizer 94% and 70% for Ox-Az. Since these trials far more data are available and aiui effectiveness averages 89% (#2 version).

Efficacy is different to effectiveness, so the first of those two sentences is largely irrelevant to the rest of the post.

[...] Recall at its maximum in UK since May, Rt was at 1.6 on 2 Oct (90% confidence, upper bound) - this was a time when a few areas were in Tier 3, but for most, restrictions were 'light'. We might assume that by July the restrictions will be lighter still.
If we used Rt = 2 then the numbers needed to be vaccinated for herd immunity is 42M (63%).

All legal restrictions lifted mid-June, we were told, so I feel you should go back to using R0 by July unless you think it's a change of plan, so I commend this Note to everyone:

Note: There is uncertainty about several (all?) of the figures I've chosen above, but to make some sense I have tried to choose 'reasonable ones'. Choosing Rt = 2.5 is certainly pessimistic but allows for a more transmissible dominant variant. Choosing 80% effectiveness is optimistic (but as the data come in we'll be able to narrow the uncertainty on that).
Conclusion: With these figures, to get to herd immunity in the summer we may need to retain some restrictions or Rt will push the herd immunity percentage up to a figure we (UK) can't reach.

I also note that then there's a big question of how we get from UK stabilisation to global immunity...

 

[Ajax Bay]

Thanks. Very useful. But not sure you've fully grasped it.

 

[Deleted User]

Bloody Hell lads!
Fair play to you for persevering with this but is there a straightforward answer to this for us thicko's reading?
Is there an agreed % of people needed to have had this before immunity is reached?

 

[Craig the cyclist]

Bloody Hell lads!
Fair play to you for persevering with this but is there a straightforward answer to this for us thicko's reading?
Is there an agreed % of people needed to have had this before immunity is reached?

Absolutely not, so ignore all the stats in this thread, apart from this one.......

100% of the statisticians presenting endless data on this thread about the level required to achieve herd immunity are wrong.

 

[classic33]

Absolutely not, so ignore all the stats in this thread, apart from this one.......

100% of the statisticians presenting endless data on this thread about the level required to achieve herd immunity are wrong.

Prove that last statement!