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Thread: Disease and pandemics thread (because it's science)

  1. #1321
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    With my allergies as bad as they are right, now, I'd never know the difference. Can't smell anything anyway.
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    Abbot Laboratories says they have a US FDA approved test that can detect positive or negative on Covid-19 infection in under 15 minutes:

    https://www.reuters.com/article/us-h...-idUSKBN21F014
    "I'm planning to live forever. So far, that's working perfectly." Steven Wright

  3. #1323
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    Here we go again... second infections of COVID-19 after cured the first time. I thought the news was already out about this, or is this something new? Unsure either way.

    https://www.npr.org/sections/goatsan...-then-positive
    Mystery In Wuhan: Recovered Coronavirus Patients Test Negative ... Then Positive
    March 27, 20209:28 AM ET

    A spate of mysterious second-time infections is calling into question the accuracy of COVID-19 diagnostic tools even as China prepares to lift quarantine measures to allow residents to leave the epicenter of its outbreak next month. It's also raising concerns of a possible second wave of cases.

    From March 18-22, the Chinese city of Wuhan reported no new cases of the virus through domestic transmission — that is, infection passed on from one person to another. The achievement was seen as a turning point in efforts to contain the virus, which has infected more than 80,000 people in China. Wuhan was particularly hard-hit, with more than half of all confirmed cases in the country.

    But some Wuhan residents who had tested positive earlier and then recovered from the disease are testing positive for the virus a second time. Based on data from several quarantine facilities in the city, which house patients for further observation after their discharge from hospitals, about 5%-10% of patients pronounced "recovered" have tested positive again.

    Some of those who retested positive appear to be asymptomatic carriers — those who carry the virus and are possibly infectious but do not exhibit any of the illness's associated symptoms — suggesting that the outbreak in Wuhan is not close to being over.
    Do good work. —Virgil Ivan "Gus" Grissom

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    Does the antibody test need to show a sufficiently strong signal along with a triple negative to mark a patient as “recovered”? Can these “recovered” be invited to join a “Health Corps” to fill community or medical needs while they wait for their jobs to return?

    Decreased B Cells on Admission was Associated with Prolonged Virus Shedding from Respiratory Tract in Coronavirus Disease 2019: A Case Control Study

    https://papers.ssrn.com/sol3/papers....act_id=3555246

    Rather than repeating Hong Kong. I hope Wuhan will do a well monitored and controlled release to discover possible reasons for reinfections.

  5. #1325
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    It seems likely that the only workable strategy is a sustained mode of operation that maintains R0 below 1. It's not necessary, or probably even possible, to maintain zero new cases, the goal instead will be to "damp the oscillations" (following the "flatten the curve" initial strategy) so that a fairly constant number of new cases can be sustained. What a sustainable number is depends on policymakers, but I might imagine something akin to the same death rate we already tolerate for the flu. In the US, that's about 1000 deaths a week, so if 3% of cases of COVID-19 reported to the medical system result in deaths, then that's 30,000 new cases per week. I think we need a form of social distancing that can keep the new cases fairly constant at something like 30,000 a week. Right now it's at about 100,000 a week, so that's not a good place to level off, we need to get it down quite a bit. Hopefully the current lockdown measures will start reducing the new cases in about another week, and maybe down to 30,000 in two weeks. The question is then, what kind of economy allows it to stay that way? Probably it will look like local measures trying to limit spread in areas of activity, which need to be identified quickly. It would mean 50,000 deaths, on the order of auto and flu deaths.a My point being, if you already have 30,000 new cases every week, there's plenty of sick people around-- it's not clear that those who recovered and tested negative are going to be a significant addition to that, though it would depend on how long they continue to be contagious. We need better data, but that's true across the board.

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    It raises an interesting psychological effect of civilised life, that we learn to accept a death rate which is in keeping with our rituals and facilities. As soon as hospitals fill up, or effectively bodies accumulate faster than the normal procedures can cope with, we move into a different psychological mood, which we could call panic. A very unfortunate effect of the current pandemic is that people are dying alone and without any ceremony because of the increased risk of infection. I even heard today on the news that a dead person could not be cremated because they had a heart pacer which no one was prepared to remove during this pandemic. The same is generally true of wars, where many norms of society have to change.
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

  7. #1327
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    Quote Originally Posted by Roger E. Moore View Post
    But some Wuhan residents who had tested positive earlier and then recovered from the disease are testing positive for the virus a second time. Based on data from several quarantine facilities in the city, which house patients for further observation after their discharge from hospitals, about 5%-10% of patients pronounced "recovered" have tested positive again.
    I'm a little confused about tests in general. If a person once had CoVid-19 and recovers, does a few weeks after recovery eliminate the ability to test that you ever had it or does the new "positive" test mean you are contagious? Are there normally different tests available to determine one or the other or both?

    When donating blood, I noticed the nurse's chart stated I was an "exceptional donor". I assumed it was because my jokes were exceptional, of course, but she said it was because their tests showed that I had never had a certain virus that could be harmful to black infants, and perhaps others. [She didn't say me jokes weren't exceptional but I liked her answer even better.]

    Also...
    Here is objective evidence that suggests the Wuhan death numbers are understated.

    Quote Originally Posted by NYPost
    China has reported 3,299 coronavirus-related deaths, with most taking place in Wuhan, the epicenter of the global pandemic. But one funeral home received two shipments of 5,000 urns over the course of two days,...
    Even if they were hoarding urns, the numbers don't add-up well.
    Last edited by George; 2020-Mar-28 at 05:09 PM.
    We know time flies, we just can't see its wings.

  8. #1328
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    Yet that story raises its own questions. Why would a single funeral parlor need that many urns? They couldn't do that many cremations. It's not just the death totals that don't add up here, maybe the story is bogus, or if true, that funeral parlor might be engaged in some shenanigans.

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    Quote Originally Posted by Ken G View Post
    Yet that story raises its own questions. Why would a single funeral parlor need that many urns? They couldn't do that many cremations. It's not just the death totals that don't add up here, maybe the story is bogus, or if true, that funeral parlor might be engaged in some shenanigans.
    That would be reasonable irony if the bad news is overstated. There are a number of sites carrying the story that comes from the Chinese source of Caixin, but I don't know of their accuracy.

    Still, there seems to be more supporting evidence in the story.

    Quote Originally Posted by Times
    Outside one funeral home, trucks shipped in about 2,500 urns on both Wednesday and Thursday, according to Chinese media outlet Caixin. Another picture published by Caixin showed 3,500 urns stacked on the ground inside. It’s unclear how many of the urns had been filled.

    People who answered the phone at six of the eight funeral homes in Wuhan said they either did not have data on how many urns were waiting to be collected, or were not authorized to disclose the numbers. Calls were not answered at the other two.
    We know time flies, we just can't see its wings.

  10. #1330
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    Or maybe they anticipated many more deaths? The Italian example is sobering. And this coming week we can expect doubling every four days. In my region we lost our first doctor yesterday. Italy has lost more than forty.
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

  11. #1331
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    Quote Originally Posted by profloater View Post
    Or maybe they anticipated many more deaths?
    Yet that would be even more strange since over 90% have recovered and they haven't had more than 100 new cases in a day in quite a while....reportedly.
    We know time flies, we just can't see its wings.

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    Quote Originally Posted by George View Post
    I'm a little confused about tests in general. If a person once had CoVid-19 and recovers, does a few weeks after recovery eliminate the ability to test that you ever had it or does the new "positive" test mean you are contagious? Are there normally different tests available to determine one or the other or both?
    The test that is most commonly being done is a PCR (polymerase chain reaction) test, which looks for viral RNA in a swab taken from the patient's nose or throat. This will detect an active current infection, but will not show whether someone had a disease some time ago. The other possibility is a serology test which uses a blood sample from the patient, looking for antibodies for a specific disease. This can show that someone had a disease well after the fact. Both of these test types have their advantages and disadvantages. And for both test types (and any medical tests, for that matter) there will always be some number of both false positives and false negatives. I'd say that with this number of people having the illness and being tested, it's completely expected that there would be a handful of cases where someone tests negative (even more than once) and then tests positive later.
    Conserve energy. Commute with the Hamiltonian.

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    The significance of these "late return to positive" tests is doubtful. We know it happens when we go looking for it. (I earlier posted a link to a report of four Chinese doctors who were discharged with two negative tests, who all went on to develop positive tests while self-isolating without symptoms at home.) So it's a thing. But the fact that you're shedding viral RNA doesn't necessarily mean that you are shedding (or harbouring) intact infective viruses.

    Grant Hutchison

  14. #1334
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    Thanks to you both for clarifying. Does each test come with an accuracy rating for both false cases?
    We know time flies, we just can't see its wings.

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    Quote Originally Posted by grant hutchison View Post
    ... But the fact that you're shedding viral RNA doesn't necessarily mean that you are shedding (or harbouring) intact infective viruses.
    So, the 'shedding of viral RNA' may occur in the form of dead (previously infected but inactive) cells here, I suppose(?)
    Either way, re-infection' can still re-emerge and can also then be passed onto others (eg: dormant zoster family of viruses .. shingles/chickenpox).. which I think may have also been what you were inferring here(?)

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    Quote Originally Posted by George View Post
    Thanks to you both for clarifying. Does each test come with an accuracy rating for both false cases?
    Tests have an associated sensitivity (a measure of their ability to avoid false negatives) and specificity (avoiding false positives). You can tune the sensitivity against the specificity by adjusting the signal threshold at which the test becomes "positive", and you choose that threshold according to the relative priority you assign to false positives and false negatives.
    The problem with that is that it assumes we have some sort of gold standard by which we can assess the test against who really does, or does not, have the disease. Whereas in fact what we've got are estimates of how good the test is at picking up SARS-CoV-2 RNA, and how good it is at rejecting other sources of RNA.
    So we're at the stage at which we can say, with some level of certainty, that SARS-CoV-2 RNA is present in the tested fluid. And if the patient is displaying COVID-19 symptoms, than we're pretty confident they have the active disease, and not some other flu-like illness. But if we have a positive test in a person who has clinically recovered, we really can't say that they "still have the disease", and we're still not sure what the presence of this RNA means in terms of transmissibility--the patient might just be shedding fragments of RNA from destroyed virions or dead cells, for instance.

    Grant Hutchison

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    Perhaps a more useful measure, rather than "this person has the disease," is "this person could communicate the disease to someone they come in contact with." That's more the issue for fighting the epidemic, moreso than the healthcare objective of treating that individual (which we generally don't use the test for anyway, we wait until they clearly need care regardless of testing). Is there a way to reinterpret these tests in that light that would be of greater use?

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    Quote Originally Posted by Ken G View Post
    Perhaps a more useful measure, rather than "this person has the disease," is "this person could communicate the disease to someone they come in contact with." That's more the issue for fighting the epidemic, moreso than the healthcare objective of treating that individual (which we generally don't use the test for anyway, we wait until they clearly need care regardless of testing). Is there a way to reinterpret these tests in that light that would be of greater use?
    I think what you're describing is exactly what it's hard for the test to do. I can't think of a good way to test the probability that someone could communicate the disease (under some interaction protocol) given the outcome of a test would be the (unethical and kind of dangerous) experiment of having a bunch of people who tested positive interact to various extents with other people and measure how many later become infected. I think you just have to use the test results as a guideline to inform your decisions, knowing that it is not perfectly accurate.
    Conserve energy. Commute with the Hamiltonian.

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    It would seem to me that a virus could present a number of antigens and therefore an animal could manufacture a number of different antibodies, one for each antigen, or even multiple antibodies for each antigen. And then there may be multiple ways of destroying viruses, without going after an antigen.
    The moment an instant lasted forever, we were destined for the leading edge of eternity.

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    Quote Originally Posted by George View Post

    Even if they were hoarding urns, the numbers don't add-up well.
    One caveat on the urns. Hubei Province was under lockdown for two months, and there are many elderly people who would have died of things other than this virus. I can imagine there might even have been an increase in natural deaths because people with problems like strokes and heart attacks and cancer might have received sub-optimum care because of the healthcare crisis.
    As above, so below

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    Quote Originally Posted by Selfsim View Post
    So, the 'shedding of viral RNA' may occur in the form of dead (previously infected but inactive) cells here, I suppose(?)
    Yes, that’s correct. One way we deal with viruses is by killing infected cells, which may have viral DNA, but you don’t get infected by the RNA. The DNA has to be incorporated into a functional unit called a virion.
    As above, so below

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    Quote Originally Posted by grant hutchison View Post
    Tests have an associated sensitivity (a measure of their ability to avoid false negatives) and specificity (avoiding false positives). You can tune the sensitivity against the specificity by adjusting the signal threshold at which the test becomes "positive", and you choose that threshold according to the relative priority you assign to false positives and false negatives.
    Ah, and you did mention this earlier in the thread. Perhaps the fact that pictures of the virus are displayed so often, that both accuracy terms could be fairly well defined with microsope comparison, though given that it's extra small, an electron microscope.

    Quote Originally Posted by Jens
    One caveat on the urns. Hubei Province was under lockdown for two months, and there are many elderly people who would have died of things other than this virus. I can imagine there might even have been an increase in natural deaths because people with problems like strokes and heart attacks and cancer might have received sub-optimum care because of the healthcare crisis.
    Yep, that's a fair point, and they may be concerned about the future of getting more urns as well (ie psuedo hoarding). If accurate data of the number of urns delivered to funeral homes over the last year throughout Hubei could be obtained, then that would be interesting to see. It's one of those things that could better tell a story if the story is wrapped in...red tape.
    We know time flies, we just can't see its wings.

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    FWIW...The following graphs show a contrast in bad news and not so bad news that's kinda interesting. The latest CFR values vary considerably and many are ugly. How Germany is doing so well is surprising to me. But the rate in new cases certainly isn't a sign of any geometric progression, at least in the prior two weeks shown.

    CFR rates March 27 .jpg
    New Case rates March 27.jpg

    [data from John Hopkins]
    We know time flies, we just can't see its wings.

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    Quote Originally Posted by Grey View Post
    I think what you're describing is exactly what it's hard for the test to do. I can't think of a good way to test the probability that someone could communicate the disease (under some interaction protocol) given the outcome of a test would be the (unethical and kind of dangerous) experiment of having a bunch of people who tested positive interact to various extents with other people and measure how many later become infected. I think you just have to use the test results as a guideline to inform your decisions, knowing that it is not perfectly accurate.
    I agree it would be hard to know what the effective R0 is for each test outcome, which is what we'd like to know. But I'll bet it's also hard to know what is the chance that a person will need care, or even that they have the disease at all (as one has to turn up the false positives enough to turn down the disastrous false negatives). These things are all hard to know, so we do the best we can. We need to know if the disease is spreading via many people with light shedding, perhaps even asymptomatic people, or if it is spreading by people who are in bed coughing their lungs out and being tended to by their family. We need to know if it is spread by small airborne droplets hanging in a crowded room for hours, or if washing hands is effective in preventing spread. There's a lot we need to know, and none of these can be tested ethically, so we will just have to make the best judgements we can. And we will have to keep doing that for about a year, because we just can't stay in our homes that long-- there won't be any economy left by then.

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    Quote Originally Posted by Grey View Post
    I see a number of potential issues. For example, if you declare most of New York City a hot zone, and don't let anyone in or out, how do you continue to supply food? If you let trucks in, but not out, you'll end up overcrowding your hot zones. And of course, since there's been relatively little testing to actually know where cases are, there's a pretty strong likelihood that no matter where you try to draw your disease free zones, there are probably people already infected inside those zones, you just don't know it yet.
    There are speculative aspects of the concept which make them against the TOS on this board. But the concept is the same as isolation procedure that are in effect in most of the world already. These measures allow for passage of the essential services. Trucks can go in and out. The only difference is that rather than having a single static zone with millions of people there are waves of shrinking zones. I will drop this discussion on this board at this point. I have started a thread on another board. Check it out if you wish:
    https://mersenneforum.org/showthread.php?t=25406

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    Quote Originally Posted by George View Post
    How Germany is doing so well is surprising to me.
    They say here that Germany, our neighbour, is doing a lot more testing than other countries and has done so from the start, and that this is the reason why their death percentage is lower. I don't recall reading how they were able to do so, logistically. Germany was also a little earlier with closing their borders to non-essential visits from foreigners (like getting cheap gas, groceries, etc).

    One has to be very careful comparing such numbers though, as there as much difference in how they are produced per country. For example, in our country there is a statistic that only three persons out of thousands have recovered. But there is no requirement to notify local health care agency that you've recovered, and it's not being tested either to save rare testkits.
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    Quote Originally Posted by slang View Post
    They say here that Germany, our neighbour, is doing a lot more testing than other countries and has done so from the start, and that this is the reason why their death percentage is lower. I don't recall reading how they were able to do so, logistically. Germany was also a little earlier with closing their borders to non-essential visits from foreigners (like getting cheap gas, groceries, etc).

    One has to be very careful comparing such numbers though, as there as much difference in how they are produced per country. For example, in our country there is a statistic that only three persons out of thousands have recovered. But there is no requirement to notify local health care agency that you've recovered, and it's not being tested either to save rare testkits.
    There is an unsubstantiated rumour that the reason Germany has such a low death rate is because they are only reporting deaths that are a direct result of Covid-19. Presumably this is from the lung damage. Any deaths where an underlying condition is exacerbated by Covid-19 leading to death from that underlying condition are not reported as Covid-19 deaths in their figures.
    Pure conjecture but conceivable. I would imagine there would be a fine line between such distinctions.

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    Quote Originally Posted by headrush View Post
    There is an unsubstantiated rumour that the reason Germany has such a low death rate is because they are only reporting deaths that are a direct result of Covid-19. Presumably this is from the lung damage. Any deaths where an underlying condition is exacerbated by Covid-19 leading to death from that underlying condition are not reported as Covid-19 deaths in their figures.
    Pure conjecture but conceivable. I would imagine there would be a fine line between such distinctions.
    I suspect that is nonsense. Germany developed a test very quickly and adopted test and trace policy early on. Without testing, the cases number must be suspect but the death toll is a reliable figure in so called western countries.
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

  29. #1349
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    Quote Originally Posted by George View Post
    [data from John Hopkins]
    Nitpick: It’s “Johns Hopkins”.

    [Mrs. Extravoice works there, so I’ve been sensitized.]


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    Quote Originally Posted by headrush View Post
    There is an unsubstantiated rumour that the reason Germany has such a low death rate is because they are only reporting deaths that are a direct result of Covid-19. Presumably this is from the lung damage. Any deaths where an underlying condition is exacerbated by Covid-19 leading to death from that underlying condition are not reported as Covid-19 deaths in their figures.
    Pure conjecture but conceivable. I would imagine there would be a fine line between such distinctions.
    As slang says, it's an artifact of their mass testing policy. They pick up cases which other countries may miss.

    Here in the US, I see (anecdotal) reports of symptomatic people not being able to get tested right away due to lack or rationing of kits.
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