igor67

I think there is likely to be some demand for a vaccine by time it is done, but possibly not. Given this is the 3rd significant outbreak in this group in the last 20 years I imagine there will be on-going interest. They may even develop a system of sorts similar (using this very loosely) to how they can identify the flu strains and then build a safe vaccine in less than a year. I imagine it depends on how similar the viable vaccine ends up being.

Best of luck on the procedure. On a similar downer note there appears to be more evidence emerging of some rather significant undercounting of the the death toll, now in Spain. I had posted about a week ago that in parts of Northern Italy the total death rate in March was substantially higher than both the historical averages for the time of year and reported Covid deaths together. At least parts of Spain are showing a similar trend. In both cases it appears that you could conservatively double the current death toll and still have some extra deaths left over. This turns out to be a common issue, the CDC has to account for routine under reporting of flu caused deaths every year, and periodically does studies to help them quantify the affect. Trying to talk numbers too seriously seems very unwise since there are plenty of differences in how and when tests are administered to both groups so you can't just use the flu percentage of undercounting. I also learned while tracking some of this down that trying to deal with data collection and all of the correction factors they need means final estimates of yearly flu deaths are not finalized for up to 2 years. Reading between the lines of their methods I suspect that dealing with the patchwork of non-standardized local reporting systems (aka Death Certificates) is a big slow down. So we are probably stuck with reliable enough numbers for the time being.

I don't have anywhere near the type of data I would want to make that type of call Jimbo. Enough maybe out there to develop a plausible idea of how that might unfold, but it would be very nuanced taking into account not just social distancing, but to what extent population density itself seems to impact the rate of spread. Those I think we have at this point some decent data for. What I'd be less confident in is how does the partial shut down affect travel between affected and less affected counties? Do people get more inclined to 'cheat' once some restrictions are lifted? I would still assume that tourism is a no go, since that is pretty much the fastest way to spread things from Chicago or to a lesser extent the Twin Cities. I'm not actually sure than for a lot of those counties, since farming and food production has still continued how much more gets opened up? Don't get me wrong if it can be plausibly safe something is better than nothing.

flu virus variations and cold virus variations are rather different things. A very crude analogy would be something like flu viruses are like canines. Different enough we could call them difference, but capable of some level of interbreeding across what we would otherwise call species boundaries. Cold viruses are often completely different biologically. So it is more akin to saying anything that lives in water is a fish. I wouldn't be overly pessimistic about treating viruses. Twenty or so years ago it was mostly true we didn't have viral treatments, but research spun out of fighting HIV helped pave the way for various antiviral therapies, none to my knowledge have shown a lot of promise against covid still complete pessimism isn't warranted.

A few things, most of the diseases we have vaccines for have mortality rates within the plausible range of covid-19 at least under current levels of treatment. A few of them are definitely higher. There are costs outside of death, most of the old diseases we have a pretty good idea of the additional costs. Though just a few years ago they realized by looking at historical data that measles biggest effect was probably that is suppressed the immune system for most people often for a year or more (sorry I don't have the citation handy). We are far from having a good idea what the level of long term cost for survivors of covid-19, but there are some signs it could involve some level of long-term lung damage. Viruses classification is based on structure, not relative threat level. It is the same in bacteria which is why you both need E.coli in your gut, and different strains are pathogenic. There is no particular biological relationship between covid and flu viruses. Hence folks looking to earlier work on other covid viruses like MERS and Sars to jump start vaccine efforts and not any of the 30-40 years worth of flu vaccines. All scientific math is modelling, especially things like gravity the normal universal law of gravitation doesn't even work well enough to support GPS. You have to adjust the model to account for relativity. Generally however you do not have to adjust the model for variations in the Earth's density to get GPS to work, but other high precision work might have to. Modelling is one of the key innovations of the entire Scientific Revolution because it forces us to turn all of fuzzy verbal logic into something that generates numerical predictions. Another key innovation is the experimental idea itself. Namely the entire notion that you could set-up a carefully controlled lab experiment with only a single variable being altered. These tools are ridiculously good, but in many scientific fields we can't do that type of lab experiment. This tends to as we are seeing in public make things messier.

I believe this is the link Chorizo was discussing https://www.kare11.com/article/news/health/coronavirus/minnesota-department-of-health-releases-covid-19-modeling/89-09e965f6-9b4c-4307-8e36-743f084fbcea I share the concern about risks of pushing a vaccine too fast. The vaccine freedom/ I don't want too/ fill-in adjective of your choice crowd have already killed people and a rushed vaccine runs the risk of giving them more 'doubt' to sow among people. If one looks at the pre-vaccine rates of these diseases on the CDC website and compares that to the modern developed world death rates from these diseases you collectively still get around 200,000 people saved per year at the US current size. And that doesn't get into the huge other costs. I have an older relative for example who spent his/her entire life on disability as a result of the brain damage caused by the high measles fever. Regrettably even folks of the generation to have a better understanding of the toll often forget about these sorts of things, because those students were sent to special schools not more integrated like they are today.

Organ recipients (immune compromised), asthma, and a big chunk of cancer patients have no diet/ exercise/ moral issues. I should know since I don't even have to go outside my teaching department to hit people in each category none of whom are anywhere close to 50. And while that is factoid status as I posted above those categories do make up a sizeable fraction of the population. Asthma alone hits 25 million people which is still quite a bit more than the unemployment number. In fact if you count just the adults with asthma you get 19.5 million which still is bigger than current unemployment. So at least for the time being it would actually do more economic damage.

Ugh, so I finally got around to tracking down some info on these chloroquinie studies with 'positive' results. I shouldn't be surprised at how bad they were, and yet I had imagined they were small scale limited studies done in good faith. I'll post a link to someone else's analysis below, but they are reputable. In this case I do not routinely analyze clinical studies, so it is easy for me to miss some of the limitations. But the short version is that the studies weren't just small sample size, they patients appear to have been cherry picked in a few different ways. The most significant is that the treatment was primarily tested on patients with mild symptoms. It is not a stretch to say I wouldn't have accepted that design from my high school students. My initial skepticism was driven by a pretty simple thing to be on the lookout for namely, how would such a drug work? The fact that the treatment involved an antibiotic for a virus was a key reason to be suspicious. https://sciencebasedmedicine.org/hydroxychloroquine-and-azithromycin-versus-covid-19/ As I posted way up thread the communication piece is hard for a lot of reasons, one is trying to find the balance between simplifying and explaining all the details. You can kind of compare my quick summary to the more robust take down in the link. Another issue, one I really focus on is appropriate skepticism. New research should always be greeted with SOME skepticism. It is the nature of research that we working on things we don't understand yet, so the conclusions from any study in any field are often incomplete or wrong. Over time though we make progress. We are stuck with limited time however and can't minutely dissect every piece of information. Situations like this and the way it is presented often turn into confirming evidence then for extreme skeptical stances against science. The antidote for that is not science cheerleading and mindless positivity. No one has actually found a good way to counteract these modern pulls in attitude.

Entertainingly though PBS was showing Wednesday Nite at the lab this weekend and they were showing one on flu from a couple of years ago. Apparently the first documented zoonotic (animal to people) transmission of a flu virus was in Broadhead, WI.

Luckily we have the complete viral genome sequence to verify it contains no signs of genetic engineering. The wide array of genetic engineering techniques all leave little pieces of extra or distinctive sequence behind. So we don't need to worry about the man made angle at all. Joseph- I think the difference here is very much a kinetic vs. thermodynamic control issue. The R value being measured for the virus under uncontrolled conditions has not changed much. So the 'thermodynamic' aka herd immunity limit is still the same 60-70% of the population. Every other model has been all about kinetics, which is a lot more sensitive to any number of changing parameters. That doesn't make the models garbage. I mean we could do the same thing in baseball and start with a nice set of predictions on the season, and then start changing the rules of the game as the season went on.

Actually since we are discussing exponential type growth relatively small adjustments in the R factor can translate to pretty big changes in how long everything takes. If I had some really good coding skills I'd whip up come sample charts.

Joseph it is very important to distinguish arm chair calculations floating around, from real calculations done by epidemiologists. As I noted above human behavior changes will necessarily alter the final calculation. But behind that one publish number or estimate are going to be a lot of data and discussion about to handle all of these different questions. If you haven't participated in that kind of scientific process it is hard to quickly convey. Having seen what passes for analysis often times in other fields it is far more rigorous, especially with this level of scrutiny. Or if you prefer a goofy example this would be like jumping out of a plane with a parachute and complaining that all of these projections about what gravity was going to do to me were nonsense.

Just to clarify the vaccine pessimism. A primary reason there is no common cold vaccine is that, the common cold is a dump category of symptoms caused by a bunch of different viruses, the majority of which are not coronaviruses. Second both SARS and MERS were coronaviruses that there has been prior success developing vaccines for. It also lacks the genetic characteristics of the flu, which allow it to change so rapidly we have to develop a new vaccine every year. Betting on a single vaccine candidate to make it all the way through would be silly, but folks have really identified a pretty large number of candidates with different methods already, so there is pretty good reason for optimism.

Chorizo I don't think you understand how big the at risk category is. Normally healthy individuals do seem quite low risk, maybe even at a tolerable risk level. But the underlying conditions category includes both diabetes and asthma, and anybody currently in cancer treatment. Diabetes is 10.5% of the population, asthma is around 8%. 65+ is 13% of the population. Now obviously we can't just the percentages together, but there are a host of other less common conditions that would need to get added in as well. So a rough ball park is 30% of Americans needing to function more or less under stay at home type orders anyway. You seem to dismiss items as projections, when they are calculations. Well validated calculations on the professional level. In some cases they have changed because of new information about the disease. But the end point number of deaths I calculated above is about as rock solid as gravity. What has clearly had a bigger impact on the calculations are actual changes in human behavior. Importantly though they are mostly changes in timing, which as we have seen is important to prevent other spin-off deaths due to lack of appropriate medical care. We've seen plenty of examples in the vaunted private sector of how poorly they are dealing with rapid shifts as well, much of the mitigation is geared to prevent that. Regrettably we've seen entirely preventable shortages like chlorquinine because of promoting of flawed information. Which has meant people who actually are known to benefit are missing out on the drug.

Just to clarify I am talking about low levels of circulation maybe early december in China and other places maybe early January again at fairly low levels probably being mistook for flu at first.

I've seen 2 reports on different genetic approaches to virus tracking that push the circulation worldwide back about a month or so. One had was focused just on New York and I think they had identified a strain that made it to New York late Jan/early Feb. The last flu numbers I had seen for yearly totals did not look unusually high. This years vaccine was generally doing quite well, but there was some oddness in that there were 2 flu strains distinct enough from each other that were circulating, so a person could actually get hit twice.

Sorry to be that guy, but this is a time to make sure we are using the terms correctly. Herd immunity is a condition that exists when enough people have resistance to a disease that it cannot meaningfully spread. Measles outbreaks the last few years help illustrate what it looks like when you start to flirt with that critical percentage, especially when undervaccinated groups congregate socially. Basically you start to see flare-ups, but it dies down quickly. It's best in this case to just refer to people as having acquired immunity to clarify. Certainly it is reasonable to anticipate a fair amount of undercounting, but the death rate spikes would have also shown up sooner if you were to assume too many earlier cases. I don't have the tools for a complete sophisticated analysis, but rough and ready works reasonably well. Last week they had revised the percentages of silent spreaders upwards to 25-50%. I would guess that 50% partially bakes in some of what we are seeing for evidence of earlier transmission already, but even if it doesn't we can apply some generous estimates and see what happens. Let's say that between earlier transmissions and current undercounting we can double the current US total to 900,000 have had the disease with symptoms. We then double again to account for the silent spreaders and get 1.8million. We round up to 2million. Which if you look at my earlier calculations means true herd immunity requires more than 100 times that many infections yet. I don't have enough experience with the equations to give a top notch estimate, but you are going to need a substantial fraction of total herd immunity to have a noticeable impact on the rate of spread.

I'm glad folks caught on that nothing is more baseball than arguing about whether or not hitting .400 in a short season should count. I would also agree that if you can't do real games then you shouldn't do it at all.

A shortened season dramatically increases the chances of someone hitting .400 again too.

MN is only testing hospitalizations, which is clearly depressing the numbers at this point. I think the most exciting news of the week was the pilot study out of China on the plasma therapy. It was of course quite small, but was quite positive and it operates on well understood principles and has a track record for other infectious disease. It helps significantly that most people can recover, so there is a potentially large supply to draw on to serve as a treatment. Unlike the completely murky was in which something like chloroquinine might possibly work. Getting to the point there would be a viable therapy is a huge point in favor of caution. We've all seen how fast it spreads even in the face of some levels of mitigation, so I think without having to be hyper technical most can see how left unchecked it would run it's course quickly and fully. Fully at this point is super easy to calculate. The accepted R factor right now is just under 3. Fully means real herd immunity, the type that you vaccinate your way toward. The percentage of the population you need to achieve herd immunity it 1-1/R. Or in this that means 2/3. So in the US that would be 220 million infected. Our best estimate of the death rate would take into account the highest estimate I've seen of the silent carriers being 50% So then we are talking 88,000 deaths out of about 3 million cases. or 2.9% Being even more generous and assuming there are a bunch of under counted mild cases but not completely silent ones we can drop that down to 2% or 4.4 million in the US people need to die to achieve herd immunity without a vaccine or a valid treatment. That works out to 1 death every 7.2 seconds spread over a calendar year compared to the current death rate of from all causes of 1 every 11 seconds. It is a sobering way to look at things because if you can't find a treatment and/or vaccine numbers like that become inevitable.

I'm actually somewhat optimistic they could pull this off. Coming off a long isolation and presumably falling infection rates I can see an enhanced testing procedure even for support personnel having minimal risk. There is definitely a high cost to the additional testing that would make this impractical for other places as early, but I can see it.

Mixed bag on the News front with a 1 day drop in New York of new cases. Oddly enough I had looked at some research last week that used some high level population genetics (similar to what is used in Ancestry.com tests) in tracking the virus and it indicated that China may not have horribly under reported its initial cases. There were fairly broad ranges on the estimates they were able to generate, but the current total was well within that range. Despite it being solid researchers and a well understood science that's not enough to convince me yet, but given that they seem to be being open with their current struggles to keep cases low as they try and re open. Of course that is probably the biggest downer news for the day that those numbers seem to start popping up as soon as they start to open.

I have no relevant insight into how long for the market, but I did see a prominent Libertarian oriented blogger suggest that he was significantly rethinking the benefits of globalization as the hyper market specialization has left everyone vulnerable to huge disruptions in supply chains. It's undoubtedly influenced by his deep reading of history and understanding that prior plagues have wreaked havoc on many an empire and helped to stimulate significant upheaval.

Not sure how not being able to get scrips filled by a private practice doctor is a point in favor of private healthcare working.

Washington state has a density of 103/ sq mi compared to WI 105, there are some indications that they are getting things under control. Louisiana is somewhat lower at 93.8 for a density. So there is certainly the potential for places to get full on as hot spots with comparable densities. Though it's not really clear what magic number the contrarians are hanging their hats on at the moment. Milwaukee certainly is perfectly dense enough. Undoubtedly NYC can generate more total bodies, but overwhelming healthcare resources can easily happen anywhere. Rural areas might in some ways be more vulnerable since so many of those hospitals have spent years sending the worst patients to nearby cities. Some of the rural counties would be at risk of running out if a single large family got sick at the same time. I looked at the state specific numbers and the MN thing is in fact super weird. It is the only state in the country where the active cases are smaller than the recovered.