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Old 17th April 2020, 01:23 PM   #1
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The One Covid-19 Science and Medicine Thread

Mod WarningMultiple threads have been opened in this Science section regarding the novel corona virus. They cross each other frequently, making it difficult to decide in which thread a comment should go. This thread has been opened for all discussions of the science, math, medicine and technology related to our current pandemic.

All other threads have been closed. The threads have not been merged because it would create a chaos of cross-talk and confused timelines. However, members should feel free to quote from those closed threads and continue those discussions here.

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Old 17th April 2020, 02:23 PM   #2
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Los Angeles County is doing serological testing to determine the extent of exposed/infected v actual case rates and fatality rates. Question came re today's Stanford study that implies a IFR around .2%

Response was that they would be discussing this joint/USC study in detail next Monday.

Question is at 30:45 into the press conference.
https://www.youtube.com/watch?v=7sHs5MJRi10
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Old 17th April 2020, 03:08 PM   #3
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Originally Posted by sir drinks-a-lot View Post
No, I still think it's likely that it will be very largely under control in the US by then. I also think there will be much fewer deaths than have been predicted by many. Of course it's now apparent we'll be talking about it for a long time, but i think it will be talking about the economic fallout, the response, future possible pandemics, etc.

Now, any answer to the question you quoted? The Johns Hopkins site still doesn't seem to be showing 30K deaths in the US. Am I looking in the wrong place?
Yes, you're looking in the wrong place.

Johns Hopkins is currently showing for the USA:
Code:
    36,721 deaths;
  692,169 confirmed cases;
    58,437 recovered;
3,541,368 tested; and,
   111,972 currently in hospital.
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Old 17th April 2020, 04:15 PM   #4
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Deleted due to not having checked the date of the article the post was discussing.
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Old 17th April 2020, 04:18 PM   #5
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Originally Posted by marting View Post
Los Angeles County is doing serological testing to determine the extent of exposed/infected v actual case rates and fatality rates. Question came re today's Stanford study that implies a IFR around .2%
Well, if that holds up it seems to indicate the numbers infected aren't vastly more than we're seeing.
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Old 17th April 2020, 04:25 PM   #6
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Originally Posted by marting View Post
Los Angeles County is doing serological testing to determine the extent of exposed/infected v actual case rates and fatality rates. Question came re today's Stanford study that implies a IFR around .2%

Response was that they would be discussing this joint/USC study in detail next Monday.

Question is at 30:45 into the press conference.
https://www.youtube.com/watch?v=7sHs5MJRi10
"85 times as many people have had the virus as they had thought"? So mortality rate is not 4%, but 1/85 of 4%, but we all know my maths.... Herd immunity, here we come!
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Old 17th April 2020, 04:52 PM   #7
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Originally Posted by Angrysoba View Post
Perhaps, then, if it does come down to male-female explanation, maybe it is not so much that women are necessarily more competent, or that men are necessarily more incompetent, but that if a leader is incompetent, that leader is more likely to be a man.

There could be a scientific reason for that!
The scientific reason is - simple maths.

Consider that, of the 138 countries in the world, only 14 are headed by women, there is a 90% chance that the head of a country will be a man.

So there is also the 90% probability that if a country’s leader is competent it will be a man.
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Old 17th April 2020, 05:03 PM   #8
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From the Chinese study posted by Nessie in the closed thread:

Our study does not rule out outdoor transmission of the virus. However, among our 7,324 identified cases in China with sufficient descriptions, only one outdoor outbreak involving two cases occurred in a village in Shangqiu, Henan. A 27-year-old man had a conversation outdoors with an individual who had returned from Wuhan on 25 January and had the onset of symptoms on 1 February.

https://www.medrxiv.org/content/10.1...058v1.full.pdf

This looks useful to say the least
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Old 17th April 2020, 05:19 PM   #9
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Here's something I found interesting:

Dag Berild, a medical doctor and Associate Professor at Oslo University Hospital, argued that the low level of antibiotic resistant bacteria in Norwegian hospitals may also have played a role in the country's lower mortality rate.

"The argument for that is that many of the coronavirus pneumonia cases are complicated by bacterial pneumonia, so if that is the case with coronavirus, then patients in a country with a low resistance rate among bacteria would have a better prognosis than those in Italy, where they have an awful lot of resistant bacteria, particularly in Lombardy."

The article is about Norway's testing capacity which some may also find interesting:

https://www.thelocal.no/20200403/how...or-coronavirus
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Old 17th April 2020, 05:48 PM   #10
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Originally Posted by novaphile View Post
Yes, you're looking in the wrong place.

Johns Hopkins is currently showing for the USA:
Code:
    36,721 deaths;
  692,169 confirmed cases;
    58,437 recovered;
3,541,368 tested; and,
   111,972 currently in hospital.

That's over 400k/~60% of confirmed cases not accounted for ( dead, hospitalized or recovered )..

What does that mean?
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Old 17th April 2020, 06:06 PM   #11
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Originally Posted by Skeptical Greg View Post
That's over 400k/~60% of confirmed cases not accounted for ( dead, hospitalized or recovered )..

What does that mean?
It just means that they are at home, self-isolating (hopefully).
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Old 17th April 2020, 07:11 PM   #12
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Originally Posted by Samson View Post
From the Chinese study posted by Nessie in the closed thread:

Our study does not rule out outdoor transmission of the virus. However, among our 7,324 identified cases in China with sufficient descriptions, only one outdoor outbreak involving two cases occurred in a village in Shangqiu, Henan. A 27-year-old man had a conversation outdoors with an individual who had returned from Wuhan on 25 January and had the onset of symptoms on 1 February.

https://www.medrxiv.org/content/10.1...058v1.full.pdf

This looks useful to say the least
Yes, and it makes sense too. The probabilities of spread outdoors are extremely low unless you are in some rowdy group. OTOH, mass transit where you are sardines in a can or grouped indoors like nursing homes is really risky.

Also the study shows the obvious. That most infections are in families and close living groups like cruise ships and aircraft carriers. At least most of the sailors on the latter are young and are at little risk even if they get the bug.
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Old 17th April 2020, 07:29 PM   #13
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Originally Posted by marting View Post
Los Angeles County is doing serological testing to determine the extent of exposed/infected v actual case rates and fatality rates. Question came re today's Stanford study that implies a IFR around .2%

Response was that they would be discussing this joint/USC study in detail next Monday.

Question is at 30:45 into the press conference.
https://www.youtube.com/watch?v=7sHs5MJRi10
Did they query the people they were testing as to whether they had, or thought that they might have had, symptoms? At least for the Santa Clara County survey, it didn't sound like they did.

I'm wondering whether Santa Clara County is representative. I believe that only about 0.05 percent of the residents tested positive, which is about a quarter of the national average.
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Old 17th April 2020, 07:30 PM   #14
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Originally Posted by Ulf Nereng View Post
Here's something I found interesting:

Dag Berild, a medical doctor and Associate Professor at Oslo University Hospital, argued that the low level of antibiotic resistant bacteria in Norwegian hospitals may also have played a role in the country's lower mortality rate.

"The argument for that is that many of the coronavirus pneumonia cases are complicated by bacterial pneumonia, so if that is the case with coronavirus, then patients in a country with a low resistance rate among bacteria would have a better prognosis than those in Italy, where they have an awful lot of resistant bacteria, particularly in Lombardy."

The article is about Norway's testing capacity which some may also find interesting:

https://www.thelocal.no/20200403/how...or-coronavirus
This suggests that the lockdown should be modified. You are allowed to do what you want as long as you do it outside and respect the 1.5 meter rule.
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Old 17th April 2020, 07:44 PM   #15
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Originally Posted by TellyKNeasuss View Post
Did they query the people they were testing as to whether they had, or thought that they might have had, symptoms? At least for the Santa Clara County survey, it didn't sound like they did.

I'm wondering whether Santa Clara County is representative. I believe that only about 0.05 percent of the residents tested positive, which is about a quarter of the national average.
No idea. They did suggest that the expected results that would be different numbers but more or less consistent with Stanford's results. I'm going to make a point of following up Monday. My major concern with serological tests is false positive rates. Especially critical when looking at small percentages. So I'm somewhat skeptical at this time.
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Old 17th April 2020, 08:08 PM   #16
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None of the antibody tests have had anything close to adequate testing to verify sensitivity and specificity. That is probably true worldwide as well but I'm only familiar with the tests being used in the US.
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Old 17th April 2020, 08:09 PM   #17
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Originally Posted by marting View Post
.....My major concern with serological tests is false positive rates. Especially critical when looking at small percentages. So I'm somewhat skeptical at this time.
The nasal swab positive rate among patients with symptoms is only about 8%. Which leaves room for lots of serum true positives. 85x 8% is not a small number.

Got any numbers for false positives on equivalent tests? Isn't HIV about 5%?

85x is given for the Stanford study, the L.A. study is not as high, but of similar magnitude. And more random, and larger sample size. I eagerly await our Serological Overlord.
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Old 17th April 2020, 08:22 PM   #18
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Originally Posted by marting View Post
Yes, and it makes sense too. The probabilities of spread outdoors are extremely low unless you are in some rowdy group. OTOH, mass transit where you are sardines in a can or grouped indoors like nursing homes is really risky.

Also the study shows the obvious. That most infections are in families and close living groups like cruise ships and aircraft carriers. At least most of the sailors on the latter are young and are at little risk even if they get the bug.
I think this result is with everybody wearing masks outside, though.
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Old 17th April 2020, 09:34 PM   #19
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Originally Posted by Skeptic Ginger View Post
None of the antibody tests have had anything close to adequate testing to verify sensitivity and specificity. That is probably true worldwide as well but I'm only familiar with the tests being used in the US.
I cannot understand how they could measure the accuracy of these antibody tests. Like the result of a test is positive. Does it mean the person has had the virus or is it a false positive? All they can do is test people who have recently recovered and if their test is negative then probably something is wrong with the test.

To find known negative cases they can go into nursing homes where they know that no one has had the virus and test these people. If they come out positive then it is a good indication that the test is faulty.
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Old 17th April 2020, 11:02 PM   #20
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The more I listen to these virologists the more they talk about not so much anti virals or fighting the virus but talking about modifying how the body deals with it. it seems like the body starts to get good at fighting the virus then at the same time starts fighting itself badly. So it seems like we should be hearing a lot more about anti inflammatories and immune suppressors. We do hear a lot about steroids bad at the start of infection but good at later stages. What does Tocilizumab do?
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Old 17th April 2020, 11:09 PM   #21
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Australia is heading down to 0 new infections and hardly anyone is wearing masks.
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Old 17th April 2020, 11:24 PM   #22
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The big problem with using immunosuppressants is that there are always opportunistic bacteria floating around, especially in hospitals. You can have impaired lung function from COVID-19, and then pick up bacterial pneumonia. To combat that, you have to add IV antibiotics, which often stresses other organs. Careful dosing and frequent monitoring are the keys, and it's devilishly tricky to balance things even when trying to support just one dangerously ill patient, let alone when non-specialist doctors are dealing with full wards of patients in the same position.
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Old 17th April 2020, 11:34 PM   #23
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Originally Posted by pipelineaudio View Post
The more I listen to these virologists the more they talk about not so much anti virals or fighting the virus but talking about modifying how the body deals with it.
Apparently we'll have some proper results in the next few days.

I'm still not expecting a magic bullet, but if they can come up with something even 50% effective it'd be a big improvement on where we're at right now.

Originally Posted by a_unique_person View Post
Australia is heading down to 0 new infections and hardly anyone is wearing masks.
Race ya!

We're running pretty neck & neck - you're a bit better than us today on cases per capita and we were better than you yesterday.

I remain unconvinced elimination of the virus is possible, but if we can keep it down to a handful of cases a day, with 100% follow up, we could easily work through it.
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Old 17th April 2020, 11:40 PM   #24
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Originally Posted by a_unique_person View Post
Australia is heading down to 0 new infections and hardly anyone is wearing masks.
Please note Australia is a long way from 0. In the last week Australia has had 320 new cases. This may be much better than the peak of 2,339 but the numbers came at a huge price. Last 13 days, that is 12 days after the lockdown began, the reduction of new cases has been 35-45% per week. In the next week Australia will get between 112 - 144 new cases.

If one criteria for the ending of the lockdown is no new cases then Australia will always be in lockdown.

Ref: https://www.health.gov.au/news/healt...current-status (but you can get similar numbers as above from any relevant reliable source).

ETA
Originally Posted by The Atheist View Post
<snip>

We're running pretty neck & neck - you're a bit better than us today on cases per capita and we were better than you yesterday.

I remain unconvinced elimination of the virus is possible, but if we can keep it down to a handful of cases a day, with 100% follow up, we could easily work through it.
If Australia and New Zealand do similar things then we can expect similar results.

ETA2. Looks like you are right. The main differences between the two countries are related to population sizes.
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Old 18th April 2020, 12:40 AM   #25
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Originally Posted by Ulf Nereng View Post
Here's something I found interesting:

Dag Berild, a medical doctor and Associate Professor at Oslo University Hospital, argued that the low level of antibiotic resistant bacteria in Norwegian hospitals may also have played a role in the country's lower mortality rate.

"The argument for that is that many of the coronavirus pneumonia cases are complicated by bacterial pneumonia, so if that is the case with coronavirus, then patients in a country with a low resistance rate among bacteria would have a better prognosis than those in Italy, where they have an awful lot of resistant bacteria, particularly in Lombardy."

The article is about Norway's testing capacity which some may also find interesting:

https://www.thelocal.no/20200403/how...or-coronavirus
We are not seeing secondary bacterial pneumonia in the same way as we do for flu.
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Old 18th April 2020, 12:41 AM   #26
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Originally Posted by Skeptic Ginger View Post
None of the antibody tests have had anything close to adequate testing to verify sensitivity and specificity. That is probably true worldwide as well but I'm only familiar with the tests being used in the US.
WHO agrees with you.
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Old 18th April 2020, 12:47 AM   #27
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Originally Posted by rjh01 View Post
I cannot understand how they could measure the accuracy of these antibody tests. Like the result of a test is positive. Does it mean the person has had the virus or is it a false positive? All they can do is test people who have recently recovered and if their test is negative then probably something is wrong with the test.

To find known negative cases they can go into nursing homes where they know that no one has had the virus and test these people. If they come out positive then it is a good indication that the test is faulty.
You can compare the commercial kit to a highly sensitive highly standardised laboratory assay. PHE have been collecting acute and convalescent bloods from known cases and there will be blood samples from pre covid that are definite negatives. So you can get a good sense of a false negative and false positive rate. There will be bloods that have been standardised and have known antibody levels that tests can be measured against.
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Old 18th April 2020, 12:53 AM   #28
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Originally Posted by Ulf Nereng View Post
Here's something I found interesting:

Dag Berild, a medical doctor and Associate Professor at Oslo University Hospital, argued that the low level of antibiotic resistant bacteria in Norwegian hospitals may also have played a role in the country's lower mortality rate.

"The argument for that is that many of the coronavirus pneumonia cases are complicated by bacterial pneumonia, so if that is the case with coronavirus, then patients in a country with a low resistance rate among bacteria would have a better prognosis than those in Italy, where they have an awful lot of resistant bacteria, particularly in Lombardy."

The article is about Norway's testing capacity which some may also find interesting:

https://www.thelocal.no/20200403/how...or-coronavirus

For this reason, they will start giving pneumococcal vaccinations to everybody 65+ and other vulnerable groups in Denmark next week.

Norway must have been better prepared for testing a large number of people from the very beginning. Do you know if this is due to the many fish farms in Norway - like in the Faroe Islands?
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Old 18th April 2020, 01:02 AM   #29
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Originally Posted by pipelineaudio View Post
The more I listen to these virologists the more they talk about not so much anti virals or fighting the virus but talking about modifying how the body deals with it. it seems like the body starts to get good at fighting the virus then at the same time starts fighting itself badly. So it seems like we should be hearing a lot more about anti inflammatories and immune suppressors. We do hear a lot about steroids bad at the start of infection but good at later stages. What does Tocilizumab do?
The vast majority of people recover with no treatment. If you give everyone immunosuppressant treatment you increase risk of other infections and might increase deaths. So you need to select out those who are very likely not to recover, and the treatment needs to be given at the right time, too soon and you are likely treating people unnecessarily, too late and it might not work.

Steroids used in SARS and MERS showed no benefit and some harm, but RCT of steroids in SARS-CoV-2 infection are under way.

Tocilizumab is a synthetic antibody that binds a chemical called interleukin 6. By binding it it inactivates it. Interleukin 6 is a chemical that is involved in driving the immune response, it is normally used to switch off the inflammatory action in arthritis and some cancers of the immune system. There are other similar drugs in trials. They are usually being given only to people with advanced disease needing ICU.
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Old 18th April 2020, 01:04 AM   #30
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Originally Posted by dann View Post
For this reason, they will start giving pneumococcal vaccinations to everybody 65+ and other vulnerable groups in Denmark next week.

Norway must have been better prepared for testing a large number of people from the very beginning. Do you know if this is due to the many fish farms in Norway - like in the Faroe Islands?
Pneumococcal vaccine is already given to the elderly and high risk groups in the UK (essentially if eligible for a flu vaccine then you are eligible for pneumonia vaccine).
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Old 18th April 2020, 01:16 AM   #31
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Originally Posted by Planigale View Post
You can compare the commercial kit to a highly sensitive highly standardised laboratory assay. PHE have been collecting acute and convalescent bloods from known cases and there will be blood samples from pre covid that are definite negatives. So you can get a good sense of a false negative and false positive rate. There will be bloods that have been standardised and have known antibody levels that tests can be measured against.
Thanks. That makes sense.
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Old 18th April 2020, 01:18 AM   #32
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Originally Posted by dann View Post
For this reason, they will start giving pneumococcal vaccinations to everybody 65+ and other vulnerable groups in Denmark next week.

Norway must have been better prepared for testing a large number of people from the very beginning. Do you know if this is due to the many fish farms in Norway - like in the Faroe Islands?
The doctor in the interview said that Norway has a high capacity to test because of the highly decentralized nature of our healthcare system. Most regional hospitals have their own testing lab, due to the long distances in Norway.

He also mentioned that there's a number of private testing labs, and this I think could be because of our large salmon farming industry.
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Old 18th April 2020, 01:28 AM   #33
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Interesting about UV-C light from Medcram:

https://www.youtube.com/watch?v=2U4DAQ3kjRs

(He also talks about Remdesivir at the start)
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Old 18th April 2020, 02:00 AM   #34
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Originally Posted by Planigale View Post
WHO agrees with you.
And he's on first.
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Old 18th April 2020, 03:37 AM   #35
dann
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Originally Posted by Ulf Nereng View Post
Interesting about UV-C light from Medcram:

https://www.youtube.com/watch?v=2U4DAQ3kjRs

(He also talks about Remdesivir at the start)

There are ongoing trials at Rigshospitalet in Copenhagen. The trials will be finished this month.
Promising drug given to first Danish corona patients (Uniavisen, March 30, 2020)
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Old 18th April 2020, 04:37 AM   #36
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Just noticed something odd about the number of new cases. It is happening in several countries, including Australia for the last 6 days. That is the number of new cases is stuck. Every day there are the same number of new cases plus or minus some noise. For example in America there have been about 30,000 new cases every day since 2 April.

I fear the lockdown is not working very well. It should be reducing this number and it is not. It is only holding it steady.
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Old 18th April 2020, 04:38 AM   #37
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Originally Posted by casebro View Post
"85 times as many people have had the virus as they had thought"? So mortality rate is not 4%, but 1/85 of 4%, but we all know my maths.... Herd immunity, here we come!
Other coronaviruses for which this has been tested confer immunity for about a year. If the same is true for this one, then herd immunity won't happen.
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Old 18th April 2020, 05:11 AM   #38
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Originally Posted by rjh01 View Post
Just noticed something odd about the number of new cases. It is happening in several countries, including Australia for the last 6 days. That is the number of new cases is stuck. Every day there are the same number of new cases plus or minus some noise. For example in America there have been about 30,000 new cases every day since 2 April.

I fear the lockdown is not working very well. It should be reducing this number and it is not. It is only holding it steady.

Don't forget that there are probably millions of so-far-untested but actually infected cases out there. The day-to-day number of people infected with the virus reflects the number of people tested more than the actual rate of infections.
The only thing that you can count on with some reliability is the number of registered deaths and hospitalizations. It took a couple of weeks for the death toll to go down in Denmark, but it did so eventually - along with the number of 1) hospitalizations, 2) patients in intensive care and 3) on ventilators.
See the three curves here: Indlagte på danske hospitaler = Corona patients in Danish hospitals

I don't know the English word for "smittetryk" (contagiousness?), the number of new infections caused by the average person infected with the virus. In Denmark, it went down from 2.6 (March 12) to 0.6 (April 14), which is actually much more than expected:
Faldende smittetryk i Danmark er 'meget overraskende', siger Statens Serum Institut (TV2.dk, April 14, 2020)
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Last edited by dann; 18th April 2020 at 05:33 AM.
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Old 18th April 2020, 05:19 AM   #39
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Originally Posted by casebro View Post
The nasal swab positive rate among patients with symptoms is only about 8%. Which leaves room for lots of serum true positives. 85x 8% is not a small number.

Got any numbers for false positives on equivalent tests? Isn't HIV about 5%?

85x is given for the Stanford study, the L.A. study is not as high, but of similar magnitude. And more random, and larger sample size. I eagerly await our Serological Overlord.
If a Covid-19 antibody test has a 95% specificity, and 5 out of 100 tests come back positive, what does that tell you (assume the test has 100% sensitivity)?
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Old 18th April 2020, 06:32 AM   #40
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Link to post quoted here.
Originally Posted by JeanTate
Turns out the WHO situation report gives a Grand Total of 36,405 for 31 March 2020.

Also:
14509/8778 = 1.65 (not 2.00)
23335/14509 = 1.61 (not 2.00)
36405/23335 = 1.56 (not 2.00)

So what?

For one, my "supposes" were wrong* even as I wrote them.

For another, anyone who read my post could have easily discovered at least these inconsistencies.

Here are the relevant numbers for three dates in April:
4 April: 56,986 (/36405 = 1.56)
8 April: 79,235 (/56986 = 1.39)
12 April: 105,592 (/79235 = 1.33)

The data suggest that the doubling time has gone from ~five days in late March to ~eight days ~two weeks later. This is a very welcome trend, if it indeed reflects accurately how the death toll from covid-19 is changing.

*In the sense that they were obviously inconsistent with what was in the WHO situation reports, although the 36405 value was not known at the time of my post.
Something of an update.

16 April: 130,885 (/105592 = 1.24)

Fitting a linear trend line to the ratio data, and extrapolating:
20 April: 1.19 (Grand Total, global covid-19 deaths: 165,860)
24 April: 1.12 (185,763)
28 April: 1.05 (195,051)

Which is good news.

However, will Russia become the new Italy (or Spain)? Etc.
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