Just curious, anyone have a plan, or preps for global pandemic?

[Saul]

Dean, according to Gordo, the man was "seriously overweight".  That's possibly the Worst possible condition to be in, when hit by the novel coronavirus.

Survivors of the pandemic tend to not have a barrel midsection.

Gordo, sorry to hear of your loss.

(A startling number of my colleagues in the math department here at UR are obese.)

  --  Saul

[Dean Pomerleau]

Saul,

I asked "how he came down with it?" (i. e. how did he become infected?), not "why did he die from it?"

--Dean 

[Todd Allen]

Fact checkers spread the idea that because the delta variant arose in India at a time when vaccines were being trialed and not in widespread use it is the unvaccinated driving viral evolution.  This appeals to those unaware variants are actually lineages which can develop countless substrains.  The many substrains of delta spreading through the vaccinated rose to prominence after widespread vaccination.  Here's a graph of delta phylogeny taken from

https://nextstrain.org/ncov/gisaid/global

 

 

Edited September 4, 2021 by Todd Allen

[Todd Allen]

2 hours ago, Dean Pomerleau said:

Clearly the vaccine doesn't provide 100% protection.

This reminds me of Ron Put's statements last spring comparing the 20,000 US deaths from covid-19 to the much greater death tolls from seasonal influenzas.  The worrying thing then was not the numbers but the trajectory, exponential growth in cases and deaths.  Looking at where we are today with vaccines still providing some protection but ignoring the trajectory, the rapid drop in protection of vaccination, I expect will be an equally grave mistake. 

[Saul]

2 hours ago, Saul said:

Dean, according to Gordo, the man was "seriously overweight".  That's possibly the Worst possible condition to be in, when hit by the novel coronavirus.

Survivors of the pandemic tend to not have a barrel midsection.

Gordo, sorry to hear of your loss.

(A startling number of my colleagues in the math department here at UR are obese.)

  --  Saul

Gordo said he spoke to the Widow -- so it seems likely that he died.

  --  Saul

Edited September 4, 2021 by Saul

[BrianA]

The Economist is keeping an updated estimate of worldwide covid deaths, and by country. Currently we're up to 15 million worldwide, around 800k in USA. These are estimates driven in part by a machine learning algo:

 

 

[Dean Pomerleau]

49 minutes ago, Saul said:

Gordo said he spoke to the Widow -- so it seems likely that he died.

  --  Saul

Saul,

Are you sure you're sharp enough to still be teaching :-).

Seriously, I know he died and nowhere did I imply otherwise. Duh.

I asked Gordo if they have any idea how he and/or his family got infected with covid. What isn't clear in your mind about the way I've phrased the question, now for the third time!?

--Dean

[Dean Pomerleau]

3 hours ago, Todd Allen said:

The many substrains of delta spreading through the vaccinated rose to prominence after widespread vaccination.  

Todd,

Cool website on the evolutionary divergence of the different variants and substrains. Clearly the tree is getting bushier with time - but what else would you expect, especially from an RNA virus and especially since concern about variants has grown so more sequencing is being done? I'm not saying your hypothesis that vaccines are driving the selection of new strains is wrong, but I'm not entirely convinced either.

Is there evidence that the rate of mutations per unit time is increasing, or that the substrains are getting more transmissible, or that the substrains are getting more transmissible as a result of vaccinations primarily and not (also) as a result of an increase in the pool of previously infected people that the virus is "trying" to find a way to reinfect?

3 hours ago, Todd Allen said:

Looking at where we are today with vaccines still providing some protection but ignoring the trajectory, the rapid drop in protection of vaccination, I expect will be an equally grave mistake. 

Definitely a troubling possibility. But it doesn't seem as dire (yet) as you seem to be suggesting. First, you cherry-picked the daily death rate in Israel to make it seem identical to the US. The 7-day average daily deaths in Israel is 2.77 deaths/million/day vs. the US which is 3.94. And why use Israel as the comparison and not the UK?

The UK 7-day average daily death rate is 0.79 deaths/million/day - 5x lower than the US. And they have a very high rate vaccinations and an even higher prevalence of antibodies from either vaccination or previous infection. Fom the official UK Office of National Statistics website:

An estimated 94.1% of the adult population in England, 92.0% in Wales, 90.4% in Northern Ireland and 93.6% in Scotland tested positive for COVID-19 antibodies in the week beginning 9 August 2021. The presence of antibodies suggests a person previously had COVID-19 or has been vaccinated.

Estimated vaccination rates continued to increase in the week beginning 2 August 2021. Across the four UK countries, 90.5% to 92.4% had received at least one dose of a COVID-19 vaccine and 76.8% to 82.5% were fully vaccinated. 

Here are the UK graphs for cases and deaths:

That UK death graph looks quite encouraging and they are 4-6 weeks further along in their Delta surge than either the US or Israel. If high rates of vaccinations were causing a waning in effectiveness and driving more transmissible and/or deadly variants, wouldn't it be much more likely to happen (or show up) in the UK, which has a population 15x larger than tiny Israel?

As of two days ago the UK is only planning to give a third vaccine doses to 1% of their population (the immunocompromised) and haven't even started yet. Word is they are likely to canceled/postponed their plan for a third shot for most adults because the evidence for waning vaccine effectiveness against hospitalization / deaths is quite weak. It looks like we will likely postpone in the US as well, at least if they listen to the scientists.

So I think your pessimism is unwarranted, or at least premature. 🙂

--Dean

Addendum: One interesting thing to consider - in England they spaced the two doses about 8-12 weeks apart, perhaps triggering a more robust immune response among the vaccinated. That might support the case for third shots in countries like the US which spaced the two doses closer. 

[corybroo]

The site mentioned by BrainA also allows for a quick graphical comparison of any two countries to get a quick visual sense of how differently they have fared.

[Saul]

1 hour ago, Dean Pomerleau said:

Saul,

Are you sure you're sharp enough to still be teaching :-).

Seriously, I know he died and nowhere did I imply otherwise. Duh.

I asked Gordo if they have any idea how he and/or his family got infected with covid. What isn't clear in your mind about the way I've phrased the question, now for the third time!?

--Dean

Sorry I misquoted the "great Dean".  I'm sure I'm sharp enough to clash horns with the pompous Dean.  Imagine misquoting Dean!

Unlike you, dean, I'm not semi-retired.  I guess you're not sharp enough to continue working.

Dean, covid (especially the delta variety) is extremely contagious -- it's unlikely that Gordo could answer your question.

(I have little doubt that I've been exposed to some form -- probably more than one -- of coronavirus -- and many other pathogens.  But I have an excellent functioning immune system (and also I'm triply vaccinated).  (Probably one of the critical factors is viral load.  I'd guess most of us, especially in urban areas, schools, and other crowded facilities are exposed.)

I have been avoiding other people's breath, from way before coronavirus appeared  -- I always had the opinion that the most dangerous source of human pathogens is other people's breath.  (Number 2 is mosquitos)

That doesn't mean that I avoid social gatherings or supermarkets.  I don't mind crowds, and don't wear a mask (except where I have to -- e.g., when in University buildings, except when teaching).  I simply avoid inhaling other people's breath.

Sorry I irked you,

  --  Saul

 

[Dean Pomerleau]

10 hours ago, Saul said:

Sorry I misquoted the "great Dean".  I'm sure I'm sharp enough to clash horns with the pompous Dean.  Imagine misquoting Dean!

Unlike you, dean, I'm not semi-retired.  I guess you're not sharp enough to continue working.

Aren't you being a little testy Saul? I wasn't irked; I was just amused by how you misinterpreted my question twice and I was just pulling your chain. Did you miss the smiley? 

10 hours ago, Saul said:

I don't mind crowds, and don't wear a mask (except where I have to -- e.g., when in University buildings, except when teaching).  I simply avoid inhaling other people's breath.

Be careful man. Even the original variant was shown to capable of infecting people more than 20 feet away indoors. You are undoubtedly very healthy and skinny, but you are still over 80 putting you at higher risk of a bad outcome. Why take the chance by being so cavalier? 

--Dean 

[Gordo]

Yea, I did not ask his widow too many questions as she was very upset, but it seems to me hardly anyone is wearing masks anymore in our region (myself included). I believe at this point everyone will be exposed, so taking excessive precautions is probably futile although I do agree that viral load is  correlated with  severity of disease and obese people should probably be masking (and fasting) if they want to improve their odds. I saw a guy at Lowes recently wearing full face respirator :

 

[Saul]

Ha ha!

Quite a picture!

Probably about 1/3 of people are wearing masks here -- paradoxically, mostly younger adults. 

Monroe county does have a high infection rate in NYS -- worse than NY city.

Dean is in Pittsburgh, which I think is a slightly bigger city than Rochester.  (But the greater Rochester area probably has a higher per capita average income.)

  --  Saul

Edited September 5, 2021 by Dean Pomerleau
Pittsburg -> Pittsburgh! :-)

[Todd Allen]

3 hours ago, Dean Pomerleau said:

I'm not saying your hypothesis that vaccines are driving the selection of new strains is wrong, but I'm not entirely convinced either.

Here's an article from 2018 discussing the process by which vaccines drive pathogens to evolve.

https://www.quantamagazine.org/how-vaccines-can-drive-pathogens-to-evolve-20180510

Quote

To conquer these diseases, some researchers have been developing immunizations that prevent disease without actually preventing infections — what are called “leaky” vaccines. And these new vaccines may incite a different, and potentially scarier, kind of microbial evolution.

Virulence, as a trait, is directly related to replication: The more pathogens that a person’s body houses, the sicker that person generally becomes. A high replication rate has evolutionary advantages — more microbes in the body lead to more microbes in snot or blood or stool, which gives the microbes more chances to infect others — but it also has costs, as it can kill hosts before they have the chance to pass on their infection. The problem with leaky vaccines, Read says, is that they enable pathogens to replicate unchecked while also protecting hosts from illness and death, thereby removing the costs associated with increased virulence. Over time, then, in a world of leaky vaccinations, a pathogen might evolve to become deadlier to unvaccinated hosts because it can reap the benefits of virulence without the costs — much as Marek’s disease has slowly become more lethal to unvaccinated chickens. This virulence can also cause the vaccine to start failing by causing illness in vaccinated hosts.

 

Edited September 5, 2021 by Todd Allen

[Dean Pomerleau]

8 hours ago, Todd Allen said:

Here's an article from 2018 discussing the process by which vaccines drive pathogens to evolve.

https://www.quantamagazine.org/how-vaccines-can-drive-pathogens-to-evolve-20180510

Thanks Todd. Very interesting article. The last paragraph from the 2018 article was interesting given our situation now:

But the most crucial need right now is for vaccine scientists to recognize the relevance of evolutionary biology to their field. Last month, when more than 1,000 vaccine scientists gathered in Washington, D.C., at the World Vaccine Congress, the issue of vaccine-induced evolution was not the focus of any scientific sessions. Part of the problem, Read says, is that researchers are afraid: They’re nervous to talk about and call attention to potential evolutionary effects because they fear that doing so might fuel more fear and distrust of vaccines by the public — even though the goal is, of course, to ensure long-term vaccine success. Still, he and Kennedy feel researchers are starting to recognize the need to include evolution in the conversation. “I think the scientific community is becoming increasingly aware that vaccine resistance is a real risk,” Kennedy said. “I think so too,” Read agreed, “but there is a long way to go.”

Here is a 2001 article in Nature by the same researcher (Read) taking about the evolution of vaccine resistance, so he has been talking about the potential problem for a long time.

The evidence you've shared shows pretty clearly (at least to me) that "leaky" vaccines can drive virus evolution and I appreciate you pointing it out. I was asking you about the quality of the evidence that vaccines are driving evolution of SARS-CoV-2. To me the evidence so far seems pretty weak if it relies on Israel data alone. But given how mutable SARS-CoV-2 is, it is definitely something to be concerned about and watch for. As I said previously, let's hope the scientists working on multi-target vaccines are successful

Your prediction of trouble ahead due to xaccine-evading variants is duly noted. Unlike with Ron's obviously flawed (even at the time) prediction that Covid deaths would only be in the neighborhood of a bad seasonal flu ywar, I'm not going to take the other side of the bet with you by predicting after this wave of Delta we'll be out of the woods. .i think that your concerns are warranted and well-grounded, but hopefully not inevitable. 

--Dean 

[Dean Pomerleau]

Gordo and Saul, 

I'm genuinely curious about your rationale for not wearing masks in public indoor spaces. My wife doesn't wear a mask anymore when she works out at her gym. I suspect for her it is a combination of peer pressure and it's uncomfortable to work out in a mask. But she does still wear one when going into a store or restaurant. So do I.

Moreover, I go to pretty great lengths to optimize my own health and to avoid harming other sentient beings. I consider wearing a mask at this time to be just another part of that effort.

I think about it like a seatbelt. Will a seatbelt prevent me from getting into a crash? No. Will it prevent 100% of injuries if I do get into a crash? No but they do offer some protection. Am I a careful driver and therefore unlikely to get into a crash? Yes. But I still wear my seatbelt because I consider it a prudent precaution and a relatively small burden.

Plus masks have the added benefit over seat belts of helping protect someone else more vulnerable than me who I might otherwise infect if I happened to have an asymptomatic infection.

Gordo how would you feel if you suspected that you were the one who had infected your friend? Saul you are our shining example of successful CR into one's elder years. It would be tragic not just for you and your family but for all of us if you got an infection and died, leaving us without a good example of how CR can be beneficial for extending healthspan and maybe lifespan.

Do you really find masks to be a significant burden? Do you consider yourself invulnerable since you are thin, relatively young (Gordo), healthy and vaccinated? Are you just sick of taking mitigation steps against covid? Do you think masks are completely ineffective? Is it a political statement you are making by not wearing a mask? Is it simply going with the crowd in your area who are largely going maskless? Or is there some other reason you choose to forgo them in indoor public spaces where they are optional?

Just curious. 

--Dean 

[Saul]

Hi Dean!

I'm vaccinated, and in the CDC's "mix and match" trial.  So, I've had my two shots of the Pfizer vaccine, and ("Mix and Match") one shot of the Moderna.  My physical age is in the 80's, but I believe my biological age is much younger -- as is probably true of most of us who are practicing serious calorie restriction.

Masks are a burden on breathing -- not good for "pranayama".

You can shroud your face in a mask, if you want to.  But I think it's presumptuous of you to preach to Gordo and me, with your prejudices.

  --  Saul

[Dean Pomerleau]

Pranayama. OK then that explains it. Best of luck Saul. 

--Dean 

[Saul]

😉

[Dean Pomerleau]

Here is a really interesting article (you may need to provide email address to read it - I used a temporary email address generator) about what is known regarding infection-acquired immunity vs vaccine-acquired immunity against different variants. Here are some highlights:

While the Israeli study [which we discussed before] indicates that infection by the original strain seems to protect against Delta, which originated in India, there have been more reinfections associated with strains originating out of South Africa and Brazil.

In the P.1 strain originating in Brazil, one study found antibody effectiveness six times weaker against the P.1 in comparison with the original SARS-CoV-2 strains. That study estimated that 25% to 61% of previously infected patients were susceptible to P.1 infection.

Similar issues have been found with the South African variant, also known as B.1.351. A vaccine trial for Novavax found that participants in the control group who were previously infected were just as likely to become ill with B.1.351 as those without natural antibodies, suggesting older strains of COVID-19 failed to provide immunity against B.1.351. By comparison, the vaccine did offer some protection.

...

“Our study shows that prior exposure to SARS-CoV-2 does not guarantee a high level of antibodies, nor does it guarantee a robust antibody response to the first vaccine dose. For people who had mild or asymptomatic infections, their antibody response to vaccination is essentially the same as it is for people who have not been previously exposed.”

...

Colorado fitness coach Bill Phillips has been an outspoken advocate for vaccination after infection after he spent two months in the hospital during his second bout with COVID-19.

Phillips, 56, decided not to get vaccinated, figuring he was in top physical condition and had antibodies that indicated a previous infection. But he caught COVID-19 again in June, ended up on a ventilator and almost died. He recently left the hospital, and is in rehab, and a wheelchair and supplemental oxygen.

“It didn’t help that I could bench press 300 pounds or run a mile straight up a hill,” Phillips told KUSA-TV in Denver. “I made a mistake. That mistake came that close to costing me my life.”

--Dean

[Todd Allen]

18 hours ago, Dean Pomerleau said:

Here is a 2001 article in Nature by the same researcher (Read) taking about the evolution of vaccine resistance, so he has been talking about the potential problem for a long time.

And still is.  Here's an editorial he wrote last week I expect you will like a lot.  I agree with most of the details but feel it falls short as it fails to address a couple crucial issues.

Vaccines could affect how the coronavirus evolves - but that’s no reason to skip your shot

[Dean Pomerleau]

Thanks Todd, 

I didn't realize Read's work had been mentioned on the Joe Rogan's show. Big time! 

Here are sections from Read's latest article you shared that summarize his position on vaccines driving SARS-CoV-2 evolution:

Evolutionary hypotheticals are important to consider. But up against the hugely beneficial impact of COVID-19 vaccines on reducing transmission and disease severity – even against the delta variant – the possibility of silent spread of more lethal variants among the vaccinated is still no argument against vaccination.

As novel variants of the coronavirus spread in the months and years ahead, it will be vital to work out whether their evolutionary advantage is arising because of reduced disease severity among the vaccinated. Delta, for instance, transmits more effectively from both unvaccinated and vaccinated people than did earlier variants. Extrapolating from our chicken work to argue against vaccination because of the delta variant has no scientific rationale: The delta variant would have become dominant even if everyone refused vaccination.

... 

Sacrificing chickens was not the solution the poultry industry adopted for Marek’s disease virus. Instead, more potent vaccines were developed. Those newer vaccines provided excellent disease control, and no lethal breakthrough variants of Marek’s have emerged in over 20 years.

There are probably ways the available COVID-19 vaccines could be improved in the future to better reduce transmission. Booster shots, larger doses or different intervals between doses might help; so too, combinations of existing vaccines. Researchers are working hard on these questions. Next-generation vaccines might be even better at blocking transmission. Nasal vaccines, for instance, might effectively curtail transmission because they more specifically target the location of transmissible virus.

As of late August 2021, more than 625,000 Americans have died from a disease that is now largely vaccine-preventable. It is sobering for me to think that some of the next to die might have avoided lifesaving vaccines because people are stoking evolutionary fears extrapolated from our research in chickens.

In the history of human and animal vaccines, there have not been many cases of vaccine-driven evolution. But in every one of them, individuals and populations have always been better off when vaccinated. At every point in the 50-year history of vaccination against Marek’s disease, an individual chicken exposed to the virus was healthier if it was vaccinated. Variants may have reduced the benefit of vaccination, but they never eliminated the benefit. Evolution is no reason to avoid vaccination.

So Read thinks leaky vaccine-driven evolution of SARS-CoV-2 is something to watch out for but the virus would be mutating to escape natural immunity without vaccines regardless so viral evolution is not a reason to eschew the widespread use of the current vaccines to save lives. Instead it is a reason to continue developing more effective vaccines. It is the arms race between humans and the virus that I mentioned last week. 

8 hours ago, Todd Allen said:

... but feel it falls short as it fails to address a couple crucial issues.

I'd very much like to hear your thoughts on those crucial issues. Is it the timing issue you are worried about? ie widespread vaccinations will accelerate selection pressure and thereby potentially make more virulent strain dominate more quickly, possibly before scientists have time to develop better vaccines to combat them? 

--Dean 

[Saul]

Of course, I agree with Dean.

  --  Saul

[Mike41]

https://www.washingtonpost.com/politics/covid-how-will-it-end/2021/09/04/44bdd69a-fed7-11eb-a664-4f6de3e17ff0_story.html
 

 

Is “IT” going to end very soon or no???

So sorry the link won’t work unless your a subscriber. Bottom line some epidemiologists claim like all pandemics this one is coming to an end due to the numbers of cases and vaccines. By mid October one influential epidemiologist claims.

Others claim that the politics on both sides is unfortunate. The anti vaccers and the fear mongerers.

 

 

 

Edited September 6, 2021 by Mike41

[Mike41]

38 minutes ago, Saul said:

Of course, I agree with Dean.

  --  Saul

I too agree with Dean.