totm april 2020 Coronavirus

[tater]

https://nypost.com/2020/04/27/ive-worked-the-coronavirus-front-line-and-i-say-its-time-to-start-opening-up/

His observations are really good. The stuff about people not seeking care is real, too, we're not even slammed here in NM, and the ER is way, way below average. Sick people are staying home out of irrational fear.

[KerikBalm]

On 4/26/2020 at 4:31 PM, tater said:

https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1

Pretty interesting.

 

Did you read the abstract all the way? The guy on twitter certainly didn't when he made a claim of some level of immunity.

"The presence of pre-existing SARS-CoV-2-reactive T cells in healthy donors is of high interest but larger scale prospective cohort studies are needed to assess whether their presence is a correlate of protection or pathology"

Of note, they mention: " in COVID-19 patients S-reactive CD4+ T cells equally targeted both N-terminal and C-terminal parts of S whereas in healthy donors S-reactive CD4+ T cells reacted almost exclusively to the Cterminal part that is a) characterized by higher homology to spike glycoprotein of human endemic "common cold" coronaviruses, and b) contains the S2 subunit of S with the cytoplasmic peptide "

The molecular biology of the S protein should not be overlooked. The spike protein (S protein) first binds to a receptor, which causes a conformational change that causes a protein cleavage and exposes the fusion peptide. The exposure of the fusion peptide allows the virus to enter an adjacent cell. The S2 form of the protein is not "visible" to the immune system until the virus has bound its target cell and is in the process of infecting it.

Furthermore, there is a thing called antibody dependent enhancement/entry (ADE). In some cases an antibody will bind the receptor portion of the S protein without inactivating it. Binding the receptor causes the S protein to act as if it bound the target cell receptor, and extend the fusion peptide. immune cells will recognize the bound antibody, and come to the virus-antibody conjugate... and get infected because the S protein wasn't neutralized. - in this case the normal target cells don't get infected because the antibodies sautrate their receptors after their production ramps up, but up to a 25% drop in leukocytes has been observed from "normal" coronavirus infection... 25% isn't like what HIV does or anything... but its also nothing to sneeze at (pun intended?).

This ADE is known to happen in other human coronaviruses. Reactivity and neutralization against one coronavirus may result in reactivity without neutralization against another coronavirus. You really need antibodies that neutralize the virus particle. T cell reactivity against S2 but not whole spike may not mean much at all.

Also, the referenced paper uses 2  mixtures of short peptides that together cover the amino acid sequence of the S1 or S2 domains, but I would advise caution in interpreting reactivity against a peptide and reactivity against the whole protein, as the 3d sturcture of the whole protein can shield certain epitopes and affect reactivity in other ways.

https://www.pnas.org/content/106/14/5871  (talks about the S protein, S1, S2, and cleavage, its not a citation for everything I said, though I can get those if you want)

 

On 4/27/2020 at 4:25 PM, tater said:

Timing matters on serological testing, you want people >20 days past onset on COVID-19:

https://covidtestingproject.org/

That time frame is in line with the results of the serological study that HUG (University Hospitals of Geneva, where I work now) just put up on a pre-print server

Edited April 29, 2020 by KerikBalm

[AHHans]

1 hour ago, KerikBalm said:

Did you read the abstract all the way? The guy on twitter certainly didn't when he made a claim of some level of immunity.

"The presence of pre-existing SARS-CoV-2-reactive T cells in healthy donors is of high interest but larger scale prospective cohort studies are needed to assess whether their presence is a correlate of protection or pathology"

Well, I did. I still like my thought that parents get protected by their kids by having been sick all the time when their kids got into kindergarten better than the alternative! ( or take your pick.)

[KerikBalm]

6 hours ago, AHHans said:

Well, I did. I still like my thought that parents get protected by their kids by having been sick all the time when their kids got into kindergarten better than the alternative! ( or take your pick.)

That would be nice, but so far in the serological virus neutralization assays I have seen (a much better surrogate for protection that reactivity of one cell type without IgG reactivity), only exposure to SARS-CoV-1 (causing the original SARS from 2003 and 2004) would offer any protection against SARS-CoV-2 (the virus causing Covid-19), among numerous types of human coronavirus that they tested... There was a bit of overlap with MERS, but not much. It seems that SARS-COV-2 is more infectious but less deadly that SARS-COV-1 and the MERS CoV... So if anything, I'd loik towards SARS-COV-2 exposure to protect against other two than vice versa

[tater]

I've seen a lot of stuff circulating about Vitamin D vs COVID-19... could that explain seasonality (in things like flu) alone? That people chose to get more sun in summer months, with more skin exposed? Seems like in the modern world, people work indoors year round, so minus some factor related to outside, it should be more like the tropics, where flu is not seasonal, but is at lower levels, all year.

If D was protective, maybe that explains kids doing better, since they spend much more time outside (and I know my kids wear short sleeves in weather I'd be wearing a jacket in, so more skin exposure)?

[AHHans]

52 minutes ago, KerikBalm said:

That would be nice, but so far [...]

Jajaja. I still think that "Saved by your kids!" is a much better slogan than "Sorry folks, you'll have to stay indoors with your stir-crazy kids for longer."

P.S. Yes, I know that it is extremely unlikely that having been exposed to relatively harmless coronaviruses helps you against SARS-CoV-2, and that it is as likely to actually be harmful (as in making it more likely that your immune system overreacts). I just think the idea is funny enough to mention it here. And I thought my wording made it clear enough that I wasn't stating an actual fact or what I thought was a fact.
P.P.S. Did I mention that I miss the sound of kids playing in the backyard? The sound of crying kids from the apartment above or below (hard to tell) doesn't have the same vibe.

Edited April 29, 2020 by AHHans
Added P.S.

[tater]

Interesting point about some of the stuff coming out (the air pollution paper might have been posted up thread somewhere):

 

[tater]

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31022-9/fulltext

Any good news is good news.

[kerbiloid]

Ouch

https://www.theguardian.com/technology/2020/apr/29/elon-musk-tweets-protest-against-us-coronavirus-lockdown

[tater]

The more you look at the COVID-19 stats, the more you see that there are cities, States, and countries that dealt with this well... and then there is NYC, and NYS leading the pack as the worst trainwrecks. To the extent that government intervention was capable of mitigating this to any degree... NY failed epically.

If your goal is to mitigate deaths, whatever NYC did... don't do that would be a good rule of thumb. Ditto NY State.

[kerbiloid]

Spoiler

  

23 minutes ago, tater said:

whatever NYC did... don't do that would be a good rule of thumb

Avoid the common touch. The common touchers become infection vectors.

(U C what I mean)

Spoiler

 

 

[tater]

This is also apparently true for flu. I'd welcome illumination for people who grok this stuff better like @KerikBalm, but assuming something like this is true, could it explain worse outcomes in places where people are in the sun less? Seasonality seems like it should be less of a thing in the modern world if the explanation for seasonality was "people close together, indoors" given air conditioning. The difference would be people elect to spend more time outdoors with their skin uncovered. Could this also explain a higher impact on population groups with darker skin?

 

[tater]

https://share-ng.sandia.gov/news/resources/news_releases/crispr_coronavirus/

[StrandedonEarth]

The situation in BC and some other places...

 

[tater]

38 minutes ago, StrandedonEarth said:

The situation in BC and some other places...

 

No it doesn't (the toon).

The curves for places not doing anything at all look pretty much the same as the places locking down. All the models predicting hospital use have been worthless. IHME eventually got NY use into it's uncertainty interval, and NY is a huge outlier in use. For the rest of the country their predictions were off by orders of magnitude. They have NM in the right ballpark now, but who cares, it's too late for prediction to be useful, planning ahead needed to happen BEFORE shutdowns in March (the point of shutdowns was to not exceed healthcare delivery).

Not even NY exceeded healthcare capacity, and they are 3X worse than Italy in deaths per capita. I was paying a lot of attention to IHME, and was texting with a friend in medical analytics (she's also an MD). She was involved with trying to plan for surges, and all the models were presumably based on Italy, and painted an awful picture of vented patients in hallways.

I'm not against flattening the curve, but I require a goal. The goal cannot be, "until a vaccine, or effective treatment," because we can't even say either will happen. Once it was clear there was no surge coming that would overwhelm the system (locality by locality, BTW, not at a Fed or even State level), restrictions should have been eased to something more sustainable. More importantly, the hospitals should be reopened immediately to normal care. My wife still can't do "elective" surgeries on people because it is mandated by the Dept of Health right now that they not. Elective surgeries like removing cancer from people. a few years from now when people die of metastatic cancer because they were forced to live with their tumor some extra months, will we have dashboards to show us the toll?

The counterfactual is if personal behavior choice alone drove any reduction in R_t. How can we tell if people washing hands, or avoiding crowds had more effect than gov mandated shutdowns?

 

 

[magnemoe]

1 hour ago, tater said:

No it doesn't (the toon).

The curves for places not doing anything at all look pretty much the same as the places locking down. All the models predicting hospital use have been worthless. IHME eventually got NY use into it's uncertainty interval, and NY is a huge outlier in use. For the rest of the country their predictions were off by orders of magnitude. They have NM in the right ballpark now, but who cares, it's too late for prediction to be useful, planning ahead needed to happen BEFORE shutdowns in March (the point of shutdowns was to not exceed healthcare delivery).

Not even NY exceeded healthcare capacity, and they are 3X worse than Italy in deaths per capita. I was paying a lot of attention to IHME, and was texting with a friend in medical analytics (she's also an MD). She was involved with trying to plan for surges, and all the models were presumably based on Italy, and painted an awful picture of vented patients in hallways.

I'm not against flattening the curve, but I require a goal. The goal cannot be, "until a vaccine, or effective treatment," because we can't even say either will happen. Once it was clear there was no surge coming that would overwhelm the system (locality by locality, BTW, not at a Fed or even State level), restrictions should have been eased to something more sustainable. More importantly, the hospitals should be reopened immediately to normal care. My wife still can't do "elective" surgeries on people because it is mandated by the Dept of Health right now that they not. Elective surgeries like removing cancer from people. a few years from now when people die of metastatic cancer because they were forced to live with their tumor some extra months, will we have dashboards to show us the toll?

The counterfactual is if personal behavior choice alone drove any reduction in R_t. How can we tell if people washing hands, or avoiding crowds had more effect than gov mandated shutdowns?

Social distancing was probably just as important but it became an priority because of the shutdown who scared the crap out of people. 
If they had not done something it would gotten much worse. How much you shut down is an mater of debate. Lots of the US shut down all non essential businesses. In Norway we shut down everything require groups or close contact so hairdressers was shut down but most  businesses and stores could keep open, lots closed because people was in quarantine and customers was not shopping.hairdressers just opened and corona hairstyle become an term. 

Sweden tried the soft approach, it did not work very well but will hardly call it an catastrophe and they had to restrict more. 
Now the hope is that you can keep this under check with social distancing and hygiene, guess we have to surf it as in heighten up if it flare up again.  
 

[tater]

11 minutes ago, magnemoe said:

Social distancing was probably just as important but it became an priority because of the shutdown who scared the crap out of people. 
If they had not done something it would gotten much worse. How much you shut down is an mater of debate. Lots of the US shut down all non essential businesses. In Norway we shut down everything require groups or close contact so hairdressers was shut down but most  businesses and stores could keep open, lots closed because people was in quarantine and customers was not shopping.hairdressers just opened and corona hairstyle become an term. 

Sweden tried the soft approach, it did not work very well but will hardly call it an catastrophe and they had to restrict more. 
Now the hope is that you can keep this under check with social distancing and hygiene, guess we have to surf it as in heighten up if it flare up again. 

The area under the curve should be the same, regardless. If 0.X% are going to die, they die regardless, it's just when they die, and if they cause other deaths due to overwhelmed healthcare.

If behavioral changes are possible that mitigate all future ID by R minus 0.whatever, and it dies out, then sure, we all have less ID to deal with going forward, and maybe the total dead is lower. I'm not trusting in a vaccine, though (although I think critical care will get better wit this disease as time goes on, US standard of care has adjusted a great deal entirely since NY started getting hammered).

[TheSaint]

A guy on another board I frequent relayed a story. He was in a Trader Joe's in the Bay Area to grab some stuff, and they had all of their mask/6-ft/one-way rules posted, and he complied with all of them. He gets to the checkout, puts his basket on the counter and waits for the cashier to check him out. The lady they had assigned to police the checkout stands starts barking at him, "You need to be inside your square!" He's looking at her like, "What the hell are you talking about?" She runs over to him (getting well within his six-foot radius) and starts jabbing her finger at him, "You need to be inside your square before he can check you out!" He looks down, and they have a square decal on the floor, about 18 inches on a side, three feet away from the register stand. And he has one foot half out of it. Life is feeling more and more like a Terry Gilliam film every day. SMH

I was talking about all this with my wife last night. The sad part is there's a certain fraction of the population who will never get over this. They're going to be wearing masks, and hoarding toilet paper, and sanitizing their Amazon boxes, and eating nothing but takeout, and yelling at everyone who comes within six feet of them for the rest of their lives.

[magnemoe]

23 minutes ago, TheSaint said:

A guy on another board I frequent relayed a story. He was in a Trader Joe's in the Bay Area to grab some stuff, and they had all of their mask/6-ft/one-way rules posted, and he complied with all of them. He gets to the checkout, puts his basket on the counter and waits for the cashier to check him out. The lady they had assigned to police the checkout stands starts barking at him, "You need to be inside your square!" He's looking at her like, "What the hell are you talking about?" She runs over to him (getting well within his six-foot radius) and starts jabbing her finger at him, "You need to be inside your square before he can check you out!" He looks down, and they have a square decal on the floor, about 18 inches on a side, three feet away from the register stand. And he has one foot half out of it. Life is feeling more and more like a Terry Gilliam film every day. SMH

I was talking about all this with my wife last night. The sad part is there's a certain fraction of the population who will never get over this. They're going to be wearing masks, and hoarding toilet paper, and sanitizing their Amazon boxes, and eating nothing but takeout, and yelling at everyone who comes within six feet of them for the rest of their lives.

And yes this situation display all the tinpot dictator wannabees very well There is three sort of peoples in this settings: the good who want to help others, the bad who use it fish for money or power and the ugly who just want love to be in an position of power. 
Under no circumstances give group 3 any sort of power at any cost. Group 2 is not perfered as they are corrupt but they are way better than 3. 

[DDE]

1 hour ago, magnemoe said:

Under no circumstances give group 3 any sort of power at any cost.

Too late. They're the ones who crawl their way to power anyway. Look at the incidence of the Dark Triad among cops.

On a related note, Russia's now down a Prime-Minister.

http://kremlin.ru/events/president/news/63297

Acting PM is Yuri Borisov, who you actually should know as Russia's defense industry curator, which includes Roscosmos.

Spoiler

 

[tater]

2 hours ago, TheSaint said:

A guy on another board I frequent relayed a story. He was in a Trader Joe's in the Bay Area to grab some stuff, and they had all of their mask/6-ft/one-way rules posted, and he complied with all of them. He gets to the checkout, puts his basket on the counter and waits for the cashier to check him out. The lady they had assigned to police the checkout stands starts barking at him, "You need to be inside your square!" He's looking at her like, "What the hell are you talking about?" She runs over to him (getting well within his six-foot radius) and starts jabbing her finger at him, "You need to be inside your square before he can check you out!" He looks down, and they have a square decal on the floor, about 18 inches on a side, three feet away from the register stand. And he has one foot half out of it. Life is feeling more and more like a Terry Gilliam film every day. SMH

I was talking about all this with my wife last night. The sad part is there's a certain fraction of the population who will never get over this. They're going to be wearing masks, and hoarding toilet paper, and sanitizing their Amazon boxes, and eating nothing but takeout, and yelling at everyone who comes within six feet of them for the rest of their lives.

Out of likes, but, yes.

People are terrible at risk assessment. It's understandable, because for normal human behavior (in the evolutionary history sense of us in our natural state) erring on the side of safety is adaptive.

The risks from COVID are more than typical seasonal flu for some populations (lower for others), but flu is none the less a very low risk, so 5X very low risk is still... very low risk. For the aged, it's a much more substantial problem, because a few % chance of death multiplied by 5 (or 10) is pretty awful.

I have yet to wear a mask anywhere other than in the storage closet of my carport (I'm much, much more afraid of hantavirus from critters in there than COVID since it has a CFR of 36%). None the less, I have cleaned out that closet. If my Governor became tyrannical enough to require one, I'd fabricate it out of cheesecloth in my kitchen (1 layer)—which is about as effective as homemade masks, or the ones I see people wearing over their chin, under their nose, etc.

I wash my hands, I have made a COVID era effort to not touch my face out of the house pretty successfully, I am not even slightly concerned about my risk of catching it out in the world at large (assuming I didn't already catch it), and I'm not terribly concerned if I do catch it. I get outside in the sun a lot, I'm not even overweight, much less obese... I'm not really at much risk.

The reality is that life is risky all the time at some level, and we could stop all kinds of needless deaths per year if no one ever left their homes. Being outside in the sun might actually be protective vs COVID, OTOH, you could get cancer from that. Running increases your CV health, but you can have ortho problems.

 

 

[kerbiloid]

Spoiler

  

11 hours ago, TheSaint said:

He looks down, and they have a square decal on the floor, about 18 inches on a side, three feet away from the register stand. And he has one foot half out of it.

He should sue that shop for no commonly used and clearly visible marks at eye level, like in all civilized countries.

Spoiler

And personally sue that woman for no smiling and "Please" in the beginning of the phrase, like we were learning in school.

Least she could just ask politely "Zurück! Stillgestanden!" and pull the plug of her MP40.

 

[DDE]

3 hours ago, kerbiloid said:

Least she could just ask politely "Zurück! Stillgestanden!" and pull the plug of her MP40.

She could've at least said the other immortal phrase:

Quote

Pick up that can!

 

[Canopus]

Are people on the KSP forum of all places really making the point that „People are dying all the Time“? 

Im kinda disappointed.

[Hotel26]

I'm going back to KSP.

Edited May 2, 2020 by Hotel26