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Author Topic: Coronavirus / COVID-19  (Read 250982 times)
Trippy
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Reply #910 on: July 16, 2020, 01:02:41 PM

They tried it but half of the hamsters freaked out and started screaming about freedom.
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Sky
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Reply #911 on: July 28, 2020, 06:05:44 AM

Some interesting stuff about the ACE2 attack vector explaining a lot of the weird symptoms: https://www.ucsf.edu/magazine/covid-body?fbclid=IwAR2T9NdqlshIiYDDj_Xd9U9dt6IInj82CZTwWAbf0Om29-C8NRczXhq3yY0
Mandella
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Reply #912 on: July 28, 2020, 06:33:37 PM

Some interesting stuff about the ACE2 attack vector explaining a lot of the weird symptoms: https://www.ucsf.edu/magazine/covid-body?fbclid=IwAR2T9NdqlshIiYDDj_Xd9U9dt6IInj82CZTwWAbf0Om29-C8NRczXhq3yY0

Thanks for that link. And it looks like I've let myself get behind the information curve.

Is it generally accepted now that 50 to 80 percent of cases are asymptomatic? That is way more than I remember reading from just a few months ago.
Trippy
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Reply #913 on: July 28, 2020, 07:08:38 PM

Some interesting stuff about the ACE2 attack vector explaining a lot of the weird symptoms: https://www.ucsf.edu/magazine/covid-body?fbclid=IwAR2T9NdqlshIiYDDj_Xd9U9dt6IInj82CZTwWAbf0Om29-C8NRczXhq3yY0
Thanks for that link. And it looks like I've let myself get behind the information curve.

Is it generally accepted now that 50 to 80 percent of cases are asymptomatic? That is way more than I remember reading from just a few months ago.
No it's not. That one doctor making that assumption based on that one antibody study in the SF Mission District. The CDC's "best guess", which they don't explain/justify, is 40%. That could be based on testing results in places like Vò, Italy, where most of the population has been tested multiple times and about 40% were asymptomatic.

Edit: here's a review of various studies that measured asymptomatic people:

Annals of Internal Medicine: Prevalence of Asymptomatic SARS-CoV-2 Infection

« Last Edit: July 28, 2020, 07:28:27 PM by Trippy »
Rasix
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Reply #914 on: August 13, 2020, 10:43:20 AM

My son's baseball league announced they're doing fall ball. Begins in a couple weeks.

Not sure how I feel about this. 95% of the kids are in very large public school districts and Arizona is still Arizona.
« Last Edit: August 13, 2020, 03:25:22 PM by Rasix »

-Rasix
Khaldun
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Reply #915 on: August 13, 2020, 11:27:16 AM

Over the past three weeks, many universities that had previously announced full or partial residential reopenings for September have reversed course and gone to being fully online.

Most small colleges are sticking to whatever they announced in June, though, which is mostly some form of partial or 'hybrid' reopening. I think the large universities just came to the conclusion that there is absolutely no way for them to successfully avoid the spread of covid-19 if they have thousands of undergrads in residence--even the wealthiest of them aren't set up to monitor the comings and goings of students, can't handle the volume of testing required, etc.

I also think some of them have lawyers who said, "You're going to get sued into oblivion if any students, staff or faculty die of covid-19 in a way that's traced to the campus". Penn State tried to pull a fast one by putting a comprehensive waiver of liability deep inside a pledge of responsible conduct that students were expected to sign before coming back (it literally said something like "no matter what, if I get sick from covid-19, I acknowledge that it's my own fault and I hereby agree to forgo any claims of liability") and there were howls of anger from students, parents and legislators. Not long afterwards, Penn State dropped that part and then said, "Hey, know what? let's not have students be in residence..."
01101010
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Reply #916 on: August 13, 2020, 11:48:58 AM

Pitt is actually having move-in this week and next in a phased system. I guess parents were contacted and given a window to be on campus. I was actually on campus earlier because my pharmacy is there. No parking anywhere for no parents moving any kids in. All the student groups that help with move-ins are no where - just a huge stack of the wheeled laundry bins they use every year in the usual spots. Such a pain in the ass to find available parking for basically no reason as the volume of kids moving back is reduced and they are not moving into the dorms, they are using the campus hotel which has their own parking lot. Typical.

Anyway, driving around the campus more than I usually do because of all that, so many packs of kids all moving in groups around campus - some masks, some not. Some walking around alone, most not. If this is what it is going to be like, looks like my co-workers are not going to be back in the office until a vaccine is out because these future adults are already screwing things up. I'll be shocked if there is not a spike around in both positives and hospitalizations probably end of Sept.

Does any one know where the love of God goes...When the waves turn the minutes to hours? -G. Lightfoot
Khaldun
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Reply #917 on: August 13, 2020, 01:44:24 PM

Pitt's a good example of another thing that made some research-1 universities blink and change course: they're in the middle of cities. It's actually just plausible that a place like Grinnell or Williams can make students be an isolated "cohort"--the town is basically an extension of the college, there's only 2000 students or so there, the setting is intimate enough that you can actually do contact tracing and sort of monitor whether students are doing dumb fucking shit like driving to a rave in Albany or whatever the fuck one would do in Des Moines in a large group of wasted-as-fuck twenty-somethings. Any big university in a city is completely fucked as far as that goes--they can't monitor students and there are a zillion ways for them to infect and be infected.
Khaldun
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Reply #918 on: August 13, 2020, 02:55:33 PM

On a completely separate subject, just to show you that if you want to be data-driven you have to accept that the road doesn't always go where you expect, here's an interesting analysis of one of our favorite subjects of conversation, Sweden: https://www.newscientist.com/article/2251615-is-swedens-coronavirus-strategy-a-cautionary-tale-or-a-success-story/

Upshot is that there may really be two simultaneous failures in the United States: that mask-wearing and compliance with social distancing was turned into a symbol of sociopolitical loyalty on the right...and that it was turned into a symbol of sociopolitical loyalty on the left. Meaning that it turns out (as has been suggested in previous discussions) that Swedes were essentially practicing social distancing (with the same economic consequences) voluntarily at roughly the same rates as in countries where social distancing was mandated by strong government or regulatory authority. And that maybe Swedes *did* develop some (at yet not well-measured) immunity. And that maybe Sweden's high per-capita death rate was mostly about a single judgmental error, which was to underestimate the vulnerability of elder care.

In the US, of course, I would still argue that this suggests that an administration that emphasized the importance of voluntary controls and acknowledged the liberty or autonomy of citizens but ALSO was absolutely unmistakeably coherent and united in its approach to the disease and strongly recommended distancing, masking, testing, might have cut in half or more the deaths. Maybe Americans are locked into an oppositional death spiral that means that if one group says, "Everyone loves apple pie", the other faction will say "Fuck you, we're going to burn apple pies by their thousands at motorcycle rallies and eat only red velvet cake" but political leadership that fuels that fire guarantees failure and death. If you leave an educated populace to cope with a pandemic while supplying them with trustworthy technical expertise and transparent political leadership, you may get roughly similar outcomes, including that your economy takes a hit because people cut back on their voluntary social interactions and travel.

So the lesson from Sweden may not be "no controls", any more than the lesson from New Zealand is "tight controls". It may be "trust, unity and truthful information".
BobtheSomething
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Reply #919 on: August 15, 2020, 11:06:48 PM

My son's baseball league announced they're doing fall ball. Begins in a couple weeks.

Not sure how I feel about this. 95% of the kids are in very large public school districts and Arizona is still Arizona.

Probably sucks for the kids who get permanent lung damage that impairs their game.  Also for the ones who spend the rest of their lives knowing they brought home the disease that killed grandma/grandpa alone and in pain.

Rasix
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Reply #920 on: August 26, 2020, 09:09:54 AM

The safety guidelines were put up for baseball, and they're pretty lackluster. They work on the assumption that no one will get sick and no one will go to games/practices while ill. The language is pretty loose as to not mandate masks in almost any situation except perhaps in the dugout.

They're trying, but it just kind of comes up short. You have to be clear about what you're going to do if/when someone gets sick on a team, and they're just dancing around that situation.  Ohhhhh, I see.

-Rasix
Khaldun
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Reply #921 on: August 27, 2020, 03:09:05 PM

Anybody know anything about a company called Everlywell? I can only find stuff about their post-Shark Tank nutritional test and then a kerfuffle with the FDA in May over a covid-19 test. Nothing since about the reliability of their testing procedure, etc.
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Reply #922 on: August 27, 2020, 04:05:12 PM

they shouldn't even be "trying"
Surlyboi
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Reply #923 on: August 27, 2020, 04:11:07 PM

My brother-in-law is a school bus driver in Delaware. He got it within a week of school opening down there. He then, of course gave it to my sister. They’ve both gotten through the worst of it but he’s still on oxygen three weeks later and they’re both experiencing long-haul syndrome after effects (lingering fatigue, foggy heads, etc.)

I’m also worried about the potential other effects, especially since the brother-in-law is diabetic.

Tuned in, immediately get to watch cringey Ubisoft talking head offering her deepest sympathies to the families impacted by the Orlando shooting while flanked by a man in a giraffe suit and some sort of "horrifically garish neon costumes through the ages" exhibit or something.  We need to stop this fucking planet right now and sort some shit out. -Kail
Trippy
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Reply #924 on: August 27, 2020, 04:35:22 PM

Anybody know anything about a company called Everlywell? I can only find stuff about their post-Shark Tank nutritional test and then a kerfuffle with the FDA in May over a covid-19 test. Nothing since about the reliability of their testing procedure, etc.
According to this Everlywell is using Fulgent Therapeutics and Assurance Scientific Laboratories for the actual testing. Fulgent is doing a good job of hiding their internal test results (can't find them at the moment) so I don't know what their internal false positive and false negative rates are. Assurance Scientific Laboratories does publish their internal test data and it looks good (under ideal circumstances):

https://assurancescientificlabs.com/wp-content/uploads/2020/07/COVID-19_Technical_Bulletin.pdf
« Last Edit: August 27, 2020, 04:39:44 PM by Trippy »
Khaldun
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Reply #925 on: August 27, 2020, 05:47:02 PM

Thanks, that's useful. I get the need to let testing producers operate under FDA authorization rather than approval, but it still seems to me that should confer an obligation to publication of results on a rolling basis if you're pushing out millions of kits. Especially since this company's previous product (the nutrition thing) got a lot of bad marks for dodgy or inconsistent results.
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Reply #926 on: August 27, 2020, 05:49:11 PM

Thanks, that's useful. I get the need to let testing producers operate under FDA authorization rather than approval, but it still seems to me that should confer an obligation to publication of results on a rolling basis if you're pushing out millions of kits. Especially since this company's previous product (the nutrition thing) got a lot of bad marks for dodgy or inconsistent results.


The FDA just dropped any requirements for EUA on Covid tests last week. There are going to be a lot of fly-by-night testing coming out soon.

'Reality' is the only word in the language that should always be used in quotes.
Khaldun
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Reply #927 on: August 27, 2020, 05:54:06 PM

Yes. So now we're going to get bullshit tests done by employers that are on the cheap and unreliable just so they can say they checked off the liability problem. Which will leave anyone who feels they were in a workplace where the employer was utterly negligent having to get entangled in complicated litigation over a decade or more about the reliability of a particular test provider. Rather than having a single national standard or even three or four approved variant tests that have met some standard of reliability. Probably the same when we get to vaccination, if we do, unless we have a new political regime in January.
Gimfain
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Reply #928 on: September 03, 2020, 12:03:21 PM

There were a study made on blood givers and they found out that 7% of blood givers had anti-bodies for covid-19. When doing randomized testing of active covid-19 on 2500 people they found 0 people with current infection. When they did randomized tests in april it was 0.9%, in may it was 0.3%. In the region where I live there isn't anyone hospitalized for covid-19. There were 2492 persons tested (not randomized) for covid-19 two weeks ago and 12 with active infection.

Given how few people have antibodies its due to  mostly voluntary social distancing, local reinforcement of common sense rules and not about herd immunity.
« Last Edit: September 03, 2020, 12:08:09 PM by Gimfain »

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MahrinSkel
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Reply #929 on: September 03, 2020, 01:44:21 PM

Meanwhile, in the land of the mud people: https://www.kpq.com/coronavirus-updates-university-reports-90-jump-in-cases-on-campus-2/

Quote
Sep 02, 6:13 am
Ole Miss reports 20 active outbreaks on campus

The University of Mississippi said it has confirmed at least 481 cases of COVID-19 among students and employees on its Oxford campus since the start of the pandemic.

Of those, 277 are active cases, mostly among students. Over the past seven days, there have been 223 new confirmed cases, an increase of more than 90%. There are currently 20 active outbreaks of three or more cases on campus, most of which are within campus housing, according to data posted on the University of Mississippi’s website.

The public research university in Oxford, Mississippi, known by its nickname Ole Miss, resumed classes on Aug. 24.

According to the student newspaper, The Daily Mississippian, emails were sent out saying residents in on-campus dormitories with a cluster of three or more cases would need to find a place to quarantine. However, some students were urged to return home or isolate themselves off-campus in nearby apartments or hotels due to the limited number of quarantine spaces on campus.

Health officials are concerned this could lead to COVID-19 spreading off-campus among the local community, according to a report by Memphis ABC affiliate WATN-TV.
So, yeah, one week from "Everything will be fine." to "Man, this risk was calculated very badly."

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Chimpy
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Reply #930 on: September 03, 2020, 02:38:44 PM

And they are not testing asymptomatic people unless they are a close contact, I am sure.

That case number is likely 10% or less of the actual number of cases around there.

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Reply #931 on: September 03, 2020, 03:19:38 PM

Sky
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Reply #932 on: September 03, 2020, 08:16:26 PM

Meanwhile in NY, where we have actual leadership and a functioning government: https://www.governor.ny.gov/news/governor-cuomo-deploys-swat-team-suny-oneonta-contain-covid-19-cluster
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Reply #933 on: September 03, 2020, 08:41:40 PM

And they are not testing asymptomatic people unless they are a close contact, I am sure.

That case number is likely 10% or less of the actual number of cases around there.

Sometimes even symptomatic people aren't tested either in this state. Just about everyone here seems to be intent on wearing a mask then completely forgetting the thing exists.

Gimfain
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Reply #934 on: September 10, 2020, 01:02:30 AM

Did an antibodies test and it showed negative so most likely its something else that made me lose taste completely for a brief time after being ill and completely wrecked my sense of smell.
« Last Edit: September 10, 2020, 01:06:15 AM by Gimfain »

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Reply #935 on: September 10, 2020, 07:02:36 AM

That is maybe not a safe conclusion: the antibody tests are known to have high rates of false negatives.

Not that it matters in some sense: you should continue to protect yourself from coronavirus regardless.
Trippy
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Reply #936 on: October 30, 2020, 03:24:18 PM

New paper from the Imperial College London and others estimating IFR based on 10 antibody studies:

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-34-ifr/

https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-10-29-COVID19-Report-34.pdf

Quote
Summary

The infection fatality ratio (IFR) is a key statistic for estimating the burden of coronavirus disease 2019 (COVID-19) and has been continuously debated throughout the current pandemic. Previous estimates have relied on data early in the epidemic, or have not fully accounted for uncertainty in serological test characteristics and delays from onset of infection to seroconversion, death, and antibody waning. After screening 175 studies, we identified 10 representative antibody surveys to obtain updated estimates of the IFR using a modelling framework that addresses the limitations listed above. We inferred serological test specificity from regional variation within serosurveys, which is critical for correctly estimating the cumulative proportion infected when seroprevalence is still low. We find that age-specific IFRs follow an approximately log-linear pattern, with the risk of death doubling approximately every eight years of age. Using these age-specific estimates, we estimate the overall IFR in a typical low-income country, with a population structure skewed towards younger individuals, to be 0.23% (0.14-0.42 95% prediction interval range). In contrast, in a typical high income country, with a greater concentration of elderly individuals, we estimate the overall IFR to be 1.15% (0.78-1.79 95% prediction interval range). We show that accounting for seroreversion, the waning of antibodies leading to a negative serological result, can slightly reduce the IFR among serosurveys conducted several months after the first wave of the outbreak, such as Italy. In contrast, uncertainty in test false positive rates combined with low seroprevalence in some surveys can reconcile apparently low crude fatality ratios with the IFR in other countries. Unbiased estimates of the IFR continue to be critical to policymakers to inform key response decisions. It will be important to continue to monitor the IFR as new treatments are introduced.
HaemishM
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Reply #937 on: October 30, 2020, 09:03:29 PM

So it's somewhere between 5 and 10 times more deadly than seasonal flus.

We are so fucked.

Jeff Kelly
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Reply #938 on: November 09, 2020, 06:04:53 AM

Today a German biotech firm has announced that they successfully completed their trials and that they have a vaccine that is „more than 90% effective”.

The plan to start the clearance process with the German analog to the FDA next week

edit: the company name is Biontech and they also request clearance with the FDA

Edit by Trippy: Pfizer press release:

https://investors.pfizer.com/investor-news/press-release-details/2020/Pfizer-and-BioNTech-Announce-Vaccine-Candidate-Against-COVID-19-Achieved-Success-in-First-Interim-Analysis-from-Phase-3-Study/default.aspx
« Last Edit: November 09, 2020, 10:29:46 AM by Trippy »
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Reply #939 on: November 09, 2020, 06:46:34 AM

Pfizer is their US partner.

This is one of the trials that when their testing protocols were released a couple of months ago got a good bit of skepticism from vaccine experts because the low bar they were looking to clear for "efficacy". And they said they would possibly stop the trial early if it showed early promising results. (I am not sure if it is this one, or the Moderna one that it just needed to show a "lack of a mild case in as few as 18 patients" to be deemed 'effective')

'Reality' is the only word in the language that should always be used in quotes.
Jeff Kelly
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Reply #940 on: November 09, 2020, 07:23:23 AM

According to the press release

Vaccine candidate was found to be more than 90% effective in preventing COVID-19 in participants without evidence of prior SARS-CoV-2 infection in the first interim efficacy analysis
Analysis evaluated 94 confirmed cases of COVID-19 in trial participants
Study enrolled 43,538 participants, with 42% having diverse backgrounds, and no serious safety concerns have been observed; safety and additional efficacy data continue to be collected
Submission for Emergency Use Authorization (EUA) to the U.S. Food and Drug Administration (FDA) planned soon after the required safety milestone is achieved, which is currently expected to occur in the third week of November
Clinical trial to continue through to final analysis at 164 confirmed cases in orde
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Reply #941 on: November 09, 2020, 07:50:56 AM

 90% would be great if it pans out. 

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Reply #942 on: November 09, 2020, 07:59:44 AM

There only being 84 cases out of 22,000 placebo recipients is what leads to questioning the 90% effective number.

It leads me to think that the people who participated in this trial were being more cautious than the population as a whole when it comes to social distancing, masking, etc.

I mean, it is great if it is truly effective.
« Last Edit: November 09, 2020, 08:01:30 AM by Chimpy »

'Reality' is the only word in the language that should always be used in quotes.
Jeff Kelly
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Reply #943 on: November 09, 2020, 08:05:46 AM

I don’t see how you could ‚improve‘ those odds without either vastly increasing the number of test subjects probably tenfold or without deliberately infecting people.

If you pre-select subjects for e.g. risky behavior it’s no longer a controlled representative study and you lose aspects of the double blind property.
Trippy
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Reply #944 on: November 09, 2020, 10:11:35 AM

Pfizer is their US partner.

This is one of the trials that when their testing protocols were released a couple of months ago got a good bit of skepticism from vaccine experts because the low bar they were looking to clear for "efficacy". And they said they would possibly stop the trial early if it showed early promising results. (I am not sure if it is this one, or the Moderna one that it just needed to show a "lack of a mild case in as few as 18 patients" to be deemed 'effective')
They changed the criteria over time so the data they have currently is stronger than their original design. I'm not a statistician so I can't say if the earlier criticisms are still valid.

https://www.statnews.com/2020/11/09/covid-19-vaccine-from-pfizer-and-biontech-is-strongly-effective-early-data-from-large-trial-indicate/
Quote
In their announcement of the results, Pfizer and BioNTech revealed a surprise. The companies said they had decided not to conduct the 32-case analysis “after a discussion with the FDA.” Instead, they planned to conduct the analysis after 62 cases. But by the time the plan had been formalized, there had been 94 cases of Covid-19 in the study. It’s not known how many were in the vaccine arm, but it would have to be nine or fewer.
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