34 votes

A bird flu pandemic would be one of the most foreseeable catastrophes in history (gifted link)

16 comments

  1. skybrian
    Link
    From the article: … … … … …

    From the article:

    The H5N1 avian flu, having mutated its way across species, is raging out of control among the nation’s cattle, infecting roughly a third of the dairy herds in California alone. Farmworkers have so far avoided tragedy, as the virus has not yet acquired the genetic tools to spread among humans. But seasonal flu will vastly increase the chances of that outcome. […]

    We might be fine. Viruses don’t always manage to adapt to new species, despite all the opportunities. But if there is a bird flu pandemic soon, it will be among the most foreseeable catastrophes in history.

    Devastating influenza pandemics arise throughout the ages because the virus is always looking for a way in, shape shifting to jump among species in ever novel forms. Flu viruses have a special trick: If two different types infect the same host — a farmworker with regular flu who also gets H5N1 from a cow — they can swap whole segments of their RNA, potentially creating an entirely new and deadly virus that has the ability to spread among humans. It’s likely that the 1918 influenza pandemic, for example, started as a flu virus of avian origin that passed through a pig in eastern Kansas. From there it likely infected its first human victim before circling the globe on a deadly journey that killed more people than World War I.

    And that’s why it’s such a tragedy that the Biden administration didn’t — or couldn’t — do everything necessary to snuff out the U.S. dairy cattle infection when the outbreak was smaller and easier to address.

    Even now, however, there is little routine testing of farmworkers or close contact tracing for those who fall ill. We still have way too little information on how the virus actually spreads among cows. Its genetic sequences are being published very late, if at all, and without the kind of data necessary to understand and trace the outbreak. And the way the virus is spreading from herd to herd makes it clear that infected cows are still being moved around rather than isolated.

    One recent study of 115 farmworkers found that about 7 percent of them showed signs of a recent, undetected H5N1 infection. They’d been going about their lives — visiting markets, churches, other homes — while harboring the potential seed of a new pandemic.

    Just a few weeks ago, a pig in a backyard farm in Oregon was found to have bird flu. It seems to have gotten it from sick poultry on the same farm. Pigs cause extra worry because they are considered to be ideal mixing vessels for various animal flu viruses to adapt and spread among humans.

    A teenager in Canada was infected, and the virus showed some key mutations that bring it closer to adapting to spread among humans. This outbreak has so far been mostly mild in humans, but historically it has been deadly, and further mutations could make it so again. That Canadian is in critical condition, unable to breathe independently.

    There’s also an infected child in California who was not known to have come into contact with any sick animals at all, which raises the terrifying possibility that he got it from another human being. And the virus levels in the wastewater in several states keep spiking.

    Biden is president for another seven weeks or so. It’s not too late for him to give the nation a parting gift. He could start taking these risks as seriously as he should have when the cattle infections were first discovered. We could get serious about mandatory testing of cows, milk and farmworkers and about isolating infected cattle herds — as we already do for birds and pigs. We could speed up development of the vaccine that’s already in the works for cows — and expedite all precautions for humans, too. It’s true that one doesn’t get proper, timely credit for disasters averted. But history will, eventually, deliver its verdict.

    19 votes
  2. [14]
    chocobean
    Link
    This didn't sit right with me. My immediate reaction is anger: How irresponsible! How ignorant! How selfish! So from the way this is written, I thought, wow, 13 with symptoms and some declined,...

    Of the 34 individuals who were exposed at that pet fair, including 13 who had respiratory symptoms, all were offered voluntary testing. Five declined. (NYT, Zeynep Tufekci)

    This didn't sit right with me. My immediate reaction is anger: How irresponsible! How ignorant! How selfish!

    So from the way this is written, I thought, wow, 13 with symptoms and some declined, right? From link within link - Hawaii Dept of Health (emphasis mine):

    To date, 54 individuals have been investigated for potential exposure. Of those, 34 were offered testing because of unprotected exposure (meaning without use of adequate personal protective equipment), to the infected birds within the past 10 days, or because they had developed respiratory symptoms within 10 days of contact with the birds.

    Twenty-nine consented to testing, including 13 who had at least one symptom of respiratory infection and 16 who had no symptoms. All the individuals who would be considered to have very high-risk exposure to the infected birds, including prolonged direct contact with visibly sick, dying, or dead birds, consented to testing. (DOH)

    54    potentially exposed
    34    potentially exposed and offered testing
    05    potentially exposed and offered testing and declined to testing
    29    potentially exposed and offered testing and consented to testing
    ---------------------------------------------------------------------------
    from the 29 above:
    13    had 1+ symptoms    
    16    had 0  symptoms    
    

    from bolded quote, of all those considered very high risk

    100%   consented to testing
    0%     declined testing
    

    So who are the 5 who declined? Did they have symptoms? Maybe. But we know for a fact that they were not in the high risk group. And there's a big difference between the wording of "potentially exposed" (Hawaii DOH) and "exposed" (Zeynep Tufekci). Tufekci is a wordsmith: he chose the articles, he chose the way to phrase the first quote. He chose to line up a long sentence with a short fragment for effect. He chose to pair the grammatically nonessential clause of "13 who had respiratory symptoms" right next to "five declined". That seems irresponsible at best and frankly, I suspect, dishonest on Tufekci's part.

    The reality of what happened is that 16 people who had no symptoms at all, offered themselves to be tested, with potentially being confirmed to carry a new and spooky potential epidemic virus and the glare of media spotlight. We don't know if the people who consented to testing had pet birds or livelihood birds at home. Folks with pets, if you knew that by consenting to tests, if you turn out positive, the government could come and destroy your pet, would you hesitate to get tested? Of those considered high risk, 100% of them stepped up and got tested, even folks with no symptoms. That's pretty good isn't it?

    13 votes
    1. [12]
      Raspcoffee
      (edited )
      Link Parent
      I want to add something else to this, a part that's rather tricky in statistics: testing people without symptoms on any kind of illness is quite often actually worse than useless unless you really...

      The reality of what happened is that 16 people who had no symptoms at all, offered themselves to be tested, with potentially being confirmed to carry a new and spooky potential epidemic virus and the glare of media spotlight. We don't know if the people who consented to testing had pet birds or livelihood birds at home. Folks with pets, if you knew that by consenting to tests, if you turn out positive, the government could come and destroy your pet, would you hesitate to get tested? Of those considered high risk, 100% of them stepped up and got tested, even folks with no symptoms.

      I want to add something else to this, a part that's rather tricky in statistics: testing people without symptoms on any kind of illness is quite often actually worse than useless unless you really understand what you're doing. Suppose you would test everyone in a country with a low amount of HIV for HIV, the majority of the tests that are positives are false positives.

      That might sound weird, but basically, every test has a chance of giving a positive result without the pathogen being present. To make this a bit easier to understand, let's say the chance of producing a false positive is 0.1% per test, and correctly gives a positive when the pathogen is present 99% of the time. Additionally, the country we test in consists 10 million people, and 5000 have the disease.

      Now, if you test all those without the pathogen, you would get about (10000000-5000) x 0.001 = 9995 false positives. (notice that I say about, not exactly, this is probability so you would almost never exactly get this number!) As for those with the pathogens, 5000 x 0.99 = 4950 positives.

      9995 false positives as opposed to 4950 actual positives. Let this sink for a bit. This hypothetical example I gave had some very decent numbers. 99% accuracy to identify the pathogen, and a legendary 0.1% of a false positives. That all sounds really nice on paper but if you do something as grand as testing everyone, you get results like this. You can't just eradicate disease by testing each and every different person.

      So usually, when you are being tested, this is because there is a reason to suspect you may have the diseases, this can be... wait for it, symptoms and exposure risk. This is why symptoms are a big factor what kind of tests you receive. 3Blue1Brown has an excellent video on this part of statistics, and how it's applicable outside of medicine, too.

      In conclusion, you are correct. Pair what I've written in this comment here and what you've said about Tufekci being selective with his choice of words and well, this feels like a deceptively written article on a very serious problem that does require attention. But with phrasing like this, you only lose to stand credibility - justifyingly so.

      That's pretty good isn't it?

      It is. As a final food for thought: We don't even know why those 5 people refused. Was someone in a hurry for personal reason while the risk was also low? Did someone have a phobia for doctors? We don't know the context of these either.

      But with the way it's phrased here too, it feels like the author wanted to presented it as something that people actively resisted health professionals.

      Edit: formatting

      12 votes
      1. [11]
        skybrian
        Link Parent
        Bayesian probability does apply here, but the way you apply it isn’t right. The math is different when testing people who have been exposed, versus testing people who haven’t been exposed. People...

        Bayesian probability does apply here, but the way you apply it isn’t right. The math is different when testing people who have been exposed, versus testing people who haven’t been exposed. People who have been exposed have a higher prior probability of having the disease - maybe not as high as people who have symptoms, but still a lot higher than the background population that hasn’t been exposed.

        This is why testing people who have been exposed is a standard public health practice and screening everyone isn’t.

        Also, I don’t see Zeynep as making any particular claim about why people did what they did.

        3 votes
        1. [10]
          Raspcoffee
          Link Parent
          You're correct, but the pitfall is that in the study it's: 05 potentially exposed and offered testing and declined to testing Which were not of the individuals of those who were at high risk....

          The math is different when testing people who have been exposed, versus testing people who haven’t been exposed.

          You're correct, but the pitfall is that in the study it's:

          05 potentially exposed and offered testing and declined to testing

          Which were not of the individuals of those who were at high risk. Whereas in the article it's:

          Of the 34 individuals who were exposed at that pet fair, including 13 who had respiratory symptoms, all were offered voluntary testing. Five declined.

          And leaves it at that. It's not as much as what is written, but more about what is not written. It's not that it's not concerning that this happens(in fact I'm in favour of reducing livestock capacity in my country, as unpopular as it would be), it's more so that, when I read the article, it feels very selectively taken out of the paper.

          This is why testing people who have been exposed is a standard public health practice and screening everyone isn’t.

          So to clarify: my complaints is not specifically with the testing that is and isn't done. It's more the way that it's presented in the article that feels like it's being taken in a different context. I'm not sure whether the author is trying to imply why certain people did what they did, but when it is written the way it is, it is very easy for someone to come to the conclusion to take the message of the DOH very differently. Whatever the reason, it does not feel like a proper way for someone to communicate the report through an opinion piece - especially with an opinion piece those are rather critical details that shouldn't be left out implicitly imo.

          2 votes
          1. [9]
            skybrian
            Link Parent
            I think it’s fair to say that this particular incident was summarized too briefly. I don’t see it as a critical detail, though, since her concern is more about what might happen in future...

            I think it’s fair to say that this particular incident was summarized too briefly. I don’t see it as a critical detail, though, since her concern is more about what might happen in future incidents?

            The main point of the article is that the US government isn’t doing enough about the risk of a bird flu pandemic and should do more, and I think that stands? The reports about it infecting humans show that it’s possible, which is supporting evidence for why it should be taken more seriously. Sometimes people decline to be tested; that’s just how it goes with public health sometimes.

            There isn’t anything we can do about it, though. The government will do what it does. Perhaps government officials read the New York Times, but they’ll make their own judgements.

            2 votes
            1. Raspcoffee
              Link Parent
              Oh yeah completely agreed. In fact, we'll pretty much need to reduce the total amount livestock if we want to reduce disease spread, combat climate change and even improve the quality of water at...

              Oh yeah completely agreed. In fact, we'll pretty much need to reduce the total amount livestock if we want to reduce disease spread, combat climate change and even improve the quality of water at times.

              About the only thing an individual can do for this is well, the classic eat less meat and dairy products. :/ But with the current stance things will need to get really bad before strong actions are taken.

              2 votes
            2. [7]
              chocobean
              Link Parent
              jumping back in here: Yes the main point stands - there's something terrible coming and we could do something about it and we should. I think I got too depressed thinking about how we're not going...

              jumping back in here: Yes the main point stands - there's something terrible coming and we could do something about it and we should.

              I think I got too depressed thinking about how we're not going to, and then laser focused on one thing that made me feel little better about how the masses behave, apologies.

              [1918 flu] killed more people than World War I.

              And yet do we have annual remembrance days about how bad it was? No. "people get sick" is a certainty and it's a tragedy we implicitly accept.

              Seeing the backlash against COVID measures, and how much society clamored to go back "to normal", and then some countries got a little too weird about restrictions and people died violent deaths instead of quiet, sickness deaths.... I think the lessons that leaders learned is hopefully, make sure folks have masks and other PPE, but also that doing anything is political suicide. Just let people do their thing and lament and wring hands and don't do anything. Offer tests, offer treatments, pay for vaccines, but otherwise let people decide how they want to be safe, and throw the vulnerable to the whims of the winds. Real estate doesn't want shut down, commerce doesn't want shut down, employers don't want shut down.

              And yes, this will be ONE of the MANY most foreseeable catastophers, but a distant second to climate change, which we are also not going to do anything about. Again, slow deaths are ignorable and people aren't going to move away from the coasts or stop living in the desert.

              1 vote
              1. [6]
                skybrian
                Link Parent
                Regarding climate change, what sort of deaths are you imagining? I don’t think of things like hurricanes, wildfires, and heat waves causing slow deaths, and not nearly as many as a pandemic, or at...

                Regarding climate change, what sort of deaths are you imagining? I don’t think of things like hurricanes, wildfires, and heat waves causing slow deaths, and not nearly as many as a pandemic, or at least not in developed countries.

                Property damage is going to keep going up, though, along with insurance costs. I wonder how that plays out?

                1 vote
                1. [5]
                  chocobean
                  Link Parent
                  climate refugees. Folks who slowly can't afford insurance; getting dropped one by one at renewal time; unable to sell property to others who also can't get new mortgage + house insurance. Heat...

                  climate refugees. Folks who slowly can't afford insurance; getting dropped one by one at renewal time; unable to sell property to others who also can't get new mortgage + house insurance. Heat deaths that mostly affect the poor and unevenly. [Edit: what I mean is that heat deaths are already happening, but it's happening to renters in small units that only have 1 side window or sublets with no windows, and folks whose air conditioning just isn't able to equalize with outside temps. The poor. They're happening but it's not like every time the weather turns 40C everyone dies: it's every time the weather turns 40C a few poor people die so they ignore it.] Marshes getting wetter [+ diseases, ticks not dying in the winter], rivers overflowing more often, flood planes flood more often, lower elevation parts of the town flood as higher elevation trees are cut for more concrete shopping centres and "exclusive communities". That kind of slow deaths.

                  The big ones like hurricanes wild fires are "faster" but they fall into "sudden catastrophes we couldn't have foreseen" and so nothing also will be done about them.

                  3 votes
                  1. [4]
                    skybrian
                    Link Parent
                    Makes sense. I think it’s a little too gloomy to say nothing is done about hurricanes. For example, South Florida’s building codes are quite strict.

                    Makes sense. I think it’s a little too gloomy to say nothing is done about hurricanes. For example, South Florida’s building codes are quite strict.

                    2 votes
                    1. [3]
                      DefinitelyNotAFae
                      Link Parent
                      Your article says the opposite. South Florida may be good, but the rest isn't, and statewide it's insufficient. That code is 22 years old, and the state legislature has been relaxing them rather...

                      Your article says the opposite. South Florida may be good, but the rest isn't, and statewide it's insufficient. That code is 22 years old, and the state legislature has been relaxing them rather than improving them.

                      Fugate warned the 2017 National Hurricane Conference in April that the Florida legislature was hell bent on abandoning mandatory code upgrades. State builders, he said, were complaining that updating the codes every three years was inconvenient. “Who’s it inconvenient to?” Fugate asked, rhetorically. “The homeowner who’s going to be paying for a home for next 30 years, that will probably go through one, if not more, tropical systems? Or to the builder or developer who’d like to build faster and cheaper?”

                      The shift toward less rigorous codes is driven by several factors, experts say: Rising anti-regulatory sentiment among state officials, and the desire to avoid anything that might hurt home sales and the tax revenue that goes with them. And fierce lobbying from home builders.”

                      And that's just one state.

                      1. [2]
                        skybrian
                        Link Parent
                        Maybe this is overly optimistic of me, but my take on it is that it’s happened before, which shows that it’s not impossible. Though, perhaps not in the short term. It might take another disaster...

                        Maybe this is overly optimistic of me, but my take on it is that it’s happened before, which shows that it’s not impossible. Though, perhaps not in the short term. It might take another disaster or two before building codes are tightened up more.

                        1 vote
                        1. DefinitelyNotAFae
                          Link Parent
                          I think this is not a realistic perspective, nor even an optimistic one. The article says that the regulations are insufficient and already being lessened. An optimistic view might be that things...

                          I think this is not a realistic perspective, nor even an optimistic one. The article says that the regulations are insufficient and already being lessened. An optimistic view might be that things could change in the future but your previous comment was claiming this thing was already good.

                          It's not too "gloomy" to say there's not enough being done about hurricanes when that's what your source says is accurate.

    2. skybrian
      Link Parent
      I read it as 5 of 34 declined. “Of” modifies 34, that’s the denominator. Clarifying what happened is worthwhile, though. Also, instead of “he chose the articles,” that should be “she.”

      I read it as 5 of 34 declined. “Of” modifies 34, that’s the denominator. Clarifying what happened is worthwhile, though.

      Also, instead of “he chose the articles,” that should be “she.”

      2 votes
  3. skybrian
    Link
    Single bird flu mutation could let it latch easily to human cells, study finds (Washington Post) ... ... I interpret this as confirming that a pandemic could happen again any time, though it...

    Single bird flu mutation could let it latch easily to human cells, study finds (Washington Post)

    Scientists from the Scripps Research Institute are reporting that it would take just a single mutation in the version of bird flu that has swept through U.S. dairy herds to produce a virus adept at latching on to human cells, a much simpler step than previously imagined.

    ...

    William Schaffner, a professor of infectious diseases at Vanderbilt University Medical Center who did not participate in the study, called the research “sobering,” adding, “I had not known it would take just one mutation in the virus for it to attach itself to the receptors on human cells.”

    ...

    James C. Paulson, one of the paper’s authors, and several other top scientists agreed that it is statistically likely the mutation has occurred in the H5N1 virus but stressed that it has yet to be detected, and other barriers remain before the virus could be transmitted from one person to another. Paulson is a professor in the Department of Molecular Medicine at Scripps.

    I interpret this as confirming that a pandemic could happen again any time, though it probably won't in any particular year.