From 60 Minutes an Epidemiological View Of What Vaccination Level Is Needed

[bhobba]

See:

Note - the link has been changed to Youtube so, fingers crossed, should work for everone now.

Can Aus or anywhere else get to over 90% - assuming the professor is right, of course?

Some people are proposing pretty draconian measures for those that do not get vaccinated. Personally, I find it not only premature but somewhat disturbing.

I am still banging my head about peoples concern with a 1 (.5 so far in Aus) in a million risk of dying from the AZ vaccine. I point out there is a 2.5 in a million risk of dying by just getting out of the bed of a morning, but it makes no difference. People, for some reason, seem to have a block about even rudimentary understanding of risk. Maybe Actuaries should be more involved in this Pandemic. The trouble is, of course, most people do not even know what an Actuary is.

Thanks
Bill

 

[phinds]

Video won't play here in US (or at least not where I am)

 

[bhobba]

Video won't play here in US (or at least not where I am)

It looks like it is region locked. That is something I can't tell when I post links up.

Here is a link that hopefully will work for everyone. It is about Professor Tony Blakely's work in this area that basically was what he said in the interview:
https://findanexpert.unimelb.edu.au...uld-mean-safely-opening-international-borders

Thanks
Bill

 

[Vanadium 50]

Me neither.

But what is magic about 90%? Why not 99%? Or 80%?

The US current "spike" is a new case rate of 5.4% of what it was at the peak. This is up from its absolute lowest of 4.6%. Deaths and hospitalizations are at an all time low - below seasonal flu when extrapolated for a year. That's with about half the population vaccinated.

Would more be better? Sure. Would a lot more be a lot better? That's tougher - there's maybe not so much room to improve left.

 

[phinds]

He says

However, even with 100% of the population vaccinated, herd immunity may not be achieved by vaccination alone until booster vaccines become available.

. I find that pretty much impossible to believe that. If the vaccine is 95% effective** then I think you WILL get herd immunity, at least for as long as the vaccines remain effective (which, I realize, we don't yet have a duration for).

EDIT: ** AND with a 95% vaccination rate

 

[bhobba]

But what is magic about 90%? Why not 99%? Or 80%?

Professor Blakely explains it in the other link I posted, which hopefully will work. It goes like this. With the R0 of the delta variant being about 5, 80% should do it from his models. But the vaccines are not 100% effective - especially against the delta variant. So we need a higher vaccination rate. His calculations show at least 90% is needed, and maybe even 100% will not do it. Our current vaccines are a bit less effective against Delta, plus with an R0 of 5, it can explode.

Thanks
Bill

 

[bhobba]

He says

. I find that pretty much impossible to believe that. If the vaccine is 95% effective then I think you WILL get herd immunity, at least for as long as the vaccines remain effective (which, I realize, we don't yet have a duration for).

At what percentage of the population vaccinated?

Thanks
Bill

 

[phinds]

At what percentage of the population vaccinated?

Thanks
Bill

OPPS .. meant to say 95% vaccinated AND 95% effective. Fauci started off last year saying 70% would do it but I think even he now agrees that that number is too low.

 

[bhobba]

OPPS .. meant to say 95% vaccinated AND 95% effective. Fauci started off last year saying 70% would do it but I think even he now agrees that that number is too low.

The professor has done the detailed calculations, and they were not posted. That is an issue for a technical forum like this. But my guess is - and it is just a guess - 95% will likely do it even with the delta variant.

Plus, since it is becoming the dominant variant, a specific vaccine may help a lot. Trouble is getting to that 95%.

Thanks
Bill

 

[Vanadium 50]

I found this to be on par with pop-science descriptions of QM or relativity.

"Herd immunity" is fine as a general concept, but it is too woolly to guide public policy. Who is your herd? If there was an outbreak in Sydney, Melbourne and Canberra, would there be calls to lock down Hobart, Darwin and Alice Springs? What about the reverse?

(Hobart? Isn't that somewhere in New Zealand? )

"Reproduction number" similarly. It varies by space and time. I hope this is obvious, but I can explain if necessary.

R = 5 is way outside the mainstream. Ontario (Canada's NSW) is at ~70% vaccination at least one dose, half that fully vaccinated, and sees R for the delta variant around 1 (1.07). The majority of their cases are delta, and have been for about a month, and case rates are about 5% of where they were at the peak.

I understand the desire to send messages that encourage the right behavior, but "if we don't reach 90% it's all for naught" seems unlikely to be the right message. A more accurate (and more likely to succeed) message is "25% is way too low - we need to get to 70% quickly".

 

[BillTre]

There are many factors that make calculating things like this fraught, in my mind.

To achieve herd immunity, you want to drive the rate at which a single infected person leads to an infection of a new host, to less than one. This will result in a statistically driven meandering walk of the population size down to zero (extinction).

• Different virus variants will have different reproductive abilities.
• The behaviors of people, that have effects on virus transmittability, will vary over time.
• Different groups of people (local populations), in different areas, will have different traits (immunization status, behaviors) affecting the ability to contract a viral infection. This will lead to a patchy distribution of rates of infection (some places will have a higher proportion of sick people than others). A virus could thrive in one area and not in others.

 

[atyy]

We expect variants to develop that will make the vaccine less effective in preventing infection, so herd immunity may not be possible, even with 100% vaccination rates. If, however, the vaccines continue to give good protection against severe disease, then we should aim for 100% vaccination among vulnerable groups, so that each vaccinated individual is protected, even if unvaccinated people are still at risk. Here are some remarks by Christian Drosten urging vaccination in this scenario.

 

[atyy]

He says

. I find that pretty much impossible to believe that. If the vaccine is 95% effective** then I think you WILL get herd immunity, at least for as long as the vaccines remain effective (which, I realize, we don't yet have a duration for).

EDIT: ** AND with a 95% vaccination rate

The 95% effectiveness of the Pfizer vaccine for symptomatic infection. However, there may be asymptomatic infection which also enables transmission. The vaccine provides about 85-95% protection against all infection (asymptomatic and symptomatic) for the original and the alpha variants. For the delta variant, the protection against all infection falls to about 79%. For the beta variant, the protection against all infection is about 75%.

https://pharmaceutical-journal.com/...hing-you-need-to-know-about-covid-19-vaccines

 

[phinds]

Trouble is getting to that 95%.

Well, I don't think "trouble" is quite adequate. I'd say there is not a snowball's chance in hell that we'll even get close to that in America. We'll be doing fantastically well if we get over 70% avg across the country and I don't think that will lead to herd immunity with all the new varieties, unless we get much better vaccines.

 

[atyy]

The 95% effectiveness of the Pfizer vaccine for symptomatic infection. However, there may be asymptomatic infection which also enables transmission. The vaccine provides about 85-95% protection against all infection (asymptomatic and symptomatic) for the original and the alpha variants. For the delta variant, the protection against all infection falls to about 79%. For the beta variant, the protection against all infection is about 75%.

https://pharmaceutical-journal.com/...hing-you-need-to-know-about-covid-19-vaccines

https://www.haaretz.com/israel-news...fections-in-israel-as-delta-spreads-1.9971842

"The Pfizer-BioNTech Coronavirus vaccine has dropped to 64 percent effectiveness in preventing infection in Israel as the delta variant continues to spread across the country, the Health Ministry said on Monday.
...
The ministry added that the vaccine is 93 percent effective in preventing hospitalizations and severe symptoms."

 

[bhobba]

"The Pfizer-BioNTech Coronavirus vaccine has dropped to 64 percent effectiveness in preventing infection in Israel as the delta variant continues to spread across the country, the Health Ministry said on Monday.
...
The ministry added that the vaccine is 93 percent effective in preventing hospitalizations and severe symptoms."

It is similar for AZ as well:
https://theconversation.com/should-...-doubles-your-protection-against-delta-163259

Regarding the CVT in Aus the fatality rate is now 3%, but they are on the lookout for the reaction and finding it more - about 1.3 per 100000 last I heard. This equates to a possibility of death of .45 in a million. Just getting out of the bed of morning has a 2.5 in a million chance of death or over 5 times higher.

In Aus we are working on vaccines for specific variants and making them here:
https://www.abc.net.au/news/2021-06...trials-in-australia-variant-booster/100229294

Sorry to say, but I think this pandemic is with us for a while yet. Imagine how much worse it would be without our modern scientific understanding and technology.

Thanks
Bill

 

[atyy]

In Aus we are working on vaccines for specific variants and making them here:
https://www.abc.net.au/news/2021-06...trials-in-australia-variant-booster/100229294

I was hoping they'd tweak the Queensland vaccine (the COVID vaccine that made people positive on HIV tests), but I guess they aren't pursuing that line of work any more? Like Novavax - it'd be nice to have a "conventional" vaccine. Also, I was intrigued by their "molecular clamp technology", which I think holds the antigen in the right shape. Pfizer/Moderna, J&J, Novavax have something that I think is similar from Jason McLellan's group at UT Austin.

 

[morrobay]

Professor Blakely explains it in the other link I posted, which hopefully will work. It goes like this. With the R0 of the delta variant being about 5, 80% should do it from his models. But the vaccines are not 100% effective - especially against the delta variant. So we need a higher vaccination rate. His calculations show at least 90% is needed, and maybe even 100% will not do it. Our current vaccines are a bit less effective against Delta, plus with an R0 of 5, it can explode.

Thanks
Bill

From the data points: index delta cases to total generated cases over time, can you show the R0 = 5 calculation ?

 

[pinball1970]

Well, I don't think "trouble" is quite adequate. I'd say there is not a snowball's chance in hell that we'll even get close to that in America. We'll be doing fantastically well if we get over 70% avg across the country and I don't think that will lead to herd immunity with all the new varieties, unless we get much better vaccines.

Or UK
We are at 50% today 2 doses and all restrictions end in 14 days.
So about 12 million with one dose only and 20 million with no dose.

That is a fair bit for the virus to aim at with a lot of people in party mode.

EDIT:

On the positive side in the last 4 months hospital admissions are still not very high in the UK and of those overnight stays and deaths is still quite low (page 15)

https://assets.publishing.service.g...ants_of_Concern_VOC_Technical_Briefing_15.pdf
So perhaps another 4 million or so vaccinated by the 19th?

Most over 50s vaccinated and those cases not leading to severe illness.

 

[bhobba]

From the data points: index delta cases to total generated cases over time, can you show the R0 = 5 calculation ?

As mentioned before, in TV info programs, and even the paper I found about it, they do not provide the technical detail that a site like this would like. From the paper:

'The Delta variant has an R0 (the number of people one infected person on average infects) of about 5.0 under pre-COVID-19 ways of living. This is twice that of the original COVID-19, which had an R0 of about 2.5. For an R0 of 5.0, theoretically, 80% of the population have to be immune — not just vaccinated — for virus transmission not to take off.'

I wish we had more detail.

As an aside just speaking to my doctor today. He is not too worried about the Delta variant and our current vaccines. What gives him optimism is the 92% protection it gives against hospitalisation.
https://www.clinicaltrialsarena.com/news/astrazeneca-vaccine-delta-variant/

A bad case of the sniffles is nothing to worry about. As a GP they see it all the time, so will make sure if it gets worse the patient will be hospitalised. The rate will be low enough not to overload the hospital system. But we must figure out a way to ensure people do get vaccinated. As I have mentioned, fingers crossed, those with vaccine hesitancy, if they talk to their doctor, hopefully will change their mind.

Thanks
Bill

 

[morrobay]

https://www.cnbc.com/2021/06/30/aus...asures-amid-delta-covid-variant-outbreak.html From this report limo driver 2 weeks ago was index case that generated 170 cases. So: R0^4.66 = 170 then 4.66 logR0 = log170. Then R0=10^.4786 = 3.01 note the exponent of growth, 4.66 is from 14days/3day generation interval. See fig,1. The generation/infection interval is about one day less than serial interval. https://pubmed.ncbi.nlm.nih.gov/32145466/

 

[atyy]

https://www.cnbc.com/2021/06/30/aus...asures-amid-delta-covid-variant-outbreak.html From this report limo driver 2 weeks ago was index case that generated 170 cases. So: R0^4.66 = 170 then 4.66 logR0 = log170. Then R0=10^.4786 = 3.01 note the exponent of growth, 4.66 is from 14days/3day generation interval. See fig,1. The generation/infection interval is about one day less than serial interval. https://pubmed.ncbi.nlm.nih.gov/32145466/

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.24.2100509
Here they use a generation time distribution with a mean of 5 days, but they also see how their results vary if it's lower or higher.

 

[bhobba]

https://www.cnbc.com/2021/06/30/aus...asures-amid-delta-covid-variant-outbreak.html From this report limo driver 2 weeks ago was index case that generated 170 cases. So: R0^4.66 = 170 then 4.66 logR0 = log170. Then R0=10^.4786 = 3.01 note the exponent of growth, 4.66 is from 14days/3day generation interval. See fig,1. The generation/infection interval is about one day less than serial interval. https://pubmed.ncbi.nlm.nih.gov/32145466/

Nice post.

Just a few comments.

It must be remembered that R0 of 5 is an estimate under pre Covid conditions. Many people, including me, are taking greater precautions regardless of mandated government mask-wearing etc. In fact, we have a growing number of people who say the government is too intrusive - people are smart enough to make their own decisions given the correct information. People that post here are highly likely to be in that camp - i.e. figure out the correct precautions for their circumstances and take them - but the general population? Anyway, pursuing that is likely taking us into politics which is not what we are on about.

Things here in Aus are at a knife-edge right now. But rest assured, at the first sign of it tipping the wrong way - total lockdown everywhere - the Australian public is strong on that point - they do not want any cases here in Aus. By just doing that, governments have been returned with virtually no opposition, i.e. just a couple of people.

Our vaccination program has been totally botched for several reasons, some of which do not reflect well on our bureaucracy:

1. We were told that CSL in Melbourne was producing over a million doses a week of AZ and producing vaccines even before approval. That turned out to be a lie. It was 400,000 as soon became apparent when GP's were only getting 50 doses a week. Still, the bureaucrats did not come clean - it was like pulling teeth getting the truth out of them. There were also significant distribution bungling I have posted about before. Again getting that information was like pulling teeth. We know it now, but not when it counted.

2. They did not consistently message the AZ CVT risks and were IMHO using the wrong methodology in explaining that risk. People should have been told even getting out of the bed of a morning carries greater risk. There are zero reasons to limit its use. All vaccines at that stage were administered by GP's who would explain the risk, and the patient can decide. But we were making 1 million doses locally of AZ and importing 300,000 doses of Pfizer per week. Again getting that 300,000 out of the bureaucrats was like pulling teeth. We are told it will increase over the coming months to a whopping over 2 million a week by year-end, outstripping local AZ production. We will see. In deciding what vaccine to get that 12 weeks is needed before you get the second dose of AZ, but 3 weeks for Pfizer needs to be considered. By the time that 12 weeks happen, there may be plenty of Pfizer. But in waiting watch it:
https://www.forbes.com/sites/victor...at-australian-birthday-party/?sh=55395ac5612f

3, There is a conflict of information coming from state and federal governments. This was highlighted by when the deputy Commonwealth Medical Officer quit and returned to private practice. He is now singing a different song - IMHO a much more rational one. He now says we have offered vaccines to all vulnerable groups. We must finish frontline workers. Then it is first in, first served on all vaccines. The government has announced we will be opening up at the beginning of next year. If you are not vaccinated by then - well, you will cop whatever the government decides. I believe it should be you must see your doctor who will explain the necessity of getting vaccinated. I am hopeful that is all that is required, but we will see. More draconian measures may be necessary, such as what is done for the Triple Antigen Vaccine. It is no jab - no pay - all government benefits stopped, including tax concessions. If even that does not work, then I think that is about as far as the government can legitimately go - but we will see. The desire of the Australian people to keep this out of Aus is powerful.

Just my take as a person living through this in Aus.

Thanks
Bill

 

[morrobay]

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.24.2100509
Here they use a generation time distribution with a mean of 5 days, but they also see how their results vary if it's lower or higher.

https://en.m.wikipedia.org/wiki/Basic_reproduction_number go to estimation methods and then down to simple model.And to first two equations: n(t) = n(0) R0^t/inf.interval. So yes they are using serial interval. And if that is 5 days applied to above data: Then R0^2.8 = 170 therefore R0= 6.25

 

[bhobba]

I was hoping they'd tweak the Queensland vaccine (the COVID vaccine that made people positive on HIV tests), but I guess they aren't pursuing that line of work any more?

Yes, they are still working on it:
https://www.abc.net.au/news/health/...19-vaccine-research-molecular-clamp/100050240

But it will not be available soon. It likely will be one of the second-generation vaccines that will start to appear probably from early next year.

Right now, correctly IMHO, the focus seems to be getting first-generation vaccines into as many as possible.

I think it likely to really bring the pandemic under control; we will need 3rd or even 4th generation vaccines.

Australia IMHO did not invest in as many first-generation vaccines as they should have. They should have fast-tracked the Covax-19 vaccine like they were doing for the UQ vaccine:
https://medicine.uq.edu.au/article/2021/06/what-covax-19-australias-most-advanced-covid-vaccine candidate

It is debatable if what I am about to say is a morally valid strategy. But Professor Petrovsky had a plan after he finished phase 1 trials to vaccinate during the Melbourne outbreak in aged care facilities as part of phase 2 trials. They had an alarmingly high death rate, so he thought the risk was worth it - as did I. With phase 2 trials complete, phase 3 could start while Australia accelerated building a manufacturing plant ready for when phase 3 is complete. IMHO Australia, lost a valuable opportunity - and possibly the world as well. Phase 2 and 3 trials should have been completed on this vaccine ages ago and should be part of the vaccines available for use right now. But as I said, it was a debatable strategy - things are always clearer in hindsight. According to Professor Petrovsky, it will be available by year-end when really it should have been available at the start of the year with a trickle earlier for high risk people in age care facilities etc.

Thanks
Bill

 

[AndreasC]

The 95% effectiveness of the Pfizer vaccine for symptomatic infection. However, there may be asymptomatic infection which also enables transmission. The vaccine provides about 85-95% protection against all infection (asymptomatic and symptomatic) for the original and the alpha variants. For the delta variant, the protection against all infection falls to about 79%. For the beta variant, the protection against all infection is about 75%.

https://pharmaceutical-journal.com/...hing-you-need-to-know-about-covid-19-vaccines

However, asymptomatic patients (in particular never-symptomatic, as opposed to pre-symptomatic) are generally thought to be less infectious than symptomatic people.

 

[morrobay]

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.24.2100509
Here they use a generation time distribution with a mean of 5 days, but they also see how their results vary if it's lower or higher.

I didn't see any reference to generation interval: time between infection events in an infector-infectee pair. Serial interval: time between symptom onsets in an infector-infectee pair. See fig (1) and conclusion: This suggests that a substantial proportion of secondary transmissions may occur prier to illness. IE, gen interval less than serial interval . https://pubmed.ncbi.nlm.nih.gov/32145466/

 

[atyy]

I didn't see any reference to generation interval: time between infection events in an infector-infectee pair. Serial interval: time between symptom onsets in an infector-infectee pair. See fig (1) and conclusion: This suggests that a substantial proportion of secondary transmissions may occur prier to illness. IE, gen interval less than serial interval . https://pubmed.ncbi.nlm.nih.gov/32145466/

They use the term "generation time" in the supplementary materials: https://www.eurosurveillance.org/do...est&checksum=8C31830EC2933219A2FD099A8DD12BC0

It looks like what they call "generation time" is taken from https://science.sciencemag.org/content/368/6491/eabb6936 which uses the term in the sense "time from infection to onward transmission".

 

[bhobba]

Things are getting bad in Syndey.

https://www.9news.com.au/national/c...rs-surge/ea055b40-4290-467c-8937-f5b069518336

Why is self-explanatory from the article and video (which is hopefully not region locked).

Thanka
Bill

 

[morrobay]

It looks like what they call "generation time" is taken from https://science.sciencemag.org/content/368/6491/eabb6936 which uses the term in the sense "time from infection to onward transmission".

Good paper. In Results: They give the R0 =2, doubling time Td = 5 days and generation time (t) of 5 days. So the R0=2 can be shown: R0=e^kt , k= ln2/Td. So R0= e^.693

 

[anorlunda]

I think it likely to really bring the pandemic under control; we will need 3rd or even 4th generation vaccines.

How do you define under control?

We have never succeeded in making the flu virus extinct. Shouldn't we expect COVID to be in circulation perpetually and require anti-COVID factors in our annual flu shots? Even then the number of annual deaths will not be zero.

https://www.cdc.gov/flu/about/burden/index.html
CDC estimates that influenza has resulted in between 9 million – 45 million illnesses, between 140,000 – 810,000 hospitalizations and between 12,000 – 61,000 deaths annually since 2010.

 

[SongDog]

How do you define under control?

We have never succeeded in making the flu virus extinct. Shouldn't we expect COVID to be in circulation perpetually and require anti-COVID factors in our annual flu shots? Even then the number of annual deaths will not be zero.

Influenzas circulate and mutate in many wild and domesticated specie, not just humans. As a result, new variants arise frequently in swine, birds, even camels. AFAIK, we don’t yet see a similar behaviour for coronaviruses.

 

[BillTre]

Influenzas circulate and mutate in many wild and domesticated specie, not just humans. As a result, new variants arise frequently in swine, birds, even camels. AFAIK, we don’t yet see a similar behaviour for coronaviruses.

Coronaviruse-19 has been found in a variety of animals (cats, ferrets, etc.), but no new mutants from them are known yet.
Give it time (and larger infected populations).

 

[bhobba]

How do you define under control?

You said it. Like the flu with the flu vaccine. There are circulating varieties each year, and we will get vaccinations for the most likely strains. Often, however, they will get it wrong, and the vaccine will not be as effective. But I think the death and hospitalisation rate will be low, possibly even lower than the flu.

Thanks
Bill

 

[pinball1970]

You said it. Like the flu with the flu vaccine. There are circulating varieties each year, and we will get vaccinations for the most likely strains. Often, however, they will get it wrong, and the vaccine will not be as effective. But I think the death and hospitalisation rate will be low, possibly even lower than the flu.

Thanks
Bill

That's where we need to get to.
Vaccines for the groups that need it. Every year.