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

  1. #2461
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    Can't believe how many cases there are all over. France is almost at 50,000 cases per day.
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    Pfizer/BioNTech have announced the interim analysis of their Phase III vaccine trial:
    Monday, November 09, 2020 - 06:45am

    • Vaccine candidate was found to be more than 90% effective in preventing COVID-19 in participants without evidence of prior SARS-CoV-2 infection in the first interim efficacy analysis
    • Analysis evaluated 94 confirmed cases of COVID-19 in trial participants
    • Study enrolled 43,538 participants, with 42% having diverse backgrounds, and no serious safety concerns have been observed; Safety and additional efficacy data continue to be collected
    • Submission for Emergency Use Authorization (EUA) to the U.S. Food and Drug Administration (FDA) planned for soon after the required safety milestone is achieved, which is currently expected to occur in the third week of November
    • Clinical trial to continue through to final analysis at 164 confirmed cases in order to collect further data and characterize the vaccine candidate’s performance against other study endpoints.
    Pretty good result, in other words. I hear it has to be stored at low temperature, which would make roll-out more difficult than it otherwise might be, but nevertheless good news, I think, if the results hold up.

    Grant Hutchison

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    How low is low temperature? I seem to recall something about dry ice in the past.
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  4. #2464
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    Quote Originally Posted by Trebuchet View Post
    How low is low temperature? I seem to recall something about dry ice in the past.
    Pfizer have quoted -70°C/-94°F, so dry ice territory. It makes the logistics difficult, but the logistics were always going to be difficult.

    Grant Hutchison

  5. #2465
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    Quote Originally Posted by Trebuchet View Post
    How low is low temperature? I seem to recall something about dry ice in the past.
    I though I had seen something suggesting that it needed to be even colder, but this article suggests that dry ice is indeed sufficient, and that Pfizer is specifically working on the logistics of putting together a dry-ice cooled container for shipping that could keep the temperature low enough for 10 days.
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  6. #2466
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    Dry ice temperature is sufficient.
    By the way, last evening 60 Minutes had an interview with the person responsible for vaccine distribution in the US. I recommend watching it if available.
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  7. #2467
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    Quote Originally Posted by grant hutchison View Post
    Pfizer have quoted -70°C/-94°F, so dry ice territory. It makes the logistics difficult, but the logistics were always going to be difficult.

    Grant Hutchison
    Wow; I know of drugs that have to be kept "on ice", like nominally 0°C (my wife's Humira comes in a styrofoam container on cold packs, and has to be stored in the refrigerator), but not that cold.
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  8. #2468
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    Quote Originally Posted by Swift View Post
    Wow; I know of drugs that have to be kept "on ice", like nominally 0°C (my wife's Humira comes in a styrofoam container on cold packs, and has to be stored in the refrigerator), but not that cold.
    The difference with this vaccine is that it's composed of messenger RNA, which is fairly fragile stuff. Minus eighty Celsius is the standard temperature for RNA storage, when it will remain intact for at least a year. In the distribution phase, when it's going to be used fairly soon after dispatch, you can get away with slightly warmer temperatures.

    Grant Hutchison

  9. #2469
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    Quote Originally Posted by grant hutchison View Post
    The difference with this vaccine is that it's composed of messenger RNA, which is fairly fragile stuff. Minus eighty Celsius is the standard temperature for RNA storage, when it will remain intact for at least a year. In the distribution phase, when it's going to be used fairly soon after dispatch, you can get away with slightly warmer temperatures.

    Grant Hutchison
    What fluid do they carry the m-RNA in? Obviously not water.
    I assume they warm it up over -70C before they inject it.
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    Quote Originally Posted by Swift View Post
    What fluid do they carry the m-RNA in? Obviously not water.
    I don't know. There doesn't yet seem to be a BNT162b2 datasheet available on-line. One will undoubtedly become available after any emergency use authorization. There are a whole load of standard vaccine excipients, but because mRNA vaccines are novel, this one probably has novel excipients too.

    Grant Hutchison

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    Sounds like this vaccine won’t be great for third world distribution but that storage requirement shouldn’t be any big issue for developed countries. Hopefully at least one of the easier to transport vaccines will give good results too.

    But wow, 90% effective or better. It gives realistic hope things could be mostly back to normal in a year. I was concerned effective vaccines might be harder to develop than hoped, but this sounds like great news.

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    Quote Originally Posted by Van Rijn View Post
    Sounds like this vaccine won’t be great for third world distribution but that storage requirement shouldn’t be any big issue for developed countries.
    I don't know what things are like in the USA, but pharmacies and doctors' offices in the UK just don't need or have fridges that maintain that sort of temperature. My Wife The Professor used to store samples in a -80°C facility owned by a large university laboratory, and there was massive competition for that resource. But then there are virus-transmission issues with getting large numbers of people vaccinated at pharmacies and offices, which often have pretty cramped facilities. So Public Health docs hereabouts have been talking about setting up vaccination facilities in tents in large open spaces, anyway--airport car-parks are one option. So maybe we'll see large refrigerated transports arriving at venues like that.
    On the other hand, Pfizer claim to have developed cool-boxes than can keep vaccine at the necessary temperature, without power, for ten days. So distribution to smaller centres may also be an option.

    Quote Originally Posted by Van Rijn View Post
    But wow, 90% effective or better. It gives realistic hope things could be mostly back to normal in a year. I was concerned effective vaccines might be harder to develop than hoped, but this sounds like great news.
    It's early days for this particular vaccine--it's an interim analysis, they won't apply for Emergency Use sign-off until they've followed all subjects for adverse events for two months (which means end of this month for the current tranche), and it'll be the end of the year before they accumulate the number of cases required by their original protocol. So there's the potential for something yet going wrong. But it's proof of concept for mRNA vaccines, there are several more in the pipeline, and they're faster to produce in quantity than older antigen-based vaccines. So, as you say, great news.

    Grant Hutchison

  13. #2473
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    Quote Originally Posted by grant hutchison View Post
    So Public Health docs hereabouts have been talking about setting up vaccination facilities in tents in large open spaces, anyway--airport car-parks are one option. So maybe we'll see large refrigerated transports arriving at venues like that.
    On the other hand, Pfizer claim to have developed cool-boxes than can keep vaccine at the necessary temperature, without power, for ten days. So distribution to smaller centres may also be an option.
    I can get dry ice at local stores and my understanding is that liquid nitrogen isn’t too hard to get either. I could imagine large ice boxes kept cold with one or the other to serve distribution sites, and those smaller boxes used for more localized distribution. Or more interest in building more refrigerators especially if it looks like this type of vaccine will become common. I imagine COVID-19 vaccine will be used as fast as it arrives for some time too, so long term storage won’t be as big an issue.

    But I wouldn’t be surprised if there is a dry ice and liquid nitrogen shortage for a time.

    It's early days for this particular vaccine--it's an interim analysis, they won't apply for Emergency Use sign-off until they've followed all subjects for adverse events for two months (which means end of this month for the current tranche), and it'll be the end of the year before they accumulate the number of cases required by their original protocol. So there's the potential for something yet going wrong.
    Sure, I’m not assuming anything is certain, but I am much more confident now it is realistic to hope for things to be returning to near normal in about a year. I was worried we could be hearing about something causing COVID-19 vaccines not to work well by now, and developers having to go back to the drawing board.

    But it's proof of concept for mRNA vaccines, there are several more in the pipeline, and they're faster to produce in quantity than older antigen-based vaccines. So, as you say, great news.
    And won’t that be interesting once we get past COVID-19 and attention is turned to other diseases? COVID-19 spurring development of this technology might have some important long term implications.

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  14. #2474
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    The BBC is reporting that the Pfizer vaccine can be stored for a few days in a normal drug fridge (-4°C) without losing potency, which makes sense, and simplifies things somewhat.

    Grant Hutchison

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    Study in Nature looks for places most likely to spread virus

    WashingtonPost.com
    Restaurants, gyms and coffee shops rank high among locations where the coronavirus is most likely to spread outside the home. That’s according to a newly published report based on data from millions of Americans, tracked by their phones as they went about daily life during the pandemic’s first wave.

    The study provides statistical support for a strategy built around limiting capacity at indoor venues — such as capping crowds at 20 percent — while allowing those locations to remain open. The researchers contend that such a strategy can make a huge dent in the infection rate while causing a far more modest drop in the total number of visits to those venues.

    Starting with a “very simple” epidemiological model, the researchers superimposed the cellphone mobility data and pressed play on a simulation of viral spread, said Northwestern University epidemiologist Jaline L. Gerardin.
    Certain venues — places of worship, full-service restaurants and gyms — disproportionately contributed to infections. In Chicago, for instance, 10 percent of sites accounted for 85 percent of predicted infections.

    The study discerned another pattern: Lower-income people, many of them essential workers, were less able to reduce their mobility during shutdowns and more likely to be exposed to crowded venues. Within low-income neighborhoods, with higher percentages of residents who are people of color, more people would be infected, which mirrors real-life patterns of transmission.
    Here is the link to the journal article in Nature

    Abstract:
    The COVID-19 pandemic dramatically changed human mobility patterns, necessitating epidemiological models which capture the effects of changes in mobility on virus spread1. We introduce a metapopulation SEIR model that integrates fine-grained, dynamic mobility networks to simulate the spread of SARS-CoV-2 in 10 of the largest US metropolitan statistical areas. Derived from cell phone data, our mobility networks map the hourly movements of 98 million people from neighborhoods (census block groups, or CBGs) to points of interest (POIs) such as restaurants and religious establishments, connecting 57k CBGs to 553k POIs with 5.4 billion hourly edges. We show that by integrating these networks, a relatively simple SEIR model can accurately fit the real case trajectory, despite substantial changes in population behavior over time. Our model predicts that a small minority of “superspreader” POIs account for a large majority of infections and that restricting maximum occupancy at each POI is more effective than uniformly reducing mobility. Our model also correctly predicts higher infection rates among disadvantaged racial and socioeconomic groups2–8 solely from differences in mobility: we find that disadvantaged groups have not been able to reduce mobility as sharply, and that the POIs they visit are more crowded and therefore higher-risk. By capturing who is infected at which locations, our model supports detailed analyses that can inform more effective and equitable policy responses to COVID-19.
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  16. #2476
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    Away back in this thread I projected the development of helmets with positive air displacement and today the BBC reports on three that are now in production. They managed to get them developed before the vaccine, But now we shall see whether they are successful in 2021.
    https://www.bbc.co.uk/news/business-54916159
    Last edited by profloater; 2020-Nov-16 at 08:56 AM. Reason: Link
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    Interim analysis of results from Moderna's mRNA vaccine report 95% protection and suggest a reduction in severity of disease in those vaccinated subjects who were infected.
    For me, this is better news than the Pfizer announcement--we're now showing good signs of passing the "has it been replicated" test for the concept of mRNA vaccines against Covid.

    Grant Hutchison

  18. #2478
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    Quote Originally Posted by grant hutchison View Post
    Interim analysis of results from Moderna's mRNA vaccine report 95% protection and suggest a reduction in severity of disease in those vaccinated subjects who were infected.
    For me, this is better news than the Pfizer announcement--we're now showing good signs of passing the "has it been replicated" test for the concept of mRNA vaccines against Covid.

    Grant Hutchison
    And also saying they don't need the super-cold temps, just an ordinary fridge.
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  19. #2479
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    Quote Originally Posted by Trebuchet View Post
    And also saying they don't need the super-cold temps, just an ordinary fridge.
    I do wonder though whether there is is an actual difference between the vaccines that makes one more temperature tolerant than the other or if one company is being more cautious than the other.

    In any event, this makes me very happy. More and more, it looks like we should start seeing the infection rate take a deep dive the further we go into next year, and with luck, it won’t come back.

    Of course the other big question is how long the immunity from the vaccines will last. Hopefully not too short.

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    Meanwhile just listening to our governor, California has had the biggest Covid-19 infection rate increase ever. We have four infection control tiers that are applied on a county by county basis. A number of counties dropped back by more than one tier in the last week. Nobody is moving to a better tier. However, so far we still aren’t as bad as some states and currently have hospital capacity, but could be overwhelmed without heavier infection control - like a strong recommendation not to gather for Thanksgiving this year.

    My goal now is to get through this winter without getting sick, and things shoud improve as the weather gets better and as vaccines start being used.

    "The problem with quotes on the Internet is that it is hard to verify their authenticity." — Abraham Lincoln

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  21. #2481
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    Quote Originally Posted by Swift View Post
    Study in Nature looks for places most likely to spread virus
    It makes sense. One interesting thing that happened in Japan is that yesterday or the day before, Hokkaido (in the north of Japan) had more cases than Tokyo (which is three times as populous). And most of the cases in Hokkaido were in Sapporo, the major city. So it seems that what has happened is that it's gotten cold there (it snowed for the first time this year a few weeks ago), and so shops are not ventilating as well, and people are catching the virus at dinners and parties and the like.
    As above, so below

  22. #2482
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    As I understand, mRNA vaccines are a good news outcome of this century, a wonderful example of development from the older and hugely significant DNA vaccines that eliminated smallpox and treat many other diseases. mRNA technology is cheaper and faster to produce. The acceleration of support for vaccine production is one positive outcome of the current pandemic. So this safety and effectiveness news is a tonic in “interesting” times.
    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

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    Quote Originally Posted by profloater View Post
    As I understand, mRNA vaccines are a good news outcome of this century, a wonderful example of development from the older and hugely significant DNA vaccines that eliminated smallpox and treat many other diseases. mRNA technology is cheaper and faster to produce. The acceleration of support for vaccine production is one positive outcome of the current pandemic. So this safety and effectiveness news is a tonic in “interesting” times.
    I don't think that "DNA vaccine" is the usual term for the vaccines that eliminating smallpox, but rather to an experimental type of vaccine where DNA is inserted into the cell nucleus to direct the production of antibodies. Normally, vaccines involved presenting cells with weakened or inactive pathogens to encourage them to learn a response. What is different about the RNA vaccines is that RNA is inserted into the cell cytoplasm to produce antibodies, so it is a way of directly programming cells. I am slightly wary, but it seems to be working pretty well.
    As above, so below

  24. #2484
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    Well the last century vaccines were modified or killed viral DNA, while these are working with less stable RNA and concentrating on the surface proteins to generate antibody resistance. As I understand it.
    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

  25. #2485
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    Vaccines come in various forms.

    Live attenuated: weak strains of live disease organism, capable of reproducing in the body, but not (under normal circumstances) of causing disease.

    Inactivated: organism that has been damaged (heat, chemicals) to prevent it reproducing in the body.

    Fractional: only specific proteins (or, for bacteria, polysaccharides) from the organism.

    The first will contain RNA or DNA (many viruses, such as coronaviruses, carry there genomes on RNA, not DNA); the second will probably contain genetic debris; the third will contain no genetic material at all.

    The new mRNA vaccines deliver a strand of messenger RNA to our bodies, which encodes for some fractional component of the disease organism. This is then transcribed by our cells to produce antigen, which then generates the immune response. You can think of it as a way of delivering a massive dose of fractional vaccine, because the amount of antigen synthesized in the body is far greater than might be administered from a single injection of antigen.

    There is more information about classical vaccine types (the first three in my list) in a document from the CDC here.

    Grant Hutchison

  26. #2486
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    Quote Originally Posted by grant hutchison View Post
    Vaccines come in various forms.

    Live attenuated: weak strains of live disease organism, capable of reproducing in the body, but not (under normal circumstances) of causing disease.

    Inactivated: organism that has been damaged (heat, chemicals) to prevent it reproducing in the body.

    Fractional: only specific proteins (or, for bacteria, polysaccharides) from the organism.

    The first will contain RNA or DNA (many viruses, such as coronaviruses, carry there genomes on RNA, not DNA); the second will probably contain genetic debris; the third will contain no genetic material at all.

    The new mRNA vaccines deliver a strand of messenger RNA to our bodies, which encodes for some fractional component of the disease organism. This is then transcribed by our cells to produce antigen, which then generates the immune response. You can think of it as a way of delivering a massive dose of fractional vaccine, because the amount of antigen synthesized in the body is far greater than might be administered from a single injection of antigen.

    There is more information about classical vaccine types (the first three in my list) in a document from the CDC here.
    Thanks for the nice explanation. I was under the mistaken impression that the mRNA would be used directly to generate the immune response, but I see that it is being used to make antigens that then generate the immune response. That makes sense. Also, just as a question, I assume that an RNA vaccine could also be used to vaccinate for a disease caused by a DNA virus, since in any case I guess the viral DNA would have to be transcribed to mRNA in the cell.
    As above, so below

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    Quote Originally Posted by profloater View Post
    Well the last century vaccines were modified or killed viral DNA, while these are working with less stable RNA and concentrating on the surface proteins to generate antibody resistance. As I understand it.
    As Grant explained, some traditional vaccines might contain DNA or RNA, and that would depend on the virus. For example, just to name some famous ones, smallpox is caused by a DNA vaccine while polio is an RNA vaccine. I think the key is that in the case of traditional vaccines, it doesn't matter if the DNA or RNA is intact, all that matters is that the body recognize it as a pathogen and generates an immune response. With an RNA (or DNA) vaccine, the RNA/DNA must be inserted into the cell to synthesize proteins, and so if it is damaged it won't be able to do that.
    As above, so below

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    Quote Originally Posted by Jens View Post
    Thanks for the nice explanation. I was under the mistaken impression that the mRNA would be used directly to generate the immune response, but I see that it is being used to make antigens that then generate the immune response. That makes sense. Also, just as a question, I assume that an RNA vaccine could also be used to vaccinate for a disease caused by a DNA virus, since in any case I guess the viral DNA would have to be transcribed to mRNA in the cell.
    Yes, all you need is mRNA that encodes a pathogen protein to which the body can mount a useful immune response--you're just tricking a person's cells into producing viral antigen for a while. You can achieve the same result with a pDNA vaccine using a DNA plasmid that encodes for an antigenic protein. They've been trialed in animals, but there are safety concerns about the DNA becoming incorporated into a cell's genome, perhaps disrupting the activity of functional genes.

    Grant Hutchison

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    Pfizer/BioNTech have now completed Phase III trials of their vaccine:

    • Primary efficacy analysis demonstrates BNT162b2 to be 95% effective against COVID-19 beginning 28 days after the first dose; 170 confirmed cases of COVID-19 were evaluated, with 162 observed in the placebo group versus 8 in the vaccine group
    • Efficacy was consistent across age, gender, race and ethnicity demographics; observed efficacy in adults over 65 years of age was over 94%
    • Safety data milestone required by U.S. Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) has been achieved
    • Data demonstrates vaccine was well tolerated across all populations with over 43,000 participants enrolled; no serious safety concerns observed; the only Grade 3 adverse event greater than 2% in frequency was fatigue at 3.8% and headache at 2.0%
    • Companies plan to submit within days to the FDA for EUA and share data with other regulatory agencies around the globe
    • The companies expect to produce globally up to 50 million vaccine doses in 2020 and up to 1.3 billion doses by the end of 2021
    Some discussion from Science here.

    Grant Hutchison

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    I’m glad to see this appears to be highly effective with older adults too. I saw this on a news site earlier, it’s good to see it is going well. Get through this winter and I expect things will start improving. Next winter will be far better.

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