Coronavirus

[GO-NAD!]

I'm pretty pissed off too. We've been patiently waiting for over a year to visit our daughter in Halifax and crap like his happens. At least we both get our first shot on Monday finally. Vaccinations are going to be the end game in opening up the borders again. No sense visiting for 2 weeks if we have to spend the entire 2 weeks in isolation.

I understand your frustration. Over the last couple of days, as we would say in Newfoundland, "the arse has gone right out of 'er". We had 52 new cases yesterday and 63 more today.

The premier also announced that since the $1000 fine for exceeding private gathering limits (maximum of 5) doesn't appear to be a sufficient deterent, he has doubled it.

 

[TLS Guy]

We are now seeing progress against Covid-19, especially in the US, UK and Israel.

However uncontrolled spread in much of the world presents a looming and worrying threat. The virus is totally out of control on the Indian subcontinent, with an absolutely horrific humanitarian catastrophe unfolding. Things remain serious in Iran and now Iraq. Japan, and especially in Tokyo are right on the brink. Parts of Europe remain in trouble, with Germany again going into lockdown.

As has been stated before, uncontrolled spread in any part of the world is a grave threat to us all.

The risks are hard to quantify. The worries are increased rates of transmission and increased pathogenicity. However the greatest is vaccine resistance and also escape from natural immunity.

Unfortunately the risks are hard to quantify and there is sparse hard data.

There is a paper in the BMJ, involving bench studies of neutralizing antibodies, on variants. The good news is that all variants except B.1.351 which originated in South Africa still seem highly susceptible to both natural and vaccine induced neutralizing antibodies. B.1.351 seems to have pretty much total escape. However this shows the limitation of this type of bench test, as we know from real world data that immune escape is far from totally lost. The answer lies in the T-cell response.

India is now producing double and triple mutants, with highly significant changes to the S-spike antigen. There is no reliable real world data that I can find, showing the impact on immunity. The fire is out of control in India, and so data is going to be hard to come by. Medical services are totally overrun. Although they have put vaccine in millions of arms, the population is 1.7 billion, and so only a very small percentage of the population are immunized. This makes it very hard to study immune escape.

My worry is that these "fires" are going to breed dangerous and problematic variants, that could send us back to the beginning and worse. I am really appalled at the lack of a coordinated world response to this.

This crisis is more likely than not, far from over.

On a personal note my wife and I became exposed on Friday. We are nearly six weeks post our second dose of the Moderna vaccine.

Our 17 year old grandson is on a sports team, and so is tested once a week by PCR. He received his first dose of the Pfizer vaccine about two weeks ago.

He was round here on Friday for a cooking lesson. We ate the fruits of the lesson that evening. After supper we watched a movie with him in the theater.

When he returned home, he found a message on his computer, informing him his test of the day before was positive for Covid-19. He was, and is well, and so is an asymptomatic spreader. He is isolating. We are following CDC guideline for the 10 days following exposure. My wife, who renewed her licenses in the spring has been a volunteer vaccine administrator and was scheduled for three days this week, and has now been cancelled for this week.

I think it was grave mistake to restart school sports activities. Rise in Minnesota cases especially the UK variant, has been very much driven by sports activities. Many teams have now become infected.

 

[GO-NAD!]

I understand your frustration. Over the last couple of days, as we would say in Newfoundland, "the arse has gone right out of 'er". We had 52 new cases yesterday and 63 more today.

The premier also announced that since the $1000 fine for exceeding private gathering limits (maximum of 5) doesn't appear to be a sufficient deterent, he has doubled it.

Another 66 today. So disheartening...

 

[Mr._Clark]

According to this news report about a MIT study, the 6 foot rule for indoor spaces makes very little difference. I have not read the entire paper, but I'm taking it with a grain of salt because it assumes that an indoor space will be well-mixed. On the other hand, there might be some truth to it.


>>>The widely used rule of staying 6 feet away from others does little to affect the risk of exposure to COVID-19 in indoor spaces, according to a new study out of MIT. . . .
A website made available by the researchers shows how this model works in different scenarios.

For example, if an infected person walks into a classroom hosting 25 people, none wearing masks and all speaking, everyone would be at risk from the coronavirus within 36 minutes, the website says. It doesn't matter if they follow the 6-foot rule.

By contrast, if all 25 people in that room were wearing a mask, the air would be safe to breathe for 20 hours, it said.

If they were all singing without a mask, they be at risk from the virus within three minutes.<<<


https://www.yahoo.com/news/staying-6-feet-apart-indoors-112732760.html


>>>The Well-Mixed Room
We first characterize the evolution of the pathogen concentration in a well-mixed room. The assumption of well mixedness is widely applied in the theoretical modeling of indoor airborne transmission (14, 16, 17), and its range of validity is discussed in SI Appendix, section 1.<<<

A guideline to limit indoor airborne transmission of COVID-19

Airborne transmission arises through the inhalation of aerosol droplets exhaled by an infected person and is now thought to be the primary transmission route of COVID-19. By assuming that the respiratory droplets are mixed uniformly through an indoor space, we derive a simple safety guideline...

www.pnas.org

 

[GO-NAD!]

According to this news report about a MIT study, the 6 foot rule for indoor spaces makes very little difference. I have not read the entire paper, but I'm taking it with a grain of salt because it assumes that an indoor space will be well-mixed. On the other hand, there might be some truth to it.


>>>The widely used rule of staying 6 feet away from others does little to affect the risk of exposure to COVID-19 in indoor spaces, according to a new study out of MIT. . . .
A website made available by the researchers shows how this model works in different scenarios.

For example, if an infected person walks into a classroom hosting 25 people, none wearing masks and all speaking, everyone would be at risk from the coronavirus within 36 minutes, the website says. It doesn't matter if they follow the 6-foot rule.

By contrast, if all 25 people in that room were wearing a mask, the air would be safe to breathe for 20 hours, it said.

If they were all singing without a mask, they be at risk from the virus within three minutes.<<<


https://www.yahoo.com/news/staying-6-feet-apart-indoors-112732760.html


>>>The Well-Mixed Room
We first characterize the evolution of the pathogen concentration in a well-mixed room. The assumption of well mixedness is widely applied in the theoretical modeling of indoor airborne transmission (14, 16, 17), and its range of validity is discussed in SI Appendix, section 1.<<<

A guideline to limit indoor airborne transmission of COVID-19

Airborne transmission arises through the inhalation of aerosol droplets exhaled by an infected person and is now thought to be the primary transmission route of COVID-19. By assuming that the respiratory droplets are mixed uniformly through an indoor space, we derive a simple safety guideline...

www.pnas.org

I keep hearing the recommendation to have good ventilation in indoor spaces to reduce possibility of transmission. However, I've yet to hear anyone define what constitutes "good" ventilation. There must be some supporting data, otherwise how can the recommendation be made? I just haven't seen or heard anything useful. Open windows might or might not be an efficient form of air exchange, but there are so many possible variables, that this method can't be relied upon. Is a modern construction home with an air exchanger sufficiently ventilated? I haven't heard anyone say.

 

[Speedskater]

There are books on 'building health'.
There are meters to measure air turn-over. But they take skill to interpret.

I would go with inspection. Number of people and how long are they there? Cubic volume room. Best guess about HVAC.

 

[Mr._Clark]

I keep hearing the recommendation to have good ventilation in indoor spaces to reduce possibility of transmission. However, I've yet to hear anyone define what constitutes "good" ventilation. There must be some supporting data, otherwise how can the recommendation be made? I just haven't seen or heard anything useful. Open windows might or might not be an efficient form of air exchange, but there are so many possible variables, that this method can't be relied upon. Is a modern construction home with an air exchanger sufficiently ventilated? I haven't heard anyone say.

There does seem to be a dearth of detailed information. It appears to me that circulation is better than stagnant air if the air is filtered or replaced with fresh air, but stagnant air is actually better than recirculating air without filtration.

The CDC has some basic guidance, but it seems like many businesses haven't really done much. I went to a small barber shop a while ago and they had the door closed even though the weather was nice. If nothing else, common sense suggests that replacing as much of the air as possible should help.

Improving Ventilation in Your Home

Ways to improve ventilation in your home.

www.cdc.gov

>>>Do open windows really make a difference?
Shaun Fitzgerald is convinced they do, and he has made it a personal mission to improve ventilation wherever he can.
He is a Royal Academy of Engineering professor at Cambridge University, but that doesn't stop him from "trying to wrench open windows that have been painted shut or haven't been maintained for years". . . . According to Dr Fitzgerald, the research shows that bringing in a good supply of fresh air to dilute and disperse the virus can cut the risk of infection by 70-80%.<<<

Coronavirus: Fresh air 'forgotten weapon' in fight

Experts are increasingly worried that the virus can accumulate in stuffy rooms.

www.bbc.com

 

[Mr._Clark]

I ran across an article (1st link below) discussing a paper (2nd link below) showing that the natural immune response in COVID patients is significantly different than the immune response from vaccines. However (paging @Swerd or @TLS Guy ) I don't really understand the following, or the significance of it:

>>>While both infection and vaccination induced robust innate and adaptive immune responses, our analysis revealed significant qualitative differences between the two types of immune challenges. In COVID-19 patients, immune responses were characterized by a highly augmented interferon response which was largely absent in vaccine recipients. Increased interferon signaling likely contributed to the observed dramatic upregulation of cytotoxic genes in the peripheral T cells and innate-like lymphocytes in patients but not in immunized subjects. Analysis of B and T cell receptor repertoires revealed that while the majority of clonal B and T cells in COVID-19 patients were effector cells, in vaccine recipients clonally expanded cells were primarily circulating memory cells. Importantly, the divergence in immune subsets engaged, the transcriptional differences in key immune populations, and the differences in maturation of adaptive immune cells revealed by our analysis have far-ranging implications for immunity to this novel pathogen.<<<

Striking difference identified between mRNA vaccination vs. SARS-CoV-2 infection immune responses

A team of scientists from the United States has recently compared the immune response elicited by natural severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) vaccination. Their findings reveal that, unlike vaccination, natural SARS-CoV-2...

www.news-medical.net

Discrete immune response signature to SARS-CoV-2 mRNA vaccination versus infection

Both SARS-CoV-2 infection and vaccination elicit potent immune responses. A number of studies have described immune responses to SARS-CoV-2 infection. However, beyond antibody production, immune responses to COVID-19 vaccines remain largely uncharacterized. Here, we performed multimodal...

www.medrxiv.org

 

[TLS Guy]

I ran across an article (1st link below) discussing a paper (2nd link below) showing that the natural immune response in COVID patients is significantly different than the immune response from vaccines. However (paging @Swerd or @TLS Guy ) I don't really understand the following, or the significance of it:

>>>While both infection and vaccination induced robust innate and adaptive immune responses, our analysis revealed significant qualitative differences between the two types of immune challenges. In COVID-19 patients, immune responses were characterized by a highly augmented interferon response which was largely absent in vaccine recipients. Increased interferon signaling likely contributed to the observed dramatic upregulation of cytotoxic genes in the peripheral T cells and innate-like lymphocytes in patients but not in immunized subjects. Analysis of B and T cell receptor repertoires revealed that while the majority of clonal B and T cells in COVID-19 patients were effector cells, in vaccine recipients clonally expanded cells were primarily circulating memory cells. Importantly, the divergence in immune subsets engaged, the transcriptional differences in key immune populations, and the differences in maturation of adaptive immune cells revealed by our analysis have far-ranging implications for immunity to this novel pathogen.<<<

Striking difference identified between mRNA vaccination vs. SARS-CoV-2 infection immune responses

A team of scientists from the United States has recently compared the immune response elicited by natural severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) vaccination. Their findings reveal that, unlike vaccination, natural SARS-CoV-2...

www.news-medical.net

Discrete immune response signature to SARS-CoV-2 mRNA vaccination versus infection

Both SARS-CoV-2 infection and vaccination elicit potent immune responses. A number of studies have described immune responses to SARS-CoV-2 infection. However, beyond antibody production, immune responses to COVID-19 vaccines remain largely uncharacterized. Here, we performed multimodal...

www.medrxiv.org

What you say is true. It is not clearly understood why vaccine immunity is better than natural infection. One reason my be is that the antigens are produced by the body in large quantities, and the infecting dose of antigen would be lower. Also in the vaccine response the host is healthy, in infections the host is weakened and sick.

Air exchange is important. I have an ERV in this house and I have it set to exchange air once an hour. However I can up it to an exchange every 20 minutes, which I did if we had to let someone in the house during covid.

It is thought that an exchange every 20 minutes reduces infectious spread enormously. In addition it has been known since the work of Sir John Charnley working on hip replacements in the fifties, that negative pressure ventilation is far superior to the usual forced air ventilation. That is why operating rooms have had negative pressure laminar flow ventilation for years. I have long thought that the life of Sir John Charnley is well worth a movie or dramatized TV series. He was a very great man on many levels.

So in terms of pandemic preparedness, air exchange and negative pressure ventilation, have a pivotal role to play. As Dr Mike Osterholm has shouting for a long time: -
"We need to stop sharing air!"

 

[haraldo]

We are now seeing progress against Covid-19, especially in the US, UK and Israel.

However uncontrolled spread in much of the world presents a looming and worrying threat. The virus is totally out of control on the Indian subcontinent, with an absolutely horrific humanitarian catastrophe unfolding. Things remain serious in Iran and now Iraq. Japan, and especially in Tokyo are right on the brink. Parts of Europe remain in trouble, with Germany again going into lockdown.

As has been stated before, uncontrolled spread in any part of the world is a grave threat to us all.

The risks are hard to quantify. The worries are increased rates of transmission and increased pathogenicity. However the greatest is vaccine resistance and also escape from natural immunity.

Unfortunately the risks are hard to quantify and there is sparse hard data.

There is a paper in the BMJ, involving bench studies of neutralizing antibodies, on variants. The good news is that all variants except B.1.351 which originated in South Africa still seem highly susceptible to both natural and vaccine induced neutralizing antibodies. B.1.351 seems to have pretty much total escape. However this shows the limitation of this type of bench test, as we know from real world data that immune escape is far from totally lost. The answer lies in the T-cell response.

India is now producing double and triple mutants, with highly significant changes to the S-spike antigen. There is no reliable real world data that I can find, showing the impact on immunity. The fire is out of control in India, and so data is going to be hard to come by. Medical services are totally overrun. Although they have put vaccine in millions of arms, the population is 1.7 billion, and so only a very small percentage of the population are immunized. This makes it very hard to study immune escape.

My worry is that these "fires" are going to breed dangerous and problematic variants, that could send us back to the beginning and worse. I am really appalled at the lack of a coordinated world response to this.

This crisis is more likely than not, far from over.

On a personal note my wife and I became exposed on Friday. We are nearly six weeks post our second dose of the Moderna vaccine.

Our 17 year old grandson is on a sports team, and so is tested once a week by PCR. He received his first dose of the Pfizer vaccine about two weeks ago.

He was round here on Friday for a cooking lesson. We ate the fruits of the lesson that evening. After supper we watched a movie with him in the theater.

When he returned home, he found a message on his computer, informing him his test of the day before was positive for Covid-19. He was, and is well, and so is an asymptomatic spreader. He is isolating. We are following CDC guideline for the 10 days following exposure. My wife, who renewed her licenses in the spring has been a volunteer vaccine administrator and was scheduled for three days this week, and has now been cancelled for this week.

I think it was grave mistake to restart school sports activities. Rise in Minnesota cases especially the UK variant, has been very much driven by sports activities. Many teams have now become infected.

take care my friends, all the best for you and your family.... these are really unprecedented times ...,. Although, in Norway we been pretty ”lucky” so far, we haven’t seen these insane fatality rates....

somehow fatality rate in Norway at some of the worst points in time was less than 1/8th what it was in UK and I dare to see what is the difference, other than we are very lucky over here

but it’s really worrying that a possible third insane wave can roll over the world once more, the real scary part would be a mutation immune to the current vaccines

we can only praise ourselves lucky as long as we are fine, take care

 

[Swerd]

@Mr._Clark – I quickly read the Introduction and Discussion sections of that paper.

https://www.medrxiv.org/content/10.1101/2021.04.20.21255677v1.full.pdf

While the paper may not be bad, it isn't clear from reading it just what the main take-home message is. It may lead to some significant discoveries, or it may be just a overview from high altitude that attempts to catalog and summarize how the immune system responds during the first several weeks after virus infection vs. after vaccination. In my opinion, it was an overview from too high an altitude. Time will tell. Too bad the authors couldn't tell us.

The most important thing to remember is this:

Infection with SARS-CoV-2, and vaccination against the virus have both been shown to stimulate immune responses and protect against subsequent infection.

Nothing in the paper suggests that one path results in better immunization than the other. Keep that in mind.

In this study, we performed a highly granular, multimodal analysis of samples from COVID-19 patients and from healthy volunteers before and after receiving the SARS-CoV-2 BNT162b2 mRNA vaccine. While both infection and immunization elicit robust humoral responses, our analysis revealed dramatic differences in cell composition and transcriptional profiles of circulating immune cells in response to the two different immune challenges.

I would translate this as follows:
The emergence of a new and dangerous viral disease has provided a truck-load of research money. Here, some scientists have used all their expensive and cool molecular biology tools to examine – for the first time – what happens during the first several weeks after virus infection and after vaccination (with Pfizer’s mRNA vaccine).

However, one major difference I saw in the paper was that virus infection – but not vaccination – resulted in heavy-duty interferon (IFN) responses:

High levels of IFN protein, IFN signaling gene products, and IFN response gene products in various cell types, indicates very high levels of inflammation. No big surprise there. Severe, even life threatening inflammation has been clinically observed for over a year in Covid-19 patients. The most interesting finding is that it was absent in vaccinated people. Achieving immunity against corona virus, while avoiding severe inflammation, is a very strong argument for getting vaccinated instead of relying on naturally occurring immunity while recovering from Covid-19. Again, no big surprise there. (Unless you watch only Faux News.)

 

[GO-NAD!]

There does seem to be a dearth of detailed information. It appears to me that circulation is better than stagnant air if the air is filtered or replaced with fresh air, but stagnant air is actually better than recirculating air without filtration.

The CDC has some basic guidance, but it seems like many businesses haven't really done much. I went to a small barber shop a while ago and they had the door closed even though the weather was nice. If nothing else, common sense suggests that replacing as much of the air as possible should help.

Improving Ventilation in Your Home

Ways to improve ventilation in your home.

www.cdc.gov

>>>Do open windows really make a difference?
Shaun Fitzgerald is convinced they do, and he has made it a personal mission to improve ventilation wherever he can.
He is a Royal Academy of Engineering professor at Cambridge University, but that doesn't stop him from "trying to wrench open windows that have been painted shut or haven't been maintained for years". . . . According to Dr Fitzgerald, the research shows that bringing in a good supply of fresh air to dilute and disperse the virus can cut the risk of infection by 70-80%.<<<

Coronavirus: Fresh air 'forgotten weapon' in fight

Experts are increasingly worried that the virus can accumulate in stuffy rooms.

www.bbc.com

Thanks for the links. I'm less concerned about the home environment - which I have more control over - than I am about public buildings. One can never be certain that any particular office building, restaurant or retail establishment has adequate ventilation. That said, my family has kept visits to such buildings to a minimum over the past year. Right now, because of the recent massive increase (relative to us) in cases means we'll be restricting that even further.

 

[Mr._Clark]

Thanks for the links. I'm less concerned about the home environment - which I have more control over - than I am about public buildings. One can never be certain that any particular office building, restaurant or retail establishment has adequate ventilation. That said, my family has kept visits to such buildings to a minimum over the past year. Right now, because of the recent massive increase (relative to us) in cases means we'll be restricting that even further.

Yeah, not knowing what HVAC system is being used in any given public place is a problem.

Now that I've had both jabs I'm not quite as concerned about it, but I still mask up with an N95 mask when going into public buildings. I'll be glad when the local case counts go down.

 

[Mr._Clark]

Good grief, just when I thought I'd heard it all, there's this:

>>>A private school in the fashionable Design District of Miami sent its faculty and staff a letter last week about getting vaccinated against Covid-19. But unlike institutions that have encouraged and even facilitated vaccination for teachers, the school, Centner Academy, did the opposite: One of its co-founders, Leila Centner, informed employees “with a very heavy heart” that if they chose to get a shot, they would have to stay away from students.<<<

A private school in Miami, citing false claims, bars vaccinated teachers from contact with students. (Published 2021)

Centner Academy advertises its support for “medical freedom from mandated vaccines,” and has recently hosted talks by antivaccine advocates.

www.nytimes.com

 

[Kvn_Walker]

Good grief, just when I thought I'd heard it all, there's this:

>>>A private school in the fashionable Design District of Miami sent its faculty and staff a letter last week about getting vaccinated against Covid-19. But unlike institutions that have encouraged and even facilitated vaccination for teachers, the school, Centner Academy, did the opposite: One of its co-founders, Leila Centner, informed employees “with a very heavy heart” that if they chose to get a shot, they would have to stay away from students.<<<

A private school in Miami, citing false claims, bars vaccinated teachers from contact with students. (Published 2021)

Centner Academy advertises its support for “medical freedom from mandated vaccines,” and has recently hosted talks by antivaccine advocates.

www.nytimes.com

You can't vaccinate against stupid.

 

[Irvrobinson]

You can't vaccinate against stupid.

Yes you can. It’s called education.

 

[panteragstk]

Yes you can. It’s called education.

 

[Kvn_Walker]

Yes you can. It’s called education.

Good luck with that. There are a lot of highly educated idiots out there.

 

[Mr._Clark]

Good luck with that. There are a lot of highly educated idiots out there.

Darwin: "I've got this."

 

[Mr._Clark]

The NY Times has an interesting article about how the Pfizer vaccine is manufactured:

How Pfizer Makes Its Covid-19 Vaccine (Published 2021)

Behind the scenes from starter cells to a finished vaccine.

www.nytimes.com