Cont: 2019-nCoV / Corona virus Pt 3

[Skeptical Greg]

You really do seem to be straining to downplay this, for some reason or another that I cannot fathom.

No, I'm personally not downplaying it.. I'm just not hand-wringing over it.

At 71, I'm supposed to be high risk. I personally feel that age is less of a factor than others, such as immune health, which tends to decline with age, but not always.

See my posts about obesity and diabetes.

 

[Skeptical Greg]

Mebbe it was the flu.

That was addressed earlier:

The list of doctors killed was not legitimate in terms of demonstrating risk of medical practitioners because it consisted heavily of very old/retired doctors who had nothing to do with the epidemic, some even in their 90s. When this was pointed out, their ages were conveniently removed from the website.

Some possibly did die from complications caused by the flu.

 

[marting]

As far as I have been able to determine, there is no reason to assume that the Covid 19 virus is as vulnerable to humidity and warm weather as flu. I don't think there is enough reliable data available yet to know one way or the other.

Heck, even if it was it wouldn't make much difference. COVID-19 has an R0 of around 2.5 while the Flu is about 1.3. It would take a much smaller environmental impact to drop Flu R0 below 1 if they both had the same sensitivity than get COVID-19 below 1. I wouldn't expect as much an impact from seasonal variations on COVID-19.

 

[EHocking]

Sure.

No, I'm personally not downplaying it.. I'm just not hand-wringing over it.

At 71, I'm supposed to be high risk. I personally feel that age is less of a factor than others, such as immune health, which tends to decline with age, but not always.

See my posts about obesity and diabetes.

I think most people accept that older people are more susceptible because of the likelihood that, at as people age, they are more likely to have an underlying or pre-existing medical condition, than younger age groups.
The figures at worldometer certainly show a correlation , but unfortunately don’t break down comorbity figures into age (or vice versa).

 

[Arcade22]

This is rubbish.

I am the first to criticize China, and it is entirely true that their Government is continuing to encroach on Hong Kong in as many ways as it can, but unlike China we have a free and open press, a professional, spirited and opinionated medical establishment.

In this situation there is absolutely no way the Hong Kong numbers are being underreported.

Yes I'm sure Gui Minhai is grateful for the freedoms he enjoyed in HK until he was kidnapped. I guess as long as people don't write gossip books about the Chinese leader they will not be disappeared and only reappear on Chinese television confessing to grave crimes and begging for forgiveness.

 

[Sherkeu]

As far as I have been able to determine, there is no reason to assume that the Covid 19 virus is as vulnerable to humidity and warm weather as flu. I don't think there is enough reliable data available yet to know one way or the other.

Except that this is not really very difficult to test. And it has been tested. Do you think the tests are wrong?

I think the largest dispute is that because it is a 'novel' virus' it may not be adequate to say the exact virus found in S. Korea is the same worldwide, as slight mutations are possible that could have big effects. But that isn't the norm. A Corona virus normally has slower mutation.

Science is kinda slow that way to say definitively one way or the other. But the growing consensus is that it survives and thrives in cool dry air, and on surfaces in that same environment. You only need to look at where it spreads to know this is a very good theory.
You could argue that a particular strain is doing 'xyz' in terms of contagion, and another behaves different, but all of them should be guarded against as if they had max spread potential.

 

[xjx388]

I have a question about the Igg/Igm tests that are seemingly flooding the market now. The FDA requires them to say that they are not diagnostic in and of themselves and that a false positive could occur if someone has had an infection with one of the other human Coronaviruses. In my mind, this renders them nearly useless.

I ask because I’m trying to advise the doctors in our clinic whether or not they should order them. I lean towards “not” because we could end up falsely diagnosing a bunch of patients and missing a punch that should be positive. I’m trying to convince them to simply wait until Abbot’s new ID Now test (we already use the system for flu, strep and RSV) is widely available in the next month or so. Their issue is that the PCR test kits are not easily obtainable from the labs that are doing it and they want to be able to offer something and they think it’s accurate enough according to the literature the test makers are publishing.

There are some smart, scientifically oriented people here: what say you?

 

[Skeptic Ginger]

You need to list the specific tests if you want an opinion on their usefulness.

Keep in mind none are useful for diagnosing a person with new onset of symptoms because even IGM won't show up for ~12 days according to a study in China I posted upthread. IGG shows up a week or so after that.

 

[Roboramma]

DR, this offer is still on the table, by the way.

How's this: I'll bet you that by Jan 1st 2021, the total number of deaths attributed to Covid19 in the USA by John's Hopkins on this website: https://coronavirus.jhu.edu/map.html will be greater than 75,000.

That 75,000 is based on your high estimate of how many deaths might occur, plus a bit. But I'd be willing to consider other terms.

As for stakes, people around here often do avatar bets, but I'd be willing to consider other stakes as well.

I find it odd that you didn't even response, considering you said you were interested in my proposal.

If you aren't confident that the number will be below 75k, I'd be happy to make the bet based on the 100k number that you've mentioned a few times in the thread.

 

[Skeptic Ginger]

The Abbott point of care test has emergency FDA approval.

I'm going to guess the little machine you need to run the test strips is going to be $5-10K. And the test strips, let's just say Abbott will make a profit on those too. Not sure which insurers if any are going to pay for the test but many probably will.

I'd be shocked if it is less and not surprised to see it even more.

The ID NOW COVID-19 EUA has not been FDA cleared or approved. It has been authorized by the FDA under an emergency use authorization for use by authorized laboratories and patient care settings. The test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens, and is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostic tests for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.

Probably going to be another month but for larger clinics that can pay for the diagnostic machine, I predict this will be a success.

I went through a page after page search for the sensitivity and specificity and it looks like you have to call and talk to a rep to find out.

I finally found this:
IN190000 v1.0 ID NOW COVID-19 Test Product Insert IN1.pdf

Analytical Reactivity (Inclusivity)
Due to the limited availability of SARS-CoV-2 isolates for inclusivity testing, an alignment was performed with the oligonucleotide primer and
probe sequences of the ID NOW COVID-19 assay with all publicly available nucleic acid sequences for the 2019-nCoV in public databases
(NCBI*and Genbank) to demonstrate the predicted inclusivity of the ID NOW COVID-19 assay. All of the alignments show 100% identity of the
ID NOW COVID-19 to the available SARS-CoV-2 sequences as of March 20, 2020.
Analytical Specificity (Cross Reactivity)
An in silico analysis for possible cross-reactions with all the organisms listed in the table below was conducted by mapping primers and probes of the
ID NOW COVID-19 target nucleic acid sequence to the sequences download from the NCBI Genbank and GISAID databases.
The ID NOW COVID-19 assay, designed for the specific detection of SARS-CoV-2, showed no significant combined homologies with human
genome, other coronaviruses, or human microflora that would predict potential ID NOW COVID-19 false results.

So they mostly tested molecules from surrogate organisms in their trials like a proof of concept. It doesn't look like that did a lot of field trials.

 

[Planigale]

I have a question about the Igg/Igm tests that are seemingly flooding the market now. The FDA requires them to say that they are not diagnostic in and of themselves and that a false positive could occur if someone has had an infection with one of the other human Coronaviruses. In my mind, this renders them nearly useless.

I ask because I’m trying to advise the doctors in our clinic whether or not they should order them. I lean towards “not” because we could end up falsely diagnosing a bunch of patients and missing a punch that should be positive. I’m trying to convince them to simply wait until Abbot’s new ID Now test (we already use the system for flu, strep and RSV) is widely available in the next month or so. Their issue is that the PCR test kits are not easily obtainable from the labs that are doing it and they want to be able to offer something and they think it’s accurate enough according to the literature the test makers are publishing.

There are some smart, scientifically oriented people here: what say you?

My concern would be that the studies I have seen published show that IgG and IgM appear relatively late. That is > 2 weeks after onset of infection
https://www.nature.com/articles/s41591-020-0819-2#Fig1
So the antibody test will be unreliable early in the infection. One would probably need to wait until at least a week after onset of symptoms to use the antibody test to diagnose the illness. PCR tests are likely to be positive earlier. A more interesting question is whether in normal people a positive antibody test means you are immune at least in the short term and should be donating convalescent serum to treat critically ill patients. Immune healthcare staff could work inn the most high risk areas.

There may be better information in a week or two as trials of antibody based assays are currently underway.

Having said that the current PCR based tests have a significant false negative rate, which may be partially an issue with quality of sample. Sputum samples are more reliable than nose / throat swabs.

If I was buying one immediately I would go for a PCR based assay, but if I could wait two weeks to make a decision I would wait and see what the antibody studies show.

 

[Capsid]

The Abbott point of care test has emergency FDA approval.

I'm going to guess the little machine you need to run the test strips is going to be $5-10K. And the test strips, let's just say Abbott will make a profit on those too. Not sure which insurers if any are going to pay for the test but many probably will.

I'd be shocked if it is less and not surprised to see it even more.

Probably going to be another month but for larger clinics that can pay for the diagnostic machine, I predict this will be a success.

I went through a page after page search for the sensitivity and specificity and it looks like you have to call and talk to a rep to find out.

I finally found this:
IN190000 v1.0 ID NOW COVID-19 Test Product Insert IN1.pdf


So they mostly tested molecules from surrogate organisms in their trials like a proof of concept. It doesn't look like that did a lot of field trials.

Deleted


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[Capsid]

I have a question about the Igg/Igm tests that are seemingly flooding the market now. The FDA requires them to say that they are not diagnostic in and of themselves and that a false positive could occur if someone has had an infection with one of the other human Coronaviruses. In my mind, this renders them nearly useless.

I ask because I’m trying to advise the doctors in our clinic whether or not they should order them. I lean towards “not” because we could end up falsely diagnosing a bunch of patients and missing a punch that should be positive. I’m trying to convince them to simply wait until Abbot’s new ID Now test (we already use the system for flu, strep and RSV) is widely available in the next month or so. Their issue is that the PCR test kits are not easily obtainable from the labs that are doing it and they want to be able to offer something and they think it’s accurate enough according to the literature the test makers are publishing.

There are some smart, scientifically oriented people here: what say you?

The antibody tests aren’t diagnostic. They show if you had the infection by antibodies in the blood. The PCR test will show if you are infected by detecting viral RNA in the throat swab.


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[Capsid]

The Abbott point of care test has emergency FDA approval.

I'm going to guess the little machine you need to run the test strips is going to be $5-10K. And the test strips, let's just say Abbott will make a profit on those too. Not sure which insurers if any are going to pay for the test but many probably will.

I'd be shocked if it is less and not surprised to see it even more.

Probably going to be another month but for larger clinics that can pay for the diagnostic machine, I predict this will be a success.

I went through a page after page search for the sensitivity and specificity and it looks like you have to call and talk to a rep to find out.

I finally found this:
IN190000 v1.0 ID NOW COVID-19 Test Product Insert IN1.pdf


So they mostly tested molecules from surrogate organisms in their trials like a proof of concept. It doesn't look like that did a lot of field trials.

This is how PCR tests are designed. The nucleic acid sequence of the virus enables the complementary sequence (primers) to be predicted in silico and synthesised.


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[GraculusTheGreenBird]

Yes I'm sure Gui Minhai is grateful for the freedoms he enjoyed in HK until he was kidnapped. I guess as long as people don't write gossip books about the Chinese leader they will not be disappeared and only reappear on Chinese television confessing to grave crimes and begging for forgiveness.

And specifically because we have a free and open press this was widely reported, and there was a public outcry amongst HK citizens which went global. It then became one of many reasons that the Chinese government rightly became so distrusted under Xi, and the main contributing factor to the anti-extradition protests that started last year, and are still ongoing.

However, Hong Kong is NOT the same as China, and we have much greater freedom and Government transparency, an independent judiciary based on British Common Law and a free press. It is completely ignorant to claim otherwise.

The medical establishment here are not CCP toadies, they are professionals. There is no way the Hong Kong numbers are being under reported.

 

[JesseCuster]

Confirmed? as in "No other cause of death possible? No chance of mal diagnosis?"

He was talking about confirmed cases, not confirmed deaths. And confirmed as in have tested positive for COVID-19.

50,000 pneumonia deaths per year, is 4,000 per month. Only when Covid passes that can there are doubtless actual covid deaths, not "Deaths attributed to covid".

That sentence doesn't make any sense to me,

Only when COVID-19 deaths pass 50,000 per yer or 4,000 per month are there "doubtless covid deaths"? Until then they're just "deaths attributed to COVID"? How does passing a certain death toll (in total, or per year or per month or whatever) make a difference as to whether a diagnosis of COVID-19 is valid?

Please explain why there needs to be a certain amount of COVID-19 deaths before you know they're actually COVID-19 deaths. We're talking about people testing positive for the COVID-19 virus and who are then dying of severe pneumonia or respiratory distress. Is there an implication that some or a significant amount of them are dying of something else by coincidence and they're being mistakenly identified of dying from COVID-19?

I dont understand.

 

[JesseCuster]

Spain has a population of 46 million and has so far recorded 10,000 deaths from COVID-19. That would make a fatality rate of 0.02% if everyone in Spain had the infection.

New York City has a population of 8 million and has so far recorded 1300 deaths. That would make for a fatality rate of 0.016% if everyone in New York City had the infection.

Given the rate at which the death tolls are rising daily in Italy, Spain and New York, how can anyone suggest with a straight face that the fatality rate might be as low as 0.01% given that those places already have had more than 0.01% of their entire population die from COVID-19 so far and those numbers are growing all the time?

Am I missing something here?

Doghouse Reilly, are you going to address this?

The claim that the fatality rate for COVID-19 might be as low as 0.01% is prima facie absurd if you accept the death tolls from Italy, Spain and New York.

And will become increasingly absurd as those figures continue to climb in these and other regions.

 

[Belz...]

It would save the small businesses (actually any size) if your central government would give them enough money to stay alive without ever having to pay it back.

Which is why I mentioned "handle the load". You can't just hand away money forever.

He's talking about the UK.

Doesn't change anything. 3000 deaths already in the UK and the worst is still to come. 8k is a certainty.

 

[Planigale]

The antibody tests aren’t diagnostic. They show if you had the infection by antibodies in the blood. The PCR test will show if you are infected by detecting viral RNA in the throat swab.


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I have seen some suggestions that if you look at IgM in SARS it is positive at time of onset of symptoms, so an IgM test might be diagnostic for symptomatic patients. I accept that PCR is probably a better earlier test but involves dealing with infective material, and it is not the most enjoyable or non-worrying experience doing throat and nose swabs on someone who has a potentially life threatening infection, I'd far rather do a pin prick blood test.
ETA
See here.
It looks like at 3 days after onset of symptoms IgM may be more reliable than PCR.
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa310/5810754
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa344/5812996

 

[Planigale]

Mebbe it was the flu.

I have seen flu; I have seen people die of flu. This is not flu. Take my word. The people coming in have a new illness. They catastrophically deteriorate from seemingly well to needing to go on a ventilator in an hour, this does not happen with flu. Now just stop with the 'it might be flu' nonsense.