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

  1. #2251
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    Ah, the subgenre of antivax SF.
    To a large extent it depends on the regulatory bodies, like the FDA, who approve vaccines for use. They're the people who balance the risk of harm against the likely benefit. Given the death toll associated with this pandemic and its economic impacts, regulatory bodies are likely to favour a shorter rather than a longer monitoring period. And that will also be influenced by whether the vaccine under examination uses tried-and-tested methods of stimulating an immune response (we have many decades of experience of a range of standard vaccine formulations), or if it has some innovative approach we haven't previously experienced (and would therefore wish to monitor for longer).
    So expect to see different countries approve different vaccines at different times during Phase III follow-up--maybe even several vaccines coming onstream in a given country from mid-2021 to mid-2023.
    The Boon Companion and I have signed up for Phase III testing, so might get vaccinated sooner than that.

    Grant Hutchison

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    Quote Originally Posted by Van Rijn View Post
    Sounds potentially very good, but from the article it hasn’t gone through peer review yet, so best to not get hopes up too high yet.
    I'm not criticising you or your statement, standards may be different in different fields, but I'm always surprised to see huge faith put in peer review. It's a total joke in my area. I can find published articles every month that show complete ignorance of and/or severe violation of things we learned in the 1960s.

    My reaction when someone tells me, "this paper has been peer reviewed" is not "oh, it must be good then", it's "there's probably a slightly lower chance that there are embarrassing and fundamental flaws that an advanced undergraduate or masters student in the field ought to be able to identify".

    I've written reviews myself, arguing that a result is (a) trivial, (b) already known for decades, or (c) wrong, and recommended rejection in language so simple even an editor should be able to understand it. The article still comes out in that journal, with few or none of the problems I cited with it corrected.

    So I consider peer review neither a necessary nor sufficient condition for a paper to be worth more than the electrons in the PDF it's found in. But maybe things are different in this field.

  3. 2020-Jul-23, 06:26 PM
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  4. #2253
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    For a someone who isn't a medic, who therefore lacks the automatic baloney-detecting reflexes that come from expert knowledge, and who is faced with the avalanche of Covid-related garbage appearing on the preprint servers, I think "not yet peer reviewed" is a fine reason to set a paper aside and not invest too much worry or optimism in what's being claimed--in the same way as "I haven't yet turned on the engine" is a good reason to withhold enthusiasm about a second-hand car.
    For experts in the field, passing peer review is most definitely only the start of the conversation. (And sometimes the conversation starts, "Who peer-reviewed this? Brighton pier?") But I'd estimate that only about 1% of Covid-related papers appearing in preprint at present will ever pass peer review, so that process represents a significant and useful filter for the layman.

    Grant Hutchison

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    Quote Originally Posted by Rolling Stone View Post
    I'm not criticising you or your statement, standards may be different in different fields, but I'm always surprised to see huge faith put in peer review. It's a total joke in my area. I can find published articles every month that show complete ignorance of and/or severe violation of things we learned in the 1960s.
    No doubt. While some may, I assure you that I don’t put great faith in just peer review for a single study. In this instance, I consider it a minimum standard. I start getting really interested if there are multiple independent studies with positive results showing up in well respected journals, getting enthusiastic responses from subject matter experts, no red flags raised.

    But we’ve had things like the hydroxychloroquine fiasco, where there were terrible studies that ultimately didn’t pass peer review, but it was getting hyped up to a ridiculous degree by obvious non-experts anyway, and it was amazing how even many doctors bought into the hype.

    So I consider peer review neither a necessary nor sufficient condition for a paper to be worth more than the electrons in the PDF it's found in. But maybe things are different in this field.
    I agree and I’m sure things aren’t different. See for instance, the case of Andrew Wakefield.

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  6. #2255
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    Quote Originally Posted by Rolling Stone View Post
    I'm not criticising you or your statement, standards may be different in different fields, but I'm always surprised to see huge faith put in peer review. It's a total joke in my area. I can find published articles every month that show complete ignorance of and/or severe violation of things we learned in the 1960s.
    Let's not derail this thread with a discussion of the general merits and failings of peer review. If you would like such a discussion, please start a dedicated thread for it. This thread already has more than enough to cover.
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  7. 2020-Jul-23, 08:39 PM
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  8. #2256
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    A new study, yet to be peer-reviewed, which stakes out the idea that disease spread aboard the Diamond Princess was significantly driven by aerosol transmission.

    https://www.medrxiv.org/content/10.1....13.20153049v1

    Article from the New York times on the same subject.

    https://www.nytimes.com/2020/07/30/h...gtype=Homepage

    From the abstract:

    Background: The current prevailing position is that coronavirus disease 2019 (COVID-19) is transmitted primarily through large respiratory droplets within close proximity (i.e., 1-2 m) of infected individuals. However, quantitative information on the relative importance of specific transmission pathways of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (i.e., droplets, aerosols, and fomites across short- and long-range distances) remains limited.

    Methods To evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we leveraged detailed information available from the Diamond Princess Cruise Ship outbreak that occurred in early 2020. We developed a framework that combines stochastic Markov chain and negative exponential dose-response modeling with available empirical data on mechanisms of SARS-CoV-2 dynamics and human behaviors, which informs a modified version of the Reed-Frost epidemic model to predict daily and cumulative daily case counts on the ship.

    We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors, including the magnitude of droplet and aerosol emissions from infected individuals, the infectious dose for deposition of droplets and aerosols to the upper and lower respiratory tracts, and others.

  9. #2257
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    From the discussion:
    There are several limitations to this modeling approach. For one, there is considerable uncertainty in our model inputs, as numerous estimates, assumptions, and implications were made because of a lack of available information, especially related to COVID-19 epidemic and mechanistic transmission characteristics, the interactions among individuals onboard the ship, and the effectiveness of infection control strategies adopted during the quarantine period. Some of these assumptions could have a significant impact on the results.
    (My bold)
    This sort of thing bedevils modelling exercises. It'll be interesting to see commentary on how reasonable their "assumption landscape" is.

    Grant Hutchison

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    New MIT study on masks: http://news.mit.edu/2020/masks-manda...ct-deaths-0805

    Masks reduce the spread of Covid-19. But just how much of an effect do they have? A study co-authored by an MIT professor finds that if the U.S. had introduced a uniform national mask mandate for employees of public-facing businesses on April 1, the number of deaths in the U.S. would likely have been 40 percent lower on June 1.
    "I'm planning to live forever. So far, that's working perfectly." Steven Wright

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    Original preprint here.
    These modelling studies based on differing dates of policy implementation in different states are interesting. The authors of the present paper seem to have missed Lyu & Wehby, which attempted something similar. Germany has also produced a similar study, which I cited on the OTB thread a while ago, and which I can dig out if anyone's interested.
    The odd thing about Lyu and Wehby (speaking from memory since I'm pressed for time, sorry), was that mask mandates were reported to have an immediate effect on case numbers as soon as they were signed, but before the implementation date. As Douglas Adams would say, "This is, of course, impossible." So that suggests people were doing something in the run-up to the mask mandate, probably influenced by the same events that led to the mask mandate--that might have been adopting masks, but it might have been a whole raft of other behavioural changes.
    Chernozhukov et al. (the current paper) model a lag between mandate and effect on case numbers, which would seem reasonable if it weren't for Lyu & Wehby's findings. They also control for other behavioural changes by using Google mobility data, which is good thing to do, but isn't particularly granular--for instance, it can give you no idea of to what extent people were physically distancing and hand-washing, or modifying other behaviours such as contact with friends.
    Finally, I'm a little suspicious of their counterfactual "if only mask mandates had been issued sooner". The world was a different place early in the pandemic, and one can imagine all kind of behavioural differences between a counterfactual early national mandate and the patchwork of later mandates which provide the data for this model.
    There are other things that puzzle me, but I haven't read carefully enough to remark on them. Again, it will be interesting to see what sort of critical response it receives--interesting that the preprint is already on version 5 after having been up for just three weeks, yet with no comments on the server.

    Grant Hutchison

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    With all the T cell immunity, and so many people having antibodies even though having been asymptomatic, and so many people losing antibodies so quick that we don't really know who has gone through the disease, we have to consider that this pandemic is almost over in the United States. Perhaps by the end of September.
    The moment an instant lasted forever, we were destined for the leading edge of eternity.

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    Quote Originally Posted by Copernicus View Post
    With all the T cell immunity, and so many people having antibodies even though having been asymptomatic, and so many people losing antibodies so quick that we don't really know who has gone through the disease, we have to consider that this pandemic is almost over in the United States. Perhaps by the end of September.
    Good luck with that.

    Grant Hutchison

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    Quote Originally Posted by Copernicus View Post
    With all the T cell immunity, and so many people having antibodies even though having been asymptomatic, and so many people losing antibodies so quick that we don't really know who has gone through the disease, we have to consider that this pandemic is almost over in the United States. Perhaps by the end of September.
    What would you consider to be an end of the pandemic? Do you just mean reaching a peak in number of new cases per day or something else? The curve is still going up in my state (California). Is it even plausible that it could hit a peak in a couple months? I would like to hope so, but I am not betting on it. Off hand, I would think for the pandemic to end, I and others would need to be able to stop social distancing and mask wearing while still being reasonably confident that we wouldn’t come down with Covid-19. My understanding is that will require an effective vaccine administered to the vast majority of the population or for the vast majority to have gotten sick and (hopefully) developed long term effective immunity. So maybe September, next year?

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    Quote Originally Posted by grant hutchison View Post
    Good luck with that.

    Grant Hutchison
    Ditto from me.
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    Quote Originally Posted by Copernicus View Post
    With all the T cell immunity, and so many people having antibodies even though having been asymptomatic, and so many people losing antibodies so quick that we don't really know who has gone through the disease, we have to consider that this pandemic is almost over in the United States. Perhaps by the end of September.
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    Goldman says we should be on the way down by my d October. If everything follows like Sweden we should be maybe a hundred deaths per day. Cases should drop to almost nothing by the end of September. There has to be a reason we aren't having close to a million cases per day in the USA.
    The moment an instant lasted forever, we were destined for the leading edge of eternity.

  18. #2266
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    Quote Originally Posted by Copernicus View Post
    Goldman says we should be on the way down by my d October. If everything follows like Sweden we should be maybe a hundred deaths per day. Cases should drop to almost nothing by the end of September. There has to be a reason we aren't having close to a million cases per day in the USA.
    Sorry, I may be forgetting something from earlier, but who is Goldman?
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    Quote Originally Posted by Copernicus View Post
    Goldman says we should be on the way down by my d October. If everything follows like Sweden we should be maybe a hundred deaths per day. Cases should drop to almost nothing by the end of September. There has to be a reason we aren't having close to a million cases per day in the USA.
    Frankly, this isnít making sense to me and again, could you explain what you would consider to be an end of the pandemic?

    If cases begin to drop in October, how can they be almost nothing in September, the prior month? Are you talking about September next year? Social distancing undoubtedly flattened the curve somewhat, but until and unless most of the population becomes immune I donít see how we can do away with distancing or (in my understanding of the term) say the pandemic is over.

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    Quote Originally Posted by Van Rijn View Post
    Frankly, this isn’t making sense to me and again, could you explain what you would consider to be an end of the pandemic?

    If cases begin to drop in October, how can they be almost nothing in September, the prior month? Are you talking about September next year? Social distancing undoubtedly flattened the curve somewhat, but until and unless most of the population becomes immune I don’t see how we can do away with distancing or (in my understanding of the term) say the pandemic is over.
    I think the claim is that new cases will be almost zero by the end of September, so deaths should be down to a hundred a day by mid-October. It doesn't seem intuitive to me.
    As above, so below

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    Quote Originally Posted by Copernicus View Post
    There has to be a reason we aren't having close to a million cases per day in the USA.
    Of course there has to be a reason, but what that reason is is up for discussion still. One possibility is that COVID-19 is not terribly infectious under certain conditions, but under certain other conditions becomes very infectious (following from the fact that there seem to have been many "super spreader" events). So one possibly for the way it has increased, i.e. steadily (never really exploding but never really going away), is that it just continues to spread depending on how often those conditions are met, and in some countries, for various reasons, the conditions are met more often than in others. In that case, whether the number of new cases in the US decreases to nothing in September will depend on how well those conditions are prevented.
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    Quote Originally Posted by Jens View Post
    I think the claim is that new cases will be almost zero by the end of September, so deaths should be down to a hundred a day by mid-October. It doesn't seem intuitive to me.
    Is that the claim? Well, I’ll wait to see if Copernicus clarifies. The posts are confusing. Meanwhile, California went back to a heavier level of closure weeks ago as numbers climbed with the June reopening. Very recently there seemed to be an improvement in numbers, but there is a report of a technical issue resulting in a significant undercount, so it is unclear if there is any real improvement. Besides, better numbers would increase the push for reopening again. At that, we’re still showing over 5000 new cases and close to 200 deaths per day. That’s just California, not the hardest hit state, but I am watching it more closely than other states. I would be absolutely astonished if the pandemic were over soon.

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    Quote Originally Posted by Jens View Post
    I think the claim is that new cases will be almost zero by the end of September, so deaths should be down to a hundred a day by mid-October. It doesn't seem intuitive to me.
    Sometimes people are in the hospital 6 to 8 weeks, so they are dying long after they got the disease. That is why even though cases are low, which could mean a few thousand a day, the deaths will linger for quite a while.
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    Quote Originally Posted by Copernicus View Post
    Sometimes people are in the hospital 6 to 8 weeks, so they are dying long after they got the disease. That is why even though cases are low, which could mean a few thousand a day, the deaths will linger for quite a while.
    This article suggests that we may only need 20 percent of people to get sick for herd immunity. https://www.inverse.com/science/coro...on-is-infected
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    Sweden's certainly telling us something. Their cases and deaths are falling (from a horrible peak that nevertheless didn't overwhelm their healthcare services), and they haven't changed their "soft lockdown" apart from (I think) doing what everyone did very belatedly--tightening up procedures in care homes, which accounted for a large proportion of Sweden's deaths. Yet serosurveillance suggests that they're nowhere near the "herd immunity" conventionally calculated from R0.
    But that "herd immunity" figure of 60-70%, so often quoted in arguments at the start of all this (particularly in the UK) is known to be naive, and it's a mystery why it was latched on to with such vigour. R is a characteristic of the virus, but also of the society in which the virus is transmitted. Different parts of society have different R values, because they interact in different ways. If you push R low (but still > 1) by imposing various social restrictions (which is what Sweden did and is still doing), then your herd immunity for that society is correspondingly decreased, and can be reached with fewer deaths.
    But if you remove all the restrictions and go back to business as usual, R increases and your necessary herd immunity jumps back towards the R0 level.
    So a bit of herd immunity in your society means you can get a bit of the way out of lockdown. That's what Mike Ryan of the WHO meant when he recently said that the rest of the world could look to Sweden to see what a post-lockdown, pre-vaccine society might look like. It's also what I meant, back in March, when I remarked on this thread that we'd all be relying on herd immunity to some extent to get out of this thing. At that point the shouting about "60% infected" and "millions of deaths" got so loud I just walked away, I'm afraid. I could have made the point better.

    Grant Hutchison
    Last edited by grant hutchison; 2020-Aug-06 at 12:42 PM.

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    Quote Originally Posted by grant hutchison View Post
    .
    So a bit of herd immunity in your society means you can get a bit of the way out of lockdown. That's what Mike Ryan of the WHO meant when he recently said that the rest of the world could look to Sweden to see what a post-lockdown, pre-vaccine society might look like. It's also what I meant, back in March, when I remarked on this thread that we'd all be relying on herd immunity to some extent to get out of this thing. At that point the shouting about "60% infected" and "millions of deaths" got so loud I just walked away, I'm afraid. I could have made the point better.

    Grant Hutchison
    There has been a lot of shouting, I agree. Having witnessed the carping from the traditional and social media, it appears to me that if a sensible, science based approach to a problem is to succeed, then more harshly imposed rules are needed. There has been and still is too much shouting from the back of the room by people who think they know better.

    This could be why the likes of Korea and possibly Germany have generally managed this crisis better than the UK and USA. Respect for (the correct) authority.

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    Quote Originally Posted by headrush View Post
    There has been a lot of shouting, I agree. Having witnessed the carping from the traditional and social media, it appears to me that if a sensible, science based approach to a problem is to succeed, then more harshly imposed rules are needed. There has been and still is too much shouting from the back of the room by people who think they know better.

    This could be why the likes of Korea and possibly Germany have generally managed this crisis better than the UK and USA. Respect for (the correct) authority.
    How about more harshly imposed rules from people who think they know better!
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    Quote Originally Posted by Copernicus View Post
    How about more harshly imposed rules from people who think they know better!
    I'm not sure how things work in other places, but where I am that's not a big concern. We are having a kind of problem now in Japan where the government is promoting domestic travel with special coupons even though infections are increasing. And I watched an interview with an epidemiologist (who knows better) who sits on some government committee, and he was asked about it. Basically, his response (I think reasonable) was that as an infectious disease expert he pushed for stricter measures, but the government also has to juggle other things, like the economic fallout, so they adopted looser measures.
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    Quote Originally Posted by Copernicus View Post
    How about more harshly imposed rules from people who think they know better!
    As long as the measures taken conform with the scientific and medical recommendations, the motives of the Powers That Be don't matter, only their actions. If such powers don't agree with the medical directives, they tend to NOT impose strict requirements.
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    Quote Originally Posted by Noclevername View Post
    As long as the measures taken conform with the scientific and medical recommendations, the motives of the Powers That Be don't matter, only their actions. If such powers don't agree with the medical directives, they tend to NOT impose strict requirements.
    There are many factors. How does this affect riots, hunger, suicide, economics.
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    There's a lot of talk in the media and elsewhere about maybe having a workable vaccine by year's end. That talk usually includes a statement that this year would be unprecedented ... it takes years to develop a vaccine.

    Well, turns out we've been at it for years. In 2008 a group of researchers started looking for a vaccine for RSV. What they learned as a result has given them a huge head start on the novel coronavirus.

    COVID-19 Vaccine Candidate with UT Ties Arrived Quickly After Years in the Making
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    Quote Originally Posted by Jim View Post
    There's a lot of talk in the media and elsewhere about maybe having a workable vaccine by year's end. That talk usually includes a statement that this year would be unprecedented ... it takes years to develop a vaccine.

    Well, turns out we've been at it for years. In 2008 a group of researchers started looking for a vaccine for RSV. What they learned as a result has given them a huge head start on the novel coronavirus.

    COVID-19 Vaccine Candidate with UT Ties Arrived Quickly After Years in the Making
    Likewise the Oxford vaccine. The ChAdOx1 vaccine vector has been used in several previous vaccines. We're fortunate this all kicked off at a time when vaccines can be assembled from tested components.

    Grant Hutchison

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