totm april 2020 Coronavirus

[sevenperforce]

And now we have a new strain in the UK that is what, 70% more infectious?

[KerikBalm]

17 minutes ago, sevenperforce said:

And now we have a new strain in the UK that is what, 70% more infectious?

Too early to tell, it may also be milder

[Scotius]

It's Christmas time after all. COVID-19 is just gift that keeps on giving.

[DDE]

1 hour ago, sevenperforce said:

in the UK

And, from what I hear, Australia. A bit too late to get worried now.

[Selective Genius]

A new 2021 DLC. Wonderful.

And I find it really disturbing that the virus mutates as soon as we have a vaccine against it. FDA said that "We would have to update the vaccines". I am pretty sure injecting saline would 'protect' me better from the virus than a vaccine, at this point...

[Codraroll]

4 hours ago, Selective Genius said:

A new 2021 DLC. Wonderful.

And I find it really disturbing that the virus mutates as soon as we have a vaccine against it. FDA said that "We would have to update the vaccines". I am pretty sure injecting saline would 'protect' me better from the virus than a vaccine, at this point...

Fortunately, the mutation appears not to have changed the structure of the virus in a way that alters the effectiveness of vaccines on it.

[sevenperforce]

2 hours ago, Codraroll said:

6 hours ago, Selective Genius said:

A new 2021 DLC. Wonderful.

And I find it really disturbing that the virus mutates as soon as we have a vaccine against it. FDA said that "We would have to update the vaccines". I am pretty sure injecting saline would 'protect' me better from the virus than a vaccine, at this point...

Fortunately, the mutation appears not to have changed the structure of the virus in a way that alters the effectiveness of vaccines on it.

Correct. The new strain is more infectious, which means its spike proteins are at least as effective as the original strain at piercing cell walls via the hACES2 receptor.  Usually when a vaccine-resistant strain emerges, it is because of some impaired functionality. If the new strain was less infectious but more deadly, then I would be worried.

If a strain is more infectious, and the target of the vaccine is the part of the virus which causes the infection, then the vaccine should be just as effective against it.

[KerikBalm]

7 hours ago, Codraroll said:

Fortunately, the mutation appears not to have changed the structure of the virus in a way that alters the effectiveness of vaccines on it.

You are making an affirmative claim on the basis of a lack of evidence. This is not proper

5 hours ago, sevenperforce said:

Correct. The new strain is more infectious, which means its spike proteins are at least as effective as the original strain at piercing cell walls via the hACES2 receptor. 

Not correct according to what is currently known.

We do NOT know that it is more infectious.

We do NOT know if it is vaccine resistant.

We DO have hints that it is more infectious.

We DO have hints that the vaccine may be less effective against this variant ... by how much, we don't know.

 

Some of its mutations are known to be associated with escape from neutralizing activity from convalescent serum or monoclonal antibodies. In particular the N439K mutation and the delta69-70 mutations, which were also present in that mink variant that everyone was concerned about.

We also see some mutations that may increase affinity for Ace2 (Y453F, and N501Y if I remember correctly off the top of my head), which should have a similar effect to the D614G mutation - which hasn't actually proven to be particularly more contagious even though it is now dominant worldwide - it may just slightly outcompete other variants within each host...

On the other hand, this new variant has a very early stop codon in the ORF8 gene, which should result in a complete loss of function. Another variant with a deletion in the ORF8 gene was determined to be milder. ORF8 is also involved in evasion of cellular immunity (as opposed to neuturalizing antibodies), which could make it MORE susceptible to the vaccine if the vaccine elicits effective cellular and humoral immunity (some vaccines only elicit the later) - which I think it does.

Then it has a number of other mutations that have completely unknown effects.

So don't go saying "correct" to affirmative claims about this strain. We don't know one way or the other at this point, and there are signs that point to valid concerns.

At the same time, don't jump to conclusions like this:

11 hours ago, Selective Genius said:

I am pretty sure injecting saline would 'protect' me better from the virus than a vaccine, at this point...

We are studying the new variant, wait for more information, do not jump to conclusions.

[sevenperforce]

44 minutes ago, KerikBalm said:

We do NOT know that it is more infectious.

We do NOT know if it is vaccine resistant.

We DO have hints that it is more infectious.

We DO have hints that the vaccine may be less effective against this variant ... by how much, we don't know.

[snip]

So don't go saying "correct" to affirmative claims about this strain. We don't know one way or the other at this point, and there are signs that point to valid concerns.

That's fair.

At the same time there is value in optimism. For example, optimism helps keep people from jumping to conclusions about saline.

[Selective Genius]

6 hours ago, sevenperforce said:

At the same time there is value in optimism.

Mate, I am just tired of this, that's all. I lost my job, can barely pay my rent, am insulted and sidelined by the relatives for being unemployed, lost the approval of the family of the girl I was with, lost a cat because I could not take her to the vet because of lockdown restrictions and then a scientist yells at me to be 'optimistic' about the future. How can somebody be optimistic with a near empty stomach and broken dignity?

At this point, I HOPE that the virus gets me and wipes me out. It would be a fresh start when I get reincarnated. All you rich people deserve to enjoy the fruits of this life and I wish you prosperity. But damn, I want a way out.

[R-T-B]

19 hours ago, Selective Genius said:

And I find it really disturbing that the virus mutates as soon as we have a vaccine against it.

This is how viruses work.  The flu does the same, every year.  It's pretty much viral evolution 101.

 

16 minutes ago, Selective Genius said:

Mate, I am just tired of this, that's all. I lost my job, can barely pay my rent, am insulted and sidelined by the relatives for being unemployed, lost the approval of the family of the girl I was with, lost a cat because I could not take her to the vet because of lockdown restrictions and then a scientist yells at me to be 'optimistic' about the future. How can somebody be optimistic with a near empty stomach and broken dignity?

At this point, I HOPE that the virus gets me and wipes me out. It would be a fresh start when I get reincarnated. All you rich people deserve to enjoy the fruits of this life and I wish you prosperity. But damn, I want a way out.

I'm sorry about your troubles...  sounds like you should talk to someone with more professionalism than you'll find here, frankly.  And I don't mean that in a condescending way.  This pandemic has a lot of people on the verge of a mental health breakdown, so you are not alone.

[Selective Genius]

2 minutes ago, R-T-B said:

you should talk to someone with more professionalism

How would I pay them though? With the money I don't have??

2 minutes ago, R-T-B said:

This is how viruses work.  The flu does the same, every year.  It's pretty much viral evolution 101.

Then why are we bothering with a vaccine, or atleast why is it being marketed as a panacea against Covid? If we could not make a vaccine against Flu which had been around since forever, how did we make one for Covid so fast?

[R-T-B]

46 minutes ago, Selective Genius said:

How would I pay them though? With the money I don't have??

I don't know, I just know we don't have the answers to mental health issues here.  I'm sorry I can't be more helpful.  I really wish I could.

If you want me to try my hand at being a doctor (which I am not), an end to your life now would make sure you never see KSP 2.

That was pretty lame, now wasn't it?  Warned you.

46 minutes ago, Selective Genius said:

Then why are we bothering with a vaccine, or atleast why is it being marketed as a panacea against Covid? If we could not make a vaccine against Flu which had been around since forever, how did we make one for Covid so fast?

I personally don't expect a mirracle cure.  It will probably have to be developed yearly.  But it should be noted some of these vaccines are mRNA based, which is an entirely new approach over the flu vaccine (basically an injection of killed virus)

Edited December 23, 2020 by R-T-B

[Selective Genius]

9 minutes ago, R-T-B said:

mRNA based

Would mRNA vaccines not work against Flu? Is this a new technology?

9 minutes ago, R-T-B said:

would make sure you never see KSP 2.

KSP 1.11 looks and feels great, if only they iron out the bugs in the next patch. The next patch is worth waiting for. And no it was not lame, pretty sure the professionals would have said the same but in a more flowery language.

Edited December 23, 2020 by Selective Genius

[KerikBalm]

On 12/23/2020 at 3:48 AM, Selective Genius said:

Mate, I am just tired of this, that's all. I lost my job, [snip]

Honestly, sometimes I think that we should have done nothing less severe neasures because of things like this.

Mostly Old people would die, but by and large they lived full lives with a quality of life better than younger generations - who are now even worse off.

We are crippling the young generation's future too buy a largely spoiled generation that caused massive problems another 5 years before something else gets them.

And I say this as someone who has benefited from the pandemic because I now work for a virology department at a hospital...

Edited December 25, 2020 by KerikBalm
Edit to add some nuance and clarify that I didn't mean to go that far

[KerikBalm]

5 hours ago, Selective Genius said:

Then why are we bothering with a vaccine, or atleast why is it being marketed as a panacea against Covid? If we could not make a vaccine against Flu which had been around since forever, how did we make one for Covid so fast?

We do have a vaccine against the flu, and it needs to be updated every year. Already based on studies of other coronaviruses, immunity after infection (and thus likely vaccination) is unreliable after 6 motnhs-1 year.

This was always going to be something that would require a yearly shot for those that are at risk. The idea is if you can vaccinate the at risk population, the rest of the population can get back to life as normal (and even if they don't get yearly vaccines, the last vaccine should provide enough protection that the newest SARS-CoV-2 strain isn't that bad).

[sevenperforce]

13 hours ago, Selective Genius said:

14 hours ago, Selective Genius said:

Mate, I am just tired of this, that's all. I lost my job, can barely pay my rent, am insulted and sidelined by the relatives for being unemployed, lost the approval of the family of the girl I was with, lost a cat because I could not take her to the vet because of lockdown restrictions and then a scientist yells at me to be 'optimistic' about the future. How can somebody be optimistic with a near empty stomach and broken dignity?

How would I pay [mental health professionals] though? With the money I don't have??

I'm sorry, man. That sucks. I'm not a mental health professional and I wouldn't attempt to give any sort of medical advice, but I truly feel for your plight. I certainly wasn't trying to yell at you. If you'd like to reach out privately, I'd be happy to learn a little bit more about your situation and see if I can find a source of no-cost counseling or therapy that you'd have access to. I happen to be rather good at that. I've really benefited tremendously from therapy.

13 hours ago, Selective Genius said:

Then why are we bothering with a vaccine, or atleast why is it being marketed as a panacea against Covid? If we could not make a vaccine against Flu which had been around since forever, how did we make one for Covid so fast?

We have highly effective vaccines against the flu, but the flu mutates rapidly enough to limit their long-term effectiveness. SARS-CoV-2 does not mutate as rapidly as the flu, and its specific mechanism of cell entry (which is what makes it so virulent) involves proteins that are susceptible to a highly targeted vaccine. We were able to do it quickly for two reasons: first, our understanding of protein-folding has gone through the roof in the last few years, and second, we skipped some of the intermediate steps that often drag this stuff out. For example, we began building factories to produce the vaccine immediately instead of waiting until it had been proven in trials.

Ordinarily a corporation would wait until a vaccine went through all its trials before investing money in production. But here, speed was more important than ROI.

13 hours ago, Selective Genius said:

Would mRNA vaccines not work against Flu? Is this a new technology?

Yes, mRNA vaccines are new technology. One of the reasons we were able to develop an mRNA vaccine for SARS-CoV-2 so rapidly is that we've been studying mRNA vaccines for the flu already. Moderna's Phase 1 clinical trials for an mRNA flu vaccine concluded in May 2019, with fairly good results. It's a little more challenging because the influenza vaccine's spike proteins bind to sialic acid, which is an extremely simple molecule. The external shape of the influenza spike protein can mutate a lot while still being able to bind to the sialic acid on the outside of host cells. In contrast, the spike proteins of SARS-CoV-2 bind to the hACES2  receptor, which is MUCH more complicated and thus requires a very specific spike protein shape, which in turn is more easily targeted.

Moderna and Pfizer both had a leg up in developing an mRNA vaccines for SARS-CoV-2 because they had already been studying the structure of the MERS-CoV spike protein. MERS-CoV binds to the DPP4 receptor, not the hACES2 receptor, but it is externally similar to the SARS-CoV-2 spike protein. Protein-folding is a very challenging problem but it's made easier when you can compare the output of two very similar codes...just like how you can more easily solve a cipher if you are able to intercept multiple messages.

This comic was back in 2014, after the 11th bi-annual CASP competition. We first began  using artificial intelligence to predict protein-fold structure in 2016 and by 2018 artificial intelligence was winning handedly. This really is the cutting edge.

The mRNA vaccine works by instructing muscle cells to produce copies of the SARS-CoV-2 spike protein, which trains the immune system to recognize and attack the spike protein and thus fight off a real infection. We were actually able to produce this mRNA sequence almost instantly, just by copying and pasting from the SARS-CoV-2 genome. However, the spike protein will become "floppy" and lose its structure if not attached to the virus. The trick was to write mRNA code that would fold a "backbone" inside the spike protein to keep it stiff without changing its external shape. And that's what scientists did, in a matter of weeks.

10 hours ago, KerikBalm said:

Honestly, sometimes I think that we should have done nothing because of things like this.

Old people would die, but by and large they lived full lives with a quality of life better than younger generations - who are now even worse off.

We are crippling the young generation's future too buy a largely spoiled generation that caused massive problems another 5 years before something else gets them.

Strongly disagree.

The past year has been a disaster but it could have been averted if governments had actually done their job. Complete lockdown. Pay everyone to stay at home for six weeks. Then reopen slowly, continuing to pay people.

The "it just affects old people" argument is BS. It doesn't just affect old people. It causes long-term disability damage to LOTS of people. A huge percentage of the population has at least SOME pre-existing condition. Yes, it kills off really old people really fast, but that's not the point.

[Starhelperdude]

I heard death makes you immune to corona, but the side effects are too big IMO

[Bill Phil]

11 hours ago, KerikBalm said:

Honestly, sometimes I think that we should have done nothing because of things like this.

Old people would die, but by and large they lived full lives with a quality of life better than younger generations - who are now even worse off.

We are crippling the young generation's future too buy a largely spoiled generation that caused massive problems another 5 years before something else gets them.

And I say this as someone who has benefited from the pandemic because I now work for a virology department at a hospital...

Doing nothing would have led to even more devastation. 

Just because we could have handled it better does not mean that nothing would be better.

[AHHans]

16 hours ago, Selective Genius said:

16 hours ago, R-T-B said:

you should talk to someone with more professionalism

How would I pay them though? With the money I don't have??

I feel with you.

I have two suggestions that may or may not help. One is to talk to a priest, pastor, rabbi, imam, or whoever might be appropriate. Here where I am, talking to a priest would give you at least someone who listens and has some experience in dealing with these kinds of problems.
The other is to look for a a self-help group. I'm fairly sure that you are not the only one who has these kinds of problems in these times. So getting together to talk about this and how the others deal with it may help you.

[KerikBalm]

2 hours ago, Bill Phil said:

Doing nothing would have led to even more devastation. 

The thing is, I am a bit of a misanthrope that thinks that overpopulation is the biggest problem in the world right now, so that kind of colors my views about what should be done. :p

2 hours ago, sevenperforce said:

The "it just affects old people" argument is BS. 

It doesn't just affect them, but it mainly affects them. Some people do develop long term side effects, but most do not.

 

But seriously, the setbacks to people's lives is severe, and giving these 20 and 30 somethings such a setback is going to have compounded effects over their whole lives.

In the other hand, if people stopped being so stupid, and actually observed the proper precautions and lockdowns, we'd only need a 2 week lockdown to be done with this virus... But people are stupid

This is the 3rd SARS-CoV to come out of China, but they kept reopening the wet markets, because people are stupid.

The population density is so high and allowing the virus to spread so easily because the earlier generations were stupid and couldn't think of the future.

This virus is a monument to the stupidity and selfishness of humanity... so... at times I see stupid and selfish behavior and almost want to root for the virus.

[R-T-B]

18 hours ago, Selective Genius said:

Would mRNA vaccines not work against Flu? Is this a new technology?

Very.  Likely to help us in the battle against the flu, honestly.

I know the light at the end of the tunnel is dim, but it's there.

Edited December 23, 2020 by R-T-B

[KerikBalm]

FYI: https://cmmid.github.io/topics/covid19/uk-novel-variant.html

Estimated 56% more transmissible, no statistically significant difference in severity has been noted- which is a bummer, because I would have bet money that this strain was at least a little milder (granted, it is one study, awaiting peer review, and as more data is gathered, we may see a difference)

[Bill Phil]

23 hours ago, KerikBalm said:

The thing is, I am a bit of a misanthrope that thinks that overpopulation is the biggest problem in the world right now, so that kind of colors my views about what should be done. :p

I'm the opposite. I'm more concerned about the negative effects of the slowing growth rate.

I don't think overpopulation is a problem, or rather, it's just one element of the world and is a very solvable issue. Not a problem in and of itself but it can feed other problems due to how the world is organized and the systems in place.

[KerikBalm]

1 hour ago, Bill Phil said:

I don't think overpopulation is a problem, or rather, it's just one element of the world and is a very solvable issue. Not a problem in and of itself but it can feed other problems due to how the world is organized and the systems in place.

I would strongly disagree, but that is a topic for another thread.

 

On 12/23/2020 at 7:10 PM, Bill Phil said:

Doing nothing would have led to even more devastation. 

I didn't say do nothing. There are intermediates between doing nothing and a full lockdown.

In Switzerland, we are getting through the 2nd wave without a full lockdown, and even that is with poor compliance amongst the population regarding proper mask wearing and social distancing.

Certainly the US f-d up by not even passing legislation to guarantee 10 days sick leave for infected people.

One shouldn't have to choose between having money for food, or infecting others. Its also ridiculous that a law would be needed.

There's a lot that can be done short of lockdown.