Coronavirus

[Swerd]

Here's a paper that may be more to your liking. As I understand it, the study (albeit involving a small number of patients) shows a correlation between a large numbers of T cells early in an infection and mild disease and the opposite with regards to neutralizing antibodies. It's interesting that one patient did not test positive for neutralizing antibodies but nevertheless cleared the virus, whereas two patients with high levels of neutralizing antibodies early in the infection had severe disease (one died).

Very interesting. I like it. This paper from Tan et al in Singapore is consistent with the results reported by Tarke et al. in San Diego.

https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1.full.pdf?fbclid=IwAR1WjabAAL3Fw1L34Nxp60iNFuJ82Fre9Bs4ywFFnchMZMdSo9kUWASVzHE

The group in San Diego looked at T-cells from patients who recovered from Covid-19 as well as from people immunized with either of the two mRNA vaccines. The group in Singapore looked at T-cells from twelve Covid-19 patients during the course of their disease, from symptom onset to convalescence or death. They analyzed the viral load in the upper respiratory tract, virus specific antibodies, and virus specific T-cells at multiple time points. They found a direct association between the early induction of virus specific T-cells and the rapid control of the virus infection. The figure below is copied from the graphical abstract of the Singapore group's paper.

I must emphasize how much work was done for this paper. They collected blood at multiple time points from 12 sick patients to analyze the levels of functional virus-specific T-cells and virus-specific antibodies. The antibody work is relatively easy to do. Blood can be collected and the cell-free portion, the plasma, can be frozen and stored for later analysis. Antibody titers (as this type of analysis is called) can be scaled up to large numbers of individual samples.

In contrast the T-cell work is much harder to do. T-cells must be partially purified from freshly collected blood, and analyzed as soon as possible before too many of the cells die. Each patient time point makes for a very long day in the lab. Multiple samples were collected from each patient. That was an impressive amount of work even if 12 patients seems like a small number. It was probably all they could manage.

Note: The term 'humoral responses' is shorthand for the immunologic response of producing antibodies circulating in the blood. See the example below from the paper:

Although rapid induction and quantity of humoral responses associate with an increase in disease severity, early induction of interferon (IFN)-γ-secreting SARS-CoV-2-specific T cells is present in patients with mild disease and accelerated viral clearance …

 

[Mr._Clark]

I have not found a link to the study yet so this looks like "science by press release" at the moment. Still, it's better than nothing.

>>>Eli Lilly and Co said on Wednesday that its combination antibody therapy to fight COVID-19 reduced the risk of hospitalization and death by 87% in a study of more than 750 high-risk COVID-19 patients.<<<

Eli Lilly's combo therapy for COVID-19 cuts serious illness and death in large study

Eli Lilly and Co said on Wednesday that its combination antibody therapy to fight COVID-19 reduced the risk of hospitalization and death by 87% in a study of more than 750 high-risk COVID-19 patients.

www.reuters.com

 

[Mr._Clark]

Another article from Reuters is not so encouraging.

>>>In a study that compared death rates among people in Britain infected with the new SARS-CoV-2 variant - known as B.1.1.7 - against those infected with other variants of the COVID-19-causing virus, scientists said the new variant’s mortality rate was “significantly higher”. . . .

In the UK study, published in the British Medical Journal on Wednesday, infection with the new variant led to 227 deaths in a sample of 54,906 COVID-19 patients, compared with 141 among the same number of patients infected with other variants.

“Coupled with its ability to spread rapidly, this makes B.1.1.7 a threat that should be taken seriously,” said Robert Challen, a researcher at Exeter University who co-led the research.<<<

UK COVID-19 variant has significantly higher death rate, study finds

A highly infectious variant of COVID-19 that has spread around the world since it was first discovered in Britain late last year is between 30% and 100% more deadly than previous dominant variants, researchers said on Wednesday.

www.reuters.com

I seem to recall reading quite a few blurbs earlier downplaying the variant. I realize there was not a lot of evidence early on, but I'm not sure what the basis was for statements such as the following:

>>>[Dr Soumya Swaminathan] And scientists have now studied this and have found that these variants do tend to spread faster, they're more transmissible or more infectious. So that's the worrying part. However, so far, they do not seem to cause more severe illness or a higher death rate or any sort of different clinical manifestations.

They seem to behave pretty much as the previous viruses were behaving and cause a pretty similar kind of disease.<<< (emphasis added)

Episode #20 - COVID-19 - Variants & Vaccines

How concerned should we be about the new variants of SARS CoV 2 which cause COVID-19? Is it unusual for viruses to change and mutate? Do vaccines protect against these variants and what can you do to protect yourself? WHO’s Chief Scientist Dr Soumya Swaminathan explains in Science in 5

www.who.int

Not everyone was downplaying it, of course.

>>>The increased transmissibility of the British variant has been accepted by scientists for some time. But British Prime Minister Boris Johnson said in a televised news conference that it could also be more deadly.

“We have been informed today that, in addition to spreading more quickly, it also now appears that there is some evidence that the new variant—the variant that was first identified in London and the southeast—may be associated with a higher degree of mortality,” said Mr. Johnson.

The government’s chief scientific adviser, Patrick Vallance, cautioned that the data about the death rates associated with the variant were still highly uncertain.<<<

U.K. Covid-19 Variant Could Be More Deadly, British Officials Say

Prime Minister Boris Johnson said the variant—which has caused Covid-19 infections across the U.K. to spike and is spreading rapidly in the U.S.—could result in higher death rates. The conclusions are still highly uncertain.

www.wsj.com

 

[cpp]

Speaking of the variant > Florida has the highest estimated concentration of cases of the B.1.1.7 variant in the US.
In recent days, more than 30% of Covid-19 samples from Florida indicate the presence of the contagious mutation that has caused havoc in the U.K We can thank our tourist for that and open travel. And now with Bike Week in full mode in Daytona and the start of Spring Break and warm weather, watch out !

 

[Swerd]

>>>Eli Lilly and Co said on Wednesday that its combination antibody therapy to fight COVID-19 reduced the risk of hospitalization and death by 87% in a study of more than 750 high-risk COVID-19 patients.<<<

At this point, I think there is enough evidence to say that the predominant immune system response against SARS-CoV-2 infection is T-cell based. This has been directly observed in both vaccinated people and in non-vaccinated people who had Covid-19 disease. In that Singapore study, those patients who quickly developed a T-cell response had good prognoses, and those patients who didn't, but did develop antibody responses, had worse prognoses. The San Diego group showed that recovered Covid-19 patients and vaccinated people both had similar looking T-cell immune responses. As time goes by, we'll see more studies of what kind of immune responses can be found as immune memory.

The Eli Lilly press release of clinical trial results showed that flooding the field with antibodies can work. That may be useful, even life saving, for Covid-19 patients who appear to have bad prognoses. But it doesn't seem to resemble the naturally occurring response where T-cell responses predominated over antibody responses.

Of course, the Eli Lilly clinical trial had nothing to say about patients' T-cell responses. But that raises an interesting question. In those patients who recovered from Covid-19 after getting IV infusions of those monoclonal antibodies, what kind(s) of long-lasting immunity can be found?

 

[TLS Guy]

Mr_Clark's articles confirm real world data from the UK, that the Pfizer and Oxford vaccines seem to be equally effective against mutant strains. The SA government wrongly stopped using the Oxford vaccine based on in vitro antibody studies. That was a serious mistake.

The US is now actively considering spacing vaccine doses further apart. This is important as the UK variant is spreading fast. Good accurate data from the UK today, shows that the UK variant is not only 74% more infectious, but the case fatality rate is increased 64%. Taken together that is very bad news, and makes the case that people should get first doses as soon as possible and get the extra 10% immunity at a later time.
I expect changed CDC guidelines shortly on this.

This may also turn out to be good news from Emory University. It is far too soon to tell.

A single pill of the investigational drug molnupiravir taken twice a day for 5 days eliminated SARS-CoV-2 from the nasopharynx of 49 participants.

However eliminating virus from the nasopharynx is one thing. Showing it alters the course of disease quite another.

Over all preliminary results from vaccinations in the UK and Israel are spectacular. It is too soon to judge the effect in the US. The irresponsible actions of many governors is going to really slow progress here and delay the results they want. It will significantly slow progress to defeat the disease, cost lives and more money. The effect of their actions will be the exact opposite of the results they, and we all desire, and harm the whole population. I wish there was a way the President could reverse their irresponsible actions.

Meanwhile here in Minnesota we have reported 14 breakthrough cases of Covid-19 more than 14 days after their second immunization. All the cases have been asymptomatic or mild. Most have been in health care workers. It seems to me this is likely from increased surveillance.

So on balance a very encouraging picture is emerging, which would be better if it were not for some very stupid governors.

 

[TLS Guy]

Changing gears, it seems Adar Poonwalla received his education in my home county, Kent. There was an article about this in Kent Online.
He attended St. Edmonds School in Canterbury.

The serum institute is now producing the Oxford vaccine at a rate of 5000 doses a minute. In India the vaccine is called Covishield and so will not show up in the AstraZeneca data. It is the same vaccine.

This shows the reach of the Oxford vaccine round the world compared to the others.

Top row: - left to right is Oxford vaccine Pfixer/Biontec

Middle row: - Moderna and the the Chinese vaccines, Sinopharm - Sinovac - San Casino.

Bottom row: - Sputnik 5 Green lines Vector institute yellow. Johnson and Johnson light blue, Baharat Biotec, an Indian vaccine that their medical community do not trust.

The Pune serum institute plant is and will dominate other vaccines world wide, especially when their new second factory come on line. This was destroyed by fire while under construction back in January. Rebuild is under way.

The new novel production facility in the UK at Oxford should come on line on three or four months. This should be able to produce new novel vaccines at speed as well as produce both mRNA and mDNA platforms as well as produce any new novel vaccines at speed.

I think this will turn out to be India's moment. I think their success will encourage massive new investment in India as a world beating high tech hub. I expect them to be a much better and more reliable partner than China.

 

[Irvrobinson]

Weird how this possible AZ vaccine side effect has shown up most prominently in Denmark:

Oxford-AstraZeneca: EU says 'no indication' vaccine linked to clots

The EU's medicines regulator reassures states after several countries suspended use of the vaccine.

www.bbc.com

Denmark, Norway and Iceland suspend use of AstraZeneca Covid vaccine over reports of blood clots

"It is important to emphasize that we have not opted out of the AstraZeneca vaccine, but that we are putting it on hold," the country's National Board of Health said.

www.cnbc.com

Edit: changed to say "possible" side effect. There's no proof this is a side effect.

 

[Trell]

Weird how this possible AZ vaccine side effect has shown up most prominently in Denmark:

Oxford-AstraZeneca: EU says 'no indication' vaccine linked to clots

The EU's medicines regulator reassures states after several countries suspended use of the vaccine.

www.bbc.com

Denmark, Norway and Iceland suspend use of AstraZeneca Covid vaccine over reports of blood clots

"It is important to emphasize that we have not opted out of the AstraZeneca vaccine, but that we are putting it on hold," the country's National Board of Health said.

www.cnbc.com

Norway as well is temporary suspending use of the AstraZeneca vaccine.

 

[Irvrobinson]

Norway as well is temporary suspending use of the AstraZeneca vaccine.

22 cases out of 3 million doses is a stretch for correlation. I suspect officials are being overly cautious so as not to stoke fears of the anti-vaxers or vaccine-worriers.

 

[Trell]

22 cases out of 3 million doses is a stretch for correlation. I suspect officials are being overly cautious so as not to stoke fears of the anti-vaxers or vaccine-worriers.

Agree that is a stretch, at least compared to so many other things that have risks. The Nordic countries have historically had a very high vaccination rate, and all vaccines have risks, so I wonder what they are up to.

 

[Irvrobinson]

Johnson & Johnson's one-shot Covid vaccine cleared for use in the EU

The vaccine has the added benefit of only requiring a single dose and can be stored in most standard refrigerators at temperatures of 2 to 8 degrees Celsius.

www.cnbc.com

 

[Swerd]

22 cases out of 3 million doses is a stretch for correlation. I suspect officials are being overly cautious so as not to stoke fears of the anti-vaxers or vaccine-worriers.

This temporary hold in using the vaccine by Denmark & Norway is a standard precaution. Similar things happen in the US and most other nations.

It gives them time to investigate each of those 22 cases, and assess whether the vaccine is a possible cause of the blood clotting. Once they sort that out, they'll do their best to resume vaccinations. It's a balancing act that drug regulatory agencies must do, as they are the last line of defense for public health. It would be negligent to ignore a rare but potentially fatal problem, as it would also be negligent to ban a much needed vaccine without good reason.

It is extremely rare that such suspensions lead to something permanent, such as an outright ban on a drug. The example in the USA that I remember was in 2004 with a class of anti-inflammatory drugs known as COX-2 Inhibitors. They were found to work no better than existing drugs like aspirin, ibuprofen, etc., and they caused significant risk of heart attacks and strokes. As a result, many of those drugs were taken off the market by their makers, before the FDA could ban them. For example Vioxx was taken off the market by it's maker Merck. One such drug remains available in the US, Celebrex, but it's label contains strong warnings.

 

[TLS Guy]

Agree that is a stretch, at least compared to so many other things that have risks. The Nordic countries have historically had a very high vaccination rate, and all vaccines have risks, so I wonder what they are up to.

It is to hide the fact they did not order and purchase enough vaccines when they should have. Patients turn up to every hospital in the world daily with blood clots. Dealing with coagulation problems is just bread and butter.

The EU are just in a huge tizzy fit, and jealous of UK progress. That is what is behind this nonsense.

 

[Irvrobinson]

It is to hide the fact they did not order and purchase enough vaccines when they should have. Patients turn up to every hospital in the world daily with blood clots. Dealing with coagulation problems is just bread and butter.

The EU are just in a huge tizzy fit, and jealous of UK progress. That is what is behind this nonsense.

While I'm not a big fan of the EU government, your reasoning doesn't make any sense. They have a shortage of vaccine, and the answer is to pause using one of them? That's nonsensical.

 

[Mr._Clark]

While I'm not a big fan of the EU government, your reasoning doesn't make any sense. They have a shortage of vaccine, and the answer is to pause using one of them? That's nonsensical.

It's dumb, but that doesn't mean it's not possible. Basically, if the citizens are torqued off at the government because the government screwed up and didn't order enough vaccine, the government can find a way to say "The vaccine isn't safe anyway, so stop yer complaining!"

I suspect there may be some of this going on in Brazil. Bolsonaro is an incompetent *ss, so he attacks the vaccines rather than taking action to address the problems there:

>>>Brazilian President Jair Bolsonaro criticized the Pfizer-BioNTech vaccine in a bizarre rant, On Thursday.

He suggested that the COVID-19 vaccine could result in people turning into crocodiles, women growing beards, and men speaking with effeminate voices, according to AFP.

Bolsonaro said: "In the Pfizer contract, it's very clear. 'We're not responsible for any side effects.' If you turn into a crocodile, that's your problem."

He continued: "If you become superhuman, if a woman starts to grow a beard or if a man starts to speak with an effeminate voice, they [Pfizer] won't have anything to do with it," he said.<<<

Brazil's Jair Bolsonaro bizarrely suggests COVID-19 vaccines could turn people into crocodiles or bearded ladies

Brazil's president suggested that the Pfizer-BioNTech vaccine has strange side effects and the country was at the "tail end of the pandemic."

www.businessinsider.com

 

[Trell]

It's dumb, but that doesn't mean it's not possible. Basically, if the citizens are torqued off at the government because the government screwed up and didn't order enough vaccine, the government can find a way to say "The vaccine isn't safe anyway, so stop yer complaining!"
...

I'm sort of rooting for that the US politicization of the pandemic stops, or at least stays there. We have enough issues without having not wearing a mask a signal of political identity, and similar idiocy.

 

[TLS Guy]

This temporary hold in using the vaccine by Denmark & Norway is a standard precaution. Similar things happen in the US and most other nations.

It gives them time to investigate each of those 22 cases, and assess whether the vaccine is a possible cause of the blood clotting. Once they sort that out, they'll do their best to resume vaccinations. It's a balancing act that drug regulatory agencies must do, as they are the last line of defense for public health. It would be negligent to ignore a rare but potentially fatal problem, as it would also be negligent to ban a much needed vaccine without good reason.

It is extremely rare that such suspensions lead to something permanent, such as an outright ban on a drug. The example in the USA that I remember was in 2004 with a class of anti-inflammatory drugs known as COX-2 Inhibitors. They were found to work no better than existing drugs like aspirin, ibuprofen, etc., and they caused significant risk of heart attacks and strokes. As a result, many of those drugs were taken off the market by their makers, before the FDA could ban them. For example Vioxx was taken off the market by it's maker Merck. One such drug remains available in the US, Celebrex, but it's label contains strong warnings.

I just watched the BBC news at 6:00 PM for today. The NHS has run its data base of the clotting incidence of vaccinated and non vaccinated patients, age corrected. The incidence is the same in both groups. So this is nonsense what they have done in Denmark, Norway, Iceland and now Austria.
The vaccine is effective and safe.

 

[TLS Guy]

While I'm not a big fan of the EU government, your reasoning doesn't make any sense. They have a shortage of vaccine, and the answer is to pause using one of them? That's nonsensical.

It has happened already. First the Germans including Merkel bad mouthed the vaccines. They had a surplus of vaccines build up even though few had been vaccinated. Then Macron of France got on the bandwagon and called the AstraZeneca vaccine barely effective.

This has been a cynical ploy. If you have messed up big time, and they have, then you reduce demand, and hey presto, the shortage disappears. If you are a Eurocrat in that dreadful organization, it makes perfect sense. Ursula Von der Lying, the president, bears huge responsibility for the fiasco, but refuses to resign. She has no electoral accountability to EU citizens whatsoever. Only 32% of the UK population are now in favor of rejoining the EU. This number continues to fall.

Here are the European vaccination rates as of March 9. The UK is vaccinating at least 250,000 a day and sometimes 500,000 a day. They will be heading to 50% very soon, and are aiming for herd immunity no later than June 21 with cancellation of all restrictions. The EU on the other hand leads with Malta, a tiny Island that got extra doses by mistake at 23%. Hungary is next because they bought Sputnik 5 and Chinese Sinopharm off the ration. They are at 15%. Denmark are at 13%, Norway at 11% and Iceland at 12%. Norway and Iceland are non EU, but I believe joined the EU purchasing consortium, but I could be wrong about that. Germany has done 10% and so has France. Germany has also started buying off the ration.
Italy has done 9.5% and confiscated a large quantity of AstraZeneca vaccine made in Italy that Australia had already purchased.

Irv, you still have a lot to learn about the EU. I have been trying to inform you of the incompetence and worse, of the EU for years. If you really understood the EU, these actions would make sense and be predictable. The EU has not been known by many in the UK as the EUSSR without good reason.

 

[Mr._Clark]

I'm sort of rooting for that the US politicization of the pandemic stops, or at least stays there. We have enough issues without having not wearing a mask a signal of political identity, and similar idiocy.

I have to say though, it might be kind of cool to turn into a crocodile. I'll bet crocodiles are immune to the corona virus.

>>>Other animals sold in pet stores including, birds, reptiles, fish, and insects do not appear to be susceptible to SARS-CoV-2 infection.<<<

Community, Work, and School

Actions that communities can take to slow the spread of COVID-19.

www.cdc.gov