Coronavirus

[Smith Corks One]

Watched an interesting podcast of This Week in Virology last night/this morning, it's long.

https://www.microbe.tv/twiv/twiv-640/

They had a guy who has a pre-published/non peer-reviewed study out there (link below) that essentially says it's more important to have cheap, quick testing available and the way to do that is to decrease sensitivity and move away from the RT-PCR gold standard. The pros of the RT-PCR are obvious. It's effective, reliable, and is very sensitive. The cons obviously are it is expensive, supplies are still limited, requires healthcare personnel to administer thus requiring PPE, can lead to long lines discouraging people from being tested, and importantly it can take a week to get the results.

This guy advocates to a different kind of testing using spit and molecular recognition on paper (paper test) which he claims are available and can be mass produced. The pros are they cost about $1-$2 per test and offer results in 10 minutes and can be done at home. The con is that it is not as sensitive. The guy, no fan of trump, claims the white house used these types of tests (albeit not the exact same one) and NYU blasted the process as not being sensitive enough. It became politicized and everyone moved away from this form of testing.

Regardless, the crux of the argument is that people who are asymptomatic or not sick enough to go to the hospital (so the vast majority of people infected) only have enough virus in their system to transmit the disease for a certain period of time. The paper test can detect the virus at that level and could be done daily allowing people to stay home, prevent spread, and thereby lowering the R effective to well below 1. As such, this is a relatively cheap, simple path forward to stop the spread, allow people back to work/school/etc, and move forward.

The last key hurdle to use this would be to get FDA approval which is unlikely as they currently require test to be a minimum of 80% as sensitive as the RT-PCR test which the paper tests can't achieve. And, there's little push to get that changed.


https://www.medrxiv.org/content/10.1101 ... 20136309v2

tl;dr: Tests are available through a completely different method right now that can be done at home in 10 minutes likely telling people if they are positive for Sars-Cov-2 and if they can transmit the disease. The cost of said test is $2.

I don’t know anything about the different types of tests, but twice in the past week (for different reasons) my wife and I went to a Walgreens drive thru testing center and got tested in no time (no wait one time, ~20 minute wait the other time). No cost to us, and swabbed our own noses. Results emailed to us within an hour. That seemed like a good deal. Anyone can do it, just need to make an appointment online.

[sighyoung]

[AWvsCBsteeeerike3]

Watched an interesting podcast of This Week in Virology last night/this morning, it's long.

https://www.microbe.tv/twiv/twiv-640/

They had a guy who has a pre-published/non peer-reviewed study out there (link below) that essentially says it's more important to have cheap, quick testing available and the way to do that is to decrease sensitivity and move away from the RT-PCR gold standard. The pros of the RT-PCR are obvious. It's effective, reliable, and is very sensitive. The cons obviously are it is expensive, supplies are still limited, requires healthcare personnel to administer thus requiring PPE, can lead to long lines discouraging people from being tested, and importantly it can take a week to get the results.

This guy advocates to a different kind of testing using spit and molecular recognition on paper (paper test) which he claims are available and can be mass produced. The pros are they cost about $1-$2 per test and offer results in 10 minutes and can be done at home. The con is that it is not as sensitive. The guy, no fan of trump, claims the white house used these types of tests (albeit not the exact same one) and NYU blasted the process as not being sensitive enough. It became politicized and everyone moved away from this form of testing.

Regardless, the crux of the argument is that people who are asymptomatic or not sick enough to go to the hospital (so the vast majority of people infected) only have enough virus in their system to transmit the disease for a certain period of time. The paper test can detect the virus at that level and could be done daily allowing people to stay home, prevent spread, and thereby lowering the R effective to well below 1. As such, this is a relatively cheap, simple path forward to stop the spread, allow people back to work/school/etc, and move forward.

The last key hurdle to use this would be to get FDA approval which is unlikely as they currently require test to be a minimum of 80% as sensitive as the RT-PCR test which the paper tests can't achieve. And, there's little push to get that changed.


https://www.medrxiv.org/content/10.1101 ... 20136309v2

tl;dr: Tests are available through a completely different method right now that can be done at home in 10 minutes likely telling people if they are positive for Sars-Cov-2 and if they can transmit the disease. The cost of said test is $2.

I don’t know anything about the different types of tests, but twice in the past week (for different reasons) my wife and I went to a Walgreens drive thru testing center and got tested in no time (no wait one time, ~20 minute wait the other time). No cost to us, and swabbed our own noses. Results emailed to us within an hour. That seemed like a good deal. Anyone can do it, just need to make an appointment online.

That seems like about the ideal execution of the current PCR testing from my understanding. And, not that it is entirely all that cumbersome, but in your situation, you still had to make the appointment, drive to a place and wait on average 10 min, drive home, get results in an hour.

Applying that model to school children, factory workers, etc still isn't feasible. And, as we're seeing when areas go through outbreaks (like Miami), that testing infrastructure starts to breakdown and result in long wait times and longer times to get results. Stands to reason that if we start relying on testing to prophylactically identify cases instead of testing symptomatic/exposed people, that excess demand is going to lead to the same situation.

Regardless, that's good to hear you were able to get tested and get results that quickly.

At the same time, the US has performed somewhere around 50M tests and I think we can effectively say that has not adequately prevented the spread. The cost is somewhere around $200 per test which comes to about $10 Billion spent on testing with no slowdown in the foreseeable future.

Conversely, iff a method is available that can be done for $2 in 10 minutes at home and that identifies individuals that currently have a transmittable concentration of virus, the US could test its entire population everyday for 2 weeks at a cost of $10B. And, doing so would have a much greater affect at slowing down the spread of the virus than the PCR testing has done.

[GeddyWrox]

Is there any indication of the number of false reads given by the at home saliva test?

[AWvsCBsteeeerike3]

Is there any indication of the number of false reads given by the at home saliva test?

I'd have to do more digging, but I think the specificity was still quite high (maybe 94%) where as PCR is closer to 99% (I think). So, you'd have more false positives. Of course, the test could be re-run pretty quickly to confirm. Given it's at 94% specificity, I think that means there's a 6% chance it's falsely positive and two positives in a row would have a 0.36% chance of being falsely positive.

Then, looking at false negatives it has more. The sensitivity I heard mentioned was 51%. But, it's not incorrectly negative 49% of the time across the board. Not going to get into the concentrations because they dont make sense to me at the moment, but once the concentration got above a certain point, the confidence shot back up into the 95%+ range. The argument made on the This Week in Virology segment was that it's not necessary to detect that lower viral connection because the virus can't be transmitted from person to person at that point.

There's some science backing this, though I can't confirm. Anecdotally, I know they've locally treated people successfully in the hospital and struggled to get two consecutive negative PCR tests. In a couple cases, they would get one then the next day it would be positive, then the next day negative, then the next day positive, etc etc etc. So, the hospital was holding people that clinically recovered, weren't showing symptoms but still had minimal, probably dead, viral RNA in their system.

[mikechamp]

The forecast is not looking too good, and I'm not referring to the weather:

US returns to 1,000 coronavirus deaths in a day and officials warn pandemic will only get worse

At least 1,000 American deaths linked to the coronavirus were reported Tuesday, and the spread shows no sign of slowing down. The harrowing death toll comes as states across the country report record-breaking numbers of new cases. More governors are making masks a requirement as overwhelmed testing labs and hospitals are raising alarm. And officials are debating whether to send children back to school in person.

The only other time this month the country crossed the threshold of 1,000 reported deaths was July 7, with 1,195 reported fatalities. According to data from Johns Hopkins University, a quarter of all days this year have seen a US death toll exceeding 1,000. Experts say the virus is now running rampant within American communities, and new data from the US Centers for Disease Control and Prevention also show infections could be more than 10 times higher than the number of reported cases in some parts of the US.

Last week, CDC Director Dr. Robert Redfield said the fall and winter will likely be "one of the most difficult times that we experienced in American public health."

https://www.kmov.com/news/us-returns-to ... f8e89.html

[AWvsCBsteeeerike3]

In some cases like this one, I really think the media does a massive disservice to the public in how they report information.

Case in point, take the idea we were talking about rapid testing earlier. Then read this article, or at least the quoted part.

https://www.msn.com/en-us/news/us/coron ... li=BBnb7Kz

As promising as the rapid tests seem to be, a significant problem prevents more doctors and clinicians from using them. Most aren't as accurate as lab-based tests, and, in some cases, they can have shockingly high rates of false negatives.

Joseph Petrosino, director of molecular virology and microbiology at Baylor College of Medicine, compares it to eating at a fast-food joint.

"If you go to a gourmet restaurant, you don't expect your meal to be ready in five minutes," he said. "But if you're on the go and you eat fast food, the quality of food is usually a sacrifice, compared to the gourmet restaurant. That's the same thing in the testing world."

One of the more popular rapid tests, Abbott Labs' ID NOW point-of-care test, which promises results in as little as five minutes and was once touted by the White House, came under fire in recent weeks after a small study found that it returned false negatives for nearly 50 percent of certain samples compared to a rival test. While other studies found more accurate results, it was enough for the FDA to issue an alert in May. The agency has received 147 adverse event reports about the test.

"The reality is that trying to do this really fast — the combination of fast and sensitive — turns out to be really a challenge," said Dr. Christopher Polage, director of the clinical microbiology laboratory at Duke University Health System.

So, that gives a pretty negative view of them right. How likely are people to trust them after reading that?

But, not until the very end do they even mention sensitivity. And, turns out, the tests aren't necessarily false negatives in context. They're simply not as sensitive and don't pick up low levels of the virus.

Is that important? Yeah, it's a pretty, pretty, pretty massive deal because it's this nuance that is at the entire crux of the argument for them but they completely ignore it.

And, that crux is this. The PCR gold standard nasal swab detects CT levels of ~40. CT levels are inversely proportional to the amount of virus in the blood. Lower CT = Higher Viral Concentration. And, it's not linear. A drop in about 3 CT levels (eg, 40 to 37) represents a 10 fold increase in the viral concentration.

Is this important? Yes, because according to Dr. Fauci CT levels of 37 or 36 and above should be interpreted as dead nucleitides which for all intents and purposes means no virus. And, the 50% of false negatives are those in this 37-40 CT level. Which may sound made up because its such a small range, but keep in mind, the viral concentration can remain at this point for weeks after the body has fought off the virus as it dies and stays in the blood from my understanding. So, the tail of the viral concentration is quite long.

Yet, the FDA is requiring sensitivities comparable to the PCR gold standard test.

Bringing me back to the crux of the argument. By requiring tests to pick up CT levels from 36-40, it's inhibiting the use/approval of rapid testing, and the only upside to include that range is to know if dead nucleitides exist on the tail end. Conversely, when the CT level is decreasing and virus is increasing, I've heard estimates that the level jumps from 40 to 35 in less than a day perhaps as little as a few hours but this level is also prior to symptom onset so a negligible amount of people are being tested on the front end in this timeframe.

tl:dr; The article blunts a nuanced conversation pointing readers towards a conclusion and away from an intimate conversation that is desperately needed. And, imo, they point readers in the wrong direction.

[GeddyWrox]

I get what you're saying here, AW. 100%.

But think how much scientific explaining you had to do to get the point across. It's just sad that so many people eschew science and learning to the point that most people can't get their heads around subtle/difficult ideas when it is urgent to national health and security to do so.

[AWvsCBsteeeerike3]

Eh, [expletive] it. Let's just let it burn its way through and see what happens, I guess. We can be the control along with Sweden.

On that note, looking at Sweden, I see they're at and have been stuck at 560ish deaths / million population which would put USA at 185K deaths before this whole things blows over.

We're almost there. *Nervous laughter*

[thrill]

Eh, [expletive] it. Let's just let it burn its way through and see what happens, I guess.

LMAO, not that we have a choice. It would be nice to have a choice, I think.