Doomwatch, 15 July 2021

There’s lots of doom stalking the earth, but mostly of the “humans are their own worst enemy” variety. There is only one active tropical cyclone – Hurricane Felicia, off the west coast of Mexico and headed out into open water. The invest area in the Atlantic is nothing to worry about, probably just a bored forecaster. There is a more serious threat potentially developing in the West Pacific that some of the models forecast to be a major storm impacting Okinawa in four or five days before heading towards Mainland China. There has been bad flooding in Germany, and in the western US heat and wild fires continue to be a problem. And the usual scattering of earthquakes, including a swarm on the California/Nevada border, and a half dozen or so volcanoes spewing ash, but none causing significant damage. Here’s a map of natural doom:

Hurricanes, Earthquakes, Volcanoes, other severe weather zones (blue/yellow) this morning (15 July)

In the “doing it to ourselves” category the SARS-COV-2 pandemic continues to do a slow burn through the population lacking natural or artificial (vaccinated) antibodies. It’s hard to get a solid handle on just how dangerous some of the new variants are. The majority of infections are now the notorious “Delta” variant (B.1.617.2 – here’s more about variants then you want to know). It does seem to have a much higher transmission rate – the variants making the rounds last year and this spring had an R of around 2, “Delta” is probably well over 3. What that means is that for the original virus, one person would infect on average two other people. “Delta” seems that one infected person can infect between 3 and 4 people. Of course that doesn’t tell you anything about the consequences of being infected – as we know, a lot of people are asymptomatic, others crash. The statistics don’t seem to indicate that conclusively, but the virus seems to be spreading within younger populations. Of course, that can be an artifact of testing bias, and that a lot of older people have had more of an opportunity to be vaccinated (or survived the virus). The research papers I’ve seen are mixed; some indicate that existing antibodies/vaccines aren’t as effective, some say it’s no big deal. The truth is probably both πŸ˜› – there is some reduction, but it’s not increasing mortality.

The media is of course excited about Delta. For Chatham County, Georgia (Savannah Area) a reporter was breathlessly saying the community transmission index “doubled since the end of June!” Technically true, it has gone from 50 to 98 between June 30 and July 14, but let’s put that in perspective: In January it was over 600 … so while the trend isn’t great as “delta” moves into the area with both cases and CTI, this isn’t something to freak out over. If you have natural or artificial antibodies, you’re in good shape. If you don’t and are an adult, you should get vaccinated unless you have a solid health reason that makes it risky. It’s as safe as any other vaccines out there (which are pretty safe all things considered).

There are a lot of unsettling geopolitical developments that do not bode well for the upcoming weeks. The situation in South Africa is out of control. This has huge implications across southern Africa, as some of the logistics and food distribution facilities looted the last few days are essential not just in South Africa but across the region. There is unrest in Cuba – how much is natural, and how much astro-turf from Miami, and where it is going is debatable. Haiti continues to be in turmoil, and the web of involvement in President Moise continues to expand. NATO continues the risky game of “poke the bear”, conducting provocative exercises across the Black Sea at the risk of goading the somewhat unstable Ukrainian regime in to taking another action in Eastern Ukraine that will result in Russia being forced to respond.

But at least Brittany now has her own lawyer now, so that’s nice.

COVID19 excess mortality – reasons for optimism?

For the last few weeks I’ve been watching the COVID-19 excess mortality statistics from NIH/CDC. As I constantly rant, the real time numbers you see on the cable “news” networks are utter rubbish: it takes several weeks for death certificates and reporting to become reliable, and of course just raw daily numbers lack context. So here is the latest reliable data charting excess mortality in the US from all causes since 2016 through late March. Above zero means more than expected; below zero means fewer people died than we would expect. The last data point (well below zero) is likely based on incomplete data, but is probably not drastically wrong. You can clearly see the bad 2017/2018 influenza season as the spike on the left side – and the very obvious and undeniable COVID-19 pandemic on the right (although people do deny it for whatever stupid reasons):

Click to embiggen

So … it is possible that in mid to late March all cause mortality in the US returned to something like statistically normal. I’m using “all cause” because that puts everything in perspective – deaths caused by everything from COVID-19, influenza, traffic accidents, crime, etc. The biggest deviations in this number over the last 20 years or more have been due to Influenza (like the spike in 2017/18), and of course now COVID-19 is the big driver. There are probably a lot of reasons for the big drop in COVID-19 related mortality – first, to be blunt, a lot of the initially vulnerable population has likely succumbed to the virus (many of them probably shouldn’t have, but that’s another rant). Second, the precautions like masking and distancing are helping, third, the vaccination program is likely starting to impact the numbers, and of course we are exiting the winter respiratory virus season.

Even given the case counts over the last couple of weeks (which were trending in the wrong direction) this trend in mortality is likely to be preserved, and the overall mortality in the US to remain in the normal range unless something changes. Have we turned the corner? Maybe … unless the variants are deadlier than expected, people get stupid about precautions too soon, etc. And other parts of the world aren’t doing so well. So don’t start partying yet – but maybe you can smile a little behind your mask …

How dangerous is COVID? How about the COVID Vaccines?

We’re starting to get enough data to draw some conclusions. TLDR: COVID is dangerous – 4.5 times more deadly than the 2017 Influenza strain, which was a bad one. With the caveat that the long term studies are still underway for a lot of at-risk populations, COVID itself is about 215 times more deadly than the vaccine. The COVID vaccine isn’t really significantly more dangerous than the Influenza vaccine. Here’s a bit more detail and context …

You can’t get this vaccine for some reason.

There is a lot of argument and discussion over the relative risk of COVID vaccines, especially in Europe with the reports of the AstraZeneca/Oxford vaccine potentially causing blood clots in some people, and the Polyethylene Glycol (PEG) in the mRNA vaccines causing anaphylaxis (allergic reactions) here in the US. Both are concerning – and there is an urgent need to figure out why certain people are more vulnerable to adverse reactions than others. Certainly those with known allergies should be very careful to check the components of each vaccine before receiving it – the CDC publishes guidelines for this, and if you have sensitivities check with your Doctor before getting a shot (or any) procedure. This is the dilemma of vaccination: it’s best for the vast majority of people, but can be dangerous for a few. But care must be taken not to blow that true statement out of proportion.

What are the overall risks – in context with other risks? Lets take a closer look at the data from the FDA’s Adverse Event Reporting System as well as the CDC’s National Center for Health Statistics data bases and a few other data bases at CDC, NHTSA, and the FBI for context. Here is what your chances of dying this year look like:

  • Chances of dying from COVID: 1 in 163
  • Chances of dying from COVID Vaccine: 1 in 35,000
  • Chances of dying from Influenza (2017 H5N1 strain): 1 in 740
  • Chances of dying from Influenza Vaccine: 1 in 100,000
  • Chances of dying in any Accident: 1 in 1,350
  • Chances of dying from Gun Violence (you are a criminal): 1 in 3,000
  • Chances of dying from Gun Violence (you are not a criminal):1 in 220,000
  • Chances of dying from a Weather or Earthquake Hazard: 1 in 2 million or so

So in context, the vaccines are not risky compared to the disease – and certainly not compared to dying in a car accident (1 in 6000 or so). There has been some reports and talk that the COVID vaccines are significantly more dangerous than the Influenza vaccines. That’s a bit hard to judge. For one thing, the COVID vaccines are being scrutinized in a way the Influenza shots have not been. But even given that, the raw numbers show that the potentially associated mortality rate is about 2.8 times higher. It’s likely that difference would disappear if similar tracking were in place, but even if true isn’t bad. So the “50 times more side effects” stuff you see circulating is overblown.

Hope that helps put things in perspective …

Binary Thinking

In reading “news” stories lately, not to mention various comments in social media about topics ranging from politics to COVID vaccines, I was struck again by the power of binary thinking, as well as how perceptions are manipulated by asking (and answering) the wrong question. Another frequent related problem is making assertions that are perhaps true, but presented out of context in such a way as to create a false perception. This usually results in the two “sides” talking past one another and a shouting match ensues; there is no shared worldview to even begin a discussion.

Here’s a concrete example regarding vaccines: In skimming a discussion about mRNA vaccines it was said by one advocate that there is no evidence or “mechanism” they cause birth defects. The problem is, that’s “true” as far as it goes but also misleading. Pregnancy was a specifically excluded condition during the trails reported so far, and all of the documentation submitted to the FDA said it was not assessed. As for mechanism, there are in fact several potential mechanisms where something could go wrong, given the rapid and complex cell division that occurs during the early stages. Is it rare? Possible or impossible? Probable? Likely? We just don’t know – there is no evidence. Last time I looked at least 18 people had become pregnant during the trials and are being closely monitored, but that’s a very small sample size, and until the children are several years old, it can’t be said for sure that there were not problems. It was also said no long term side effects have been reported. That is true but highly misleading: the vaccines were only developed less than a year ago, so there hasn’t been enough time for any long term effects to develop or reach a statistical threshold. So therein lies the problem – saying “there is no evidence” when there have been very limited (or no) studies is absolutely not the same thing as saying “there have been detailed studies an no problem was found.” That’s a distinction that is lost on many people.

For the record on this subject, here is what CDC says as of 7 January 2021: Based on how mRNA vaccines work, experts believe they are unlikely to pose a specific risk for people who are pregnant. However, the actual risks of mRNA vaccines to the pregnant person and her fetus are unknown because these vaccines have not been studied in pregnant women. We know COVID19 presents risks to pregnant women, so if in a high risk group (like a health care provider) it might make sense to be vaccinated with an mRNA vaccine despite the unknowns. Work from home and sensible about social distancing, etc? Maybe best to wait. It’s not an easy call, based on an objective view of the available data.

Again, this isn’t to be anti-vaccine. There are rational risk-benefit arguments for some, and over time as more data is collected and if the early results hold up, increasingly large segments of the population to take these vaccines. What bothers me is that people present it as a binary, “no brainier” choice. It’s just not that straightforward and it is hubris to assert that it is.

Unfortunately there is no shortage of hubris, exaggeration, and binary thinking in order to sway opinions in our public dialogue these days. I could cite many examples, from election fraud (it probably didn’t impact the results, but that’s not the point: the US election system is broken, with deep structural flaws such that it doesn’t meet standards it imposes on other countries), to social debates like LGBTQ issues or abortion or climate change or …

In short, it takes objectivity and careful analysis to reach good conclusions. This is especially hard given the political parties benefit from a sharply divided electorate, advocates for various issues minimize or are even blind to potentially adverse consequences, and demand you “take a stand”, and of course the media industry profits from the noise and drama all that creates. Please don’t feed that process, and try to understand that many situations are not sound-byte simple.

In short, life is complex. Don’t fall into the trap of absolutes.

Not a big Star Wars fan, but it has its moments.

COVID19 Mortality: A look back

TLDR: The 27 March 2020 forecast all population symptomatic case fatality rate based on the Diamond Princess cruse ship data was 1.71%. The current (20 January 2021) US symptomatic case fatality rate is 1.67%. So while the public perceptions and actions have been shifting, the bottom line hasn’t changed that much, and while there was a lot of uncertainty back then, the early work wasn’t bad. Here’s some more background, including a rant about people who think people aren’t dying from this, and a look back at the mortality forecasts made early last year.

Our first solid look at COVID19 in a controlled environment was the cruse ship “Diamond Princess”. Almost exactly one year ago, on January 20, 2020, the ship departed Yokohama on a three hour tour, um, on a round trip tour of Southeast Asia timed to coincide with the Lunar New Year celebrations. A single passenger from China brought with him a hitchhiker: the SARS-COV-2 virus. Over the ensuing weeks (which included some dumb measures by the Japanese Government that made things worse), something like over a third of the passengers and crew are thought to have contracted the virus. Around 400 of the passengers and crew became sick enough to be classified as symptomatic, nearly 200 of those were hospitalized, and about 10 or 12 had a primary cause of death being from the disease which is now called COVID19.

So where do things stand? I again rant that real time death counters seen on “news” outlets are disgusting displays of much that is wrong with American “Journalism.” Let’s look at the National Center for Health Statistics data, which is probably the most authoritative/reliable source. These statistics are updated weekly; those of you with wonky tendencies may want to read the technical notes, but the bottom line is that mortality statistics take time to compile in the US. Nationally, only 60% of death records are submitted to NCHS within 10 DAYS of death! Lets ltake a look at the week of December 26th. As of the 14th of January (two weeks after), the number of reported deaths were 41,796. As of yesterday that number is up to 72,710 … now, that’s a worse than usual example due to the holidays, but it shows the dangers of relying on the “real time” data. The Johns Hopkins data sets that many in the media are using are quite good, but they are not definitive, and the sensationalist abuse of this data is not helping. Again, pandemics are “slow motion” disasters. They rarely evolve from hour to hour or day to day, it’s more of a week to week process, with the decisions of millions of individuals influencing the course of the outbreak. The hype is stressful, distracting, and given the politics, divisive, as it encourages people who think they are being railroaded to believe there isn’t a problem.

But there is. I’ve posted similar graphics before, but here it is again, updated through yesterday. The blue line is shows total reported deaths. The orange line is expected deaths based on the US population at the time. The yellow line is “non-COVID related deaths” as classified by the ICD–10 codes. The “expected” line is wavy because more people die in winter than summer – usually due to Influenza and Pneumonia. You can very clearly see that the 2017-18 influenza season was bad, and that 2018-19 was mild. The 2019-2020 season was pretty normal – until in early February something drastic happened. That “something” was the SARS-COV-2 virus. Even if the only data you had was the blue line – reported deaths – you’d know that there was a new disease stalking the land. Look carefully at the orange line – non-COVID deaths – and how high it is during the summer. Contrary to what some with an ax to grind are saying, it seems that we were more than likely under-counting COVID deaths rather than over counting them, although it is possible that some people died who would not have otherwise because they did not seek medical care out of fear, or some other indirectly related causes. In any event, reported deaths are obviously well above normal, there is obviously some new disease running through the population, and anyone who is saying otherwise is simply wrong.

Click to embiggen …

Looking back at the early mortality forecasts, my own forecasts were off by a factor of two – the estimates from late March/Early April were on the order of 200,000 by now, but reported US fatalities recently topped 400,000. I had assumed average people would demonstrate more common sense than they did (yeah, you can rarely go wrong assuming people are idiots but despite being on doomwatch I try to be optimistic πŸ˜› ). I also thought the initial reaction would be stronger nationally, and widespread masking start earlier, than how it played out. I never really thought the vaccines would be ready by now – and I’m still rather pessimistic it will have the impacts the vaccine chorus is singing. First, this is a corona virus: other beasties of this type are responsible for about 20-30% common cold cases, and they mutate so rapidly the immune system can’t keep up; it’s unrealistic to expect vaccines to keep up, although it’s also wrong to discount them, as like with influenza vaccines, they can provide some protection even against unrelated strains. Second, despite the PR deluge, the efficacy hasn’t really been statistically demonstrated to the usual standards, and the quality control and massive rollout have created problems that have harmed the process. Cheerleading and glossing over things like adverse reaction rates isn’t really great way to build confidence. As I have said, I am absolutely in favor of vaccines – but I’m also in favor of a careful, “first do no harm” approach to public policy that a rushed “do something NOW” process rarely allows. Appearances do matter, but the data matters more.

When I teach emergency management, the very first thing I try to get decision makers to understand is that no matter what they do, they are going to kill people. There is almost never such a thing as “erring on the side of caution” because all actions have consequences – and as I often point out, economic harm also causes physical harm, a fact that is often overlooked. Ultimately the trick is to figure out policies that will cause the least harm in the long run.

As the COVID19 pandemic shows, that’s a very difficult thing to do.

The Vaccine question

My guess is every engineering student since the mid 1940’s has had to watch the video of the Tacoma Narrows Bridge collapse. Other professions have similar cautionary tales of hubris, short cuts, innocent mistakes, misunderstanding of nature, and things that went terribly wrong. They are often clear in hindsight, but lost in the immediate noise and pressure of crisis decision making. Often progress requires risk – but the two require a rational balance. Now that a number of potential vaccines are approaching approval and distribution, everyone from government officials to individuals are soon facing difficult decisions: who gets what vaccine, when or if to take it, and what level of persuasion (or even coercion) should be used to get people to take them. Yes, these are difficult decisions, and to be blunt anyone who says it’s a “no brainer,” simple, or obvious is either fostering an agenda, being disingenuous, or doesn’t know what they are talking about. These questions are even more difficult because several of the potential vaccines on the verge of distribution are using technologies that have never seen wide spread distribution and use. Compounding that are issues of politics, National pride, and commercialism. The details are complex, and most of the simplified explanations I’ve seen (and more than a few technical ones as well) are biased either towards “trust us; don’t worry” or “it could be a beaker full of death.”

The answers to all of life’s questions may be found in Star Trek (the original, not the later crap).

As with most issues, the truth lies well within the extremes, but the the decisions are ultimately fairly straightforward. We have to weigh the consequences of COVID19 (to society and the economy as well as physical health) against the effectiveness and risks (known and unknown) of the various vaccines. Given the complexity, both advocates and detractors (some quite vocal) among the general public really don’t fully understand how any of the vaccines work or their implications. For the vaccines under development, there are four broad classes (link goes to Nature article with good graphics). The major vaccines that have been approved or are closest to certification are in three classes: killed virus (the Chinese Sinovac), viral vector, such as those based on the Human adenovirus (like the Gamaleya vaccine) or Chimpanzee adenovirus (AstraZeneca/Oxford); and those based on nucleic acid – the mRNA vaccines (Pfizer, Moderna). The killed virus approach is how most current vaccines work. The viral vector vaccines are fairly recent, but there are a few that have been approved and in use for over a decade. The mRNA vaccines are substantively different. And it is here we have a bit of a problem.

mRNA vaccines and related technology have only seen small scale experimental use, usually in the context of cancer or other deadly diseases, and have never before been certified. In theory they should be safe, perhaps even safer than traditional approaches, but there are some potential risks and more than a few unknowns. At least some viral vector based technology has been around for 17 years and Gameleya, for instance, has a number of vaccines (including an Ebola vaccine) that have been approved and in use for years. For those vaccines there have also been long term studies as to adverse reactions. So while the actual vaccine for SARS-COV-2 is new (since, obviously, the virus is new), the vaccine methodology itself isn’t – in fact, one was in development after the SARS-COV-1 scare back in 2008. For the mRNA vaccines there have been no long term trials or monitoring, and no previous vaccines approved for human use based on these technologies. Another factor is that the various studies are not using consistent criteria and methodologies. This is a distinction lost on many in the media, such as the NY Times article last Sunday discussing the commencement of distribution in China (Sinovac), Russia (Gamaleya’s SputnikV), versus Great Britain (the Pfizer vax). The FDA briefing materials for the Thursday Pfizer approval meeting also glosses over this issue, but is clear there are a lot of unknowns.

With all of the vaccines, there are unknowns, and always some side effects. How effective is it in the real world? And by “effective”, be very careful how that is defined – some of the criteria in the current Phase III studies seem like pretty low bars compared to past studies. Do they minimize transmission, protect the person inoculated from getting sick, minimize (but not prevent) symptoms? How long does immunity last – and how do the inevitable mutations impact effectiveness? But the ultimate question is do the advantages in reducing the consequences of COVID outweigh the potential side effects of the vaccine – especially given the need for mass inoculations of 80%+ of the population? There is little doubt that the benefit/cost radio of vaccination will be in favor of vaccination if – and it’s still a big IF – they work as the early results indicate, and adverse reaction rates are similar to other vaccines. But can we assume that? Most advocates are. With the mRNA vaccines there are additional unknowns as to the long term impact of the underlying delivery methodology. Again, in theory it should be as safe, and perhaps even safer than more traditional approaches using a live, killed approaches. But we just don’t know. While the short-term impacts seem low based on the early trials, they are just that: short term, relatively small scale studies (weeks to months, thousands of people). No one knows what, if any, the long term consequences of this kind of vaccine as a whole might be when applied to the general population over time. It’s never been done before. There is no reason at the moment to suspect there is some hidden gotcha – but the designer of the Tacoma Narrows Bridge didn’t think it would rip itself apart either.

Opinion and Conclusion: As I have said before, COVID-19 falls in a gray area. If it were causing wide scale deaths across a wide range of groups, and mRNA vaccines were the only viable option, then maybe we would need to “roll the bones” with a new technology. And yet, COVID is bad. But for all the disruption and pain COVID has caused, it’s not smallpox or the black death, much less the FGC-347601 virus Dr. McCoy had to deal with (and recall in that tale, the disease itself was actually an unforeseen side effect of a noble original objective).

Make no mistake: mRNA therapies have the potential to be a major innovation in the treatment of all kinds of diseases from cancer to COVID. But while pressure often leads to rapid advances, we’ve also seen far too often in the history of technical advances that the temporal or economic pressure to do something now leads to catastrophe. Tacoma Narrows. Challenger. Mars Climate Orbiter. The pharmaceutical industry isn’t immune either: Thalidomide, or more recently Vioxx. Darvocet. That said, don’t fall into the anti-vaxxer trap of seeing every adverse reaction as evidence of a conspiracy. It’s painful to say it but a certain adverse reaction rate is acceptable in light of the impacts of the pandemic. And, yes, Big Pharma sees this as a huge money making opportunity, and that requires monitoring and regulation. But Pharma have done a lot of good work, and in the present system, being profitable is how things get done.

When you weigh all the factors, in my opinion it is simply too soon for the wide scale application of some of these vaccines in relation to the risk from COVID (again, not to minimize that risk). Much of the harm of this virus has been self inflicted – a coherent global response would have cut the economic impact five fold, and the death toll by a third in my estimation. If everyone would just behave responsibly, between mitigation and other measures we would have some time to sort this out. Let’s take a deep breath, proceed cautiously, roll out the various vaccines in a reasonable way and not get hung up on national pride (noting some vendors in China have an unfortunate reputation), or commercialism, while moving expeditiously to apply new technologies in parallel as they are validated. The rollout of the new, untested vaccines can and should be spaced over several years. Supply chain issues may force that in practice anyway, but that should have been the plan from the start. And foreign developed vaccines – properly vetted for safety, without nationalistic biases – should be allowed in as part of the mix. The Gamaleya vaccine is likely a prime example. But even the vaccines based on established methodologies need more testing.

I think it is reckless to push the wide spread distribution of novel vaccines on tens of millions of people until there is a longer safety and performance baseline. As noted above we have absolutely no idea what the medium term (2-3 years), much less long term (5-10 years) implications are with respect to adverse outcomes for some of these approaches. It is especially reckless where there are several candidate vaccines with more well understood risks. Maybe the mRNA based vaccines are fantastic, but not only do we not know, we don’t even have the data to know and won’t for several years. To coerce hundreds of millions of people to take these vaccines in an experiment of this magnitude is simply unethical. Should ever increasing numbers try it? Of course – with an appreciation of the risks, under careful supervision and long term monitoring. Those at highest risk? Absolutely – although I’d be careful with otherwise healthy members of the health care community upon which we depend. Tens or hundreds of Millions? It’s just too soon.

Don’t mistake this post as “anti-vax“. It isn’t. I got a flu shot back in September. I get other vaccinations and boosters as needed for travel, etc. For what it’s worth, I’ll try to get one of the vaccines based on established methodologies when available, or, as a number of biomedical researchers have said – usually privately but in this link one does publicly – wait a couple of years until there is a longer term baseline regarding both effectiveness and adverse reactions. The bottom line is that in every medical decision, you have to weigh the pros and cons. Primum non nocere – first, do no harm. Are we doing that by rushing out the novel COVID vaccines for mass vaccination? Needless to say, I’m concerned.

Addendum: I’m not a physician, but I do understand a lot of the issues surrounding this at a fairly detailed level More importantly, I am pretty knowledgeable (some would say expert) in emergency management decision making and how things go wrong in complex scientific and technical processes. To be absolutely clear, I’m not advising anyone not to get one of the new vaccines. I think a lot of people probably should get them. At the moment there is no reason to suspect there is anything wrong with them. In fact many if not most of the fears of the mRNA vaccines are way overblown. But that doesn’t mean it isn’t rational to have some concerns, and saying “we don’t have any reason to suspect there is anything wrong” is VERY VERY DIFFERENT from saying “here is a 5 year followup study that shows nothing is wrong”. Read the actual FDA briefing materials to see how often the word unknown is used. There are lots of competing blog posts and opinionating on all of this, and much of it lacks nuance. Don’t be stampeded into one position or another out of fear. Fear is the mind killer …

Pandemic Update: things still going great (for the virus …)

With the late season storms both here and in the West Pacific, and the developing catastrophe in Nicaragua/Honduras, haven’t formally checked in to see how the virus is doing until today … Yep, the virus is doing fine. Humans? Not so much. True, it’s not a Monty Python style dystopian “bring out your dead” kind of pandemic, but a lot of people are still passing away from this thing who would not have otherwise died. How do we know this? Forget the death counters popular on TV. As I have discussed before, the absolute numbers aren’t nearly as important as the concept of excess mortality – how many people are we losing who wouldn’t have died otherwise? For some more background on that take a look at this post. For those paying attention let’s jump right to the numbers. Here is the overall US chart for deviations in mortality over the last four years, as of the last week of October. Above average is above normal, below zero is below average. No, the numbers aren’t any more recent than the end of October. I’m so tired of ranting about the craptacular public health data reporting system in this stupid country, a system that is even worse than the stupid election system that can’t manage to count live ballots any better than it can dead bodies – the gallows humor there writes itself these days.

Click to embiggen this utterly depressing graphic.

So it’s absolutely, unambiguously clear: something is killing ‘Muricans this year at greater numbers than past years, and it’s pretty clear it’s the SARS-COV-2 virus that causes COVID-19. And it’s not “just the flu”. “Just a bad flu” is what that spike in late 2017/early 2018 is. No, it’s not “Spanish Flu” bad, much less the Black Death, but it’s bad enough. Even correcting for the mild 2019 influenza season, (which is partly responsible for the early spike in COVID deaths – vulnerable people who would have died in 2019 lived into 2020 to fall victim to COVID instead), COVID has really distorted the mortality statistics.

What about the State of Georgia? Here’s that graph. Note with ha smaller sample size, it is “noisier”, but clearly the same story …

Yet another depressing graphic.

Before anybody says “oh, it’s getting better!” Remember these numbers are a couple of weeks old, and the lag between infection and death is around 4 weeks, so this is maybe 6 weeks behind the curve. The last few entries are certainly low as it can take four weeks or so to collect all the mortality data (insert primal scream here).

This graph looks like the normal cycling of a mostly out of control virus, where people notice it’s bad, react, it drops some, then they get complacent, and it rebounds, as well as the fact that we are seeing the virus move in to different populations in different areas. The other problem is that we are entering the normal respiratory virus season, and, flawed as they are, the other metrics – case counts, hospitalizations, positivity rates, and so forth – are all trending upwards. So it’s likely these numbers are about to trend higher.

Again, the problem with SARS-COV-2/COVID19 is that it’s bad – but not bad enough. It slots nicely into a place that scares some people in to overreacting, and others into under reacting, exacerbating existing fault lines in society depending on where you fall on the security/freedom and personal/collective responsibility prioritization scales.

So what do we do? Mostly it’s common sense. But that is in remarkably short supply. The problem is a critical mass of the population across the country (and even world)has to act responsibly. Otherwise the slow burn – punctuated with flare ups – will continue. And with flare-ups politicians will feel forced to “do something” dramatic, most likely things like shutdowns and restrictions which won’t work in the long run, but will further the social and political divisions, not to mention the incredibly fragile economic situation. An interesting question arises: If the mortality rate settles in to a new, higher value, say 20-30% above the previous average, will people ultimately just accept that and get on with life? It’s going to be interesting to watch the media coverage with respect to the statistics as the likely change in administration progresses. Will things actually be better next year, or will they just seem better with an (on the surface anyway) more coherent approach and a vaccine? When will the media give up on coverage and move on to other stories? Hard to say. Those are all issues just as important – maybe more so – as the biology and epidemiology of the virus itself.

I’m also very afraid that the vaccine won’t be the deus ex machina that people are hoping it will be. For starters, the 90%+ effectiveness reports are unlikely to be seen in widespread use. Those number always come down once things move in to general use, so there’s an expectations problem building. There’s also a fair enough chance one or more of several potentially unfavorable scenarios will come to pass – not the least of which will be that in the rush to get vaccines out, long term adverse reactions will start to crop up in six months or a year once widespread vaccination takes off. The other is potential risk is that immunity will decline rapidly and be seasonal at best. Great for the bottom line of Big Pharma, probably not so good for the rest of us.

Sense some frustration here? Yep. COVID19 long ago stopped being a mostly scientific problem, and after the behavior of both political parties in the US the last few years, only a hard core political activist affiliated with one of the tribes can be optimistic (aka delusional) about all this. Those of us in the real world will just have to continue to suffer through their shenanigans and try to keep out of the way …

So how’s the COVID pandemic going? Pretty good, if you are the SARS-COV-2 virus …

As I frequently rant, various phenomena have their own pace, or temporal domain. With hurricanes, it’s about 12 to 24 hours. With a pandemic, it depends on the disease, but for COVID19 it’s about two weeks. You can’t force that into some other paradigm like a 24 hour news cycle, or political campaign, or whatever. It just doesn’t work, and leads to stress, confusion, and bad decisions. I’d add that each phenomena also has a natural spatial domain or geographic region that makes sense to analyze. Those geographies don’t usually match our arbitrary political geographies. For example, what sense does it make to have a hurricane warning that extends to the Savannah River, “forcing” the evacuation of Hilton Head, when you can stand on the north end of Tybee under only a tropical storm warning, with no evacuation in force, and look across the river/sound and wave at the folks fleeing in terror. OK, a little exaggeration, but not much sometimes. With the pandemic, given different approaches (masks vs not), people moving back and forth (Effingham being a “bedroom” community of Chatham as a local Savannah GA example), not to mention the inconsistencies in reporting, it’s hard to define a spatial domain that works. The point, in scientific terms, is that the temporal and spatial characteristics of some phenomena doesn’t always fit with our arbitrary temporal and spatial definitions. That leads to a lot of noise that – you guessed it – people with agendas can exploit to say “things are great!” or “things are terrible!” and, based on the data, they are both somewhat right and somewhat wrong.

But for those of us who care about reality, how are things? Well, the virus is doing fine. Which isn’t good news for us who are foodbags for the thing. I’ve basically given up on a lot of the statistics based on case counts and positive results. It’s just too noisy. The main thing I’m watching closely right now is the excess mortality numbers, and how that compares with both reported COVID mortality and the expected mortality. In other words, how many more people are dying than the longer term statistics suggest should be the case? Now, that doesn’t tell us that COVID is responsible for all of those deaths, it does tell us if something unusual is going on, and from other evidence it is clear COVID is in fact responsible for most of them (a fact that some folks just can’t seem to get a handle on).

Here I’m using the from the National Vital Statistics System. Death reports are subject to delays, so for example today the “latest” data is only as of the end of September, since it takes around ten working days for reports to filter up to CDC – longer for some jurisdictions (yeah, unbelievable, but there it is). Despite all the flaws, this is probably giving us the most complete overall picture of the impact of the virus. So the “temporal” domain for our analysis is going to be number of reported deaths per calendar week. That helps reduce errors caused by weekends, Mondays, and Fridays, as well as just normal day-to-day fluctuations. For the spatial domain, lets look at the whole US, and some selected states. Even that is a bit risky due to reporting differences, etc. but we can see some interesting things at the state level. So here is a plot of the ratio of the number of reported deaths divided by the expected (based on the previous 10 years) number of deaths, per week for the 39 weeks of 2020 thus far.

Excess Mortality Ratio for 2020

So clearly, NYC had a Very Bad Spring with a lot of people dying who shouldn’t have. You can try to argue “well, it was older people, or in nursing homes, or people already sick” or some such excuses but the simple fact is that it wasn’t their time. Something (and we know it was COVID) was killing people over and above the usual causes of death. As you look at other states you can see different progressions – a mostly under control slow burn in Washington State, later peaks such as in the South East (GA/FL) and Arizona, etc. For the US as a whole, it’s the bigger population states driving things, but there was clearly the NY (and NJ) crash in the spring followed by a slow burn and second much smaller peak in mid summer. Lower population and rural states are starting to catch up a bit in the stats, but as you can see with a state like South Dakota it’s noisier.

What does it mean, and what does it indicate for the future? The virus continues to do a series of waves through different parts of the country. Now that fall/winter are here, we can expect another “wave” in the higher populated states since a) most people were not exposed to the first wave and b) compliance with mitigation measures is variable. Since states aren’t in isolation, and any “reservoir” of the virus will enable it to get back in to areas with it under control, that seems inevitable. One thing is that a lot of those vulnerable in, say, NYC were taken out by the first wave. However, people age, get sick with chronic diseases, etc., so there are now all new victims waiting to be infected. I suspect we will see “waves” of deaths rippling through the next year – probably no big spikes like the original NEUS spike, but lots of “slow burns” and increases in the rate between 10 and 30 percent above the normal mortality rate in most jurisdictions.

So what do you do? Same as it ever was – mask when encountering someone outside your household in an indoor environment for sure, or outside with prolonged contact; hand hygiene. Get a flu shot if it’s ok for you to do so – for one thing, we really want to not have any more confusion between flu and COVID than necessary, and it may give your immune system a little boost that might help. Try to take care of yourself and stay healthy. Because I doubt there is going to be a miracle vaccine for this thing, and it will just be a fact of life for the foreseeable future …

The President, the Virus, and the limits of Testing

I would hope everyone is praying for a swift recovery of the President. If there is one thing this country doesn’t need right now it’s more uncertainty and disruption thrown into the Election. As for commenting on the situation, I think it illustrates some vital points to understand about the virus that causes COVID19 and how our society needs to try to react to it. Of course, everything is a mine field given how emotional and split everyone is over politics. So I’m going to try to discuss in a somewhat neutral way a vital issue: the limits of testing. That does mean pointing out how the White House made a mistake about testing. Please don’t try to read between the lines on this with respect to my politics – there is no agenda here. Of course I have an opinion, and I think I’ve decided which one I’m going to vote against, but I’m not happy about it, and to be clear I don’t support either side.

I’ve ranted a lot about the problems with testing here in the US, and what is happening in the White House seems to be a classic case of the misapplication of a technique designed for one thing and using it for something else. The first thing you need to understand is how COVID acts in a person. The New York Times has a surprisingly good article on the progression of the disease today. I think their COVID coverage is still free. They have a lot of simple graphics that do a nice job of (literally) charting the disease; the key graphic is this, with the danger zone of 2-3 days marked:

From the New York Times: progression of COVID19. https://www.nytimes.com/interactive/2020/10/02/science/charting-a-coronavirus-infection.html

The problem is that the kind of test used by the White House to test visitors, the Abbott ID Now system, is designed to determine if someone who has symptoms has COVID19 or something else. The advantage of this (vs. the more sensitive PCR test) is speed: you get an answer in 15 minutes vs. overnight at best. But … if you look at the graph, the time of peak viral load (the therefore infectiousness) is generally before the onset of symptoms. Worse, at that stage (between the first pink vertical line and the when the green “symptoms” line starts), the test has a 30% miss rate. So someone could have the virus – and be spreading it – and the Abbott test will miss it about 1 in 3 times. Let’s say you have 200 people in the inner circle. If it’s like the rest of the population in areas of community spread were in the 10-20% exposure range. Taking the low number, that’s 20 people. With a one in three miss rate on the daily tests, and the period of infectious but not symptomatic, you would statistically over a period of a couple months have three to five people wandering around for at least a day spreading the virus. That’s why other measures – masks, hygiene – are essential even with routine testing and temperature checks. No one measure is a silver bullet – but like layers of Kevlar in a bullet proof jacket, taken together they can beat this thing.

I suspect what happened is that the White House didn’t fully appreciate this. They were testing everyone on the staff, felt comfortable with that, and it probably wasn’t clear that this system wasn’t designed as a wide scale preventative measure. It was designed to test people who were already sick. Whose fault was that? Did the manufacturer oversell the product? Did that technical detail get lost in the rush to put something in place? Did they just ignore advice and engage in wishful thinking? All of the above (I’d put my bet here)? To be clear, this mistake isn’t limited to the White House – I know of at least one medical facility that has been doing the same thing (treating the rapid test as exclusionary rather than confirmatory), so they aren’t alone. The bottom line is that it was statistically pretty much inevitable that there was going to be an outbreak within the White House.

It is absolutely vital to realize that in the short to medium term there is no single solution for dealing with this virus. Testing is useful – but has limits. A vaccine will be useful – but will likely have significant limits. Masks are useful – but have limits. Shutdowns at one time could have been useful – but (IMNSHO) are no longer given the cost/benefits. Social Distancing is useful but has limits. Hygiene is always a good idea. Immunity may or may not be a thing. It is utterly insane that the US political system has decided that some of these are “Democrat” solutions, and some are “Republican” solutions.

Doomwatch, Tuesday 29 Sept 2020

Numerous potential flashpoints of doom out there … but nothing as of this morning above the “that might get bad soon.”

Tropics: Typhoon Kujira is off of Japan, no threat to land. Tropical Depression 18-E is off the coast of Mexico, again no threat to land. Closer to home (well, mine πŸ™‚ ) a system is moving across the Caribbean that the global models are showing spinning up in a few days as it approaches the Yucatan Peninsula. NHC gives this a 50% chance of forming something in the next five days. Some of the usual suspects are already flogging the potential for the system to spin up. Here is what the GFS model is showing for next Wednesday, a sort of organized depression/minimal storm approaching the Mexican coast, and a second thing trying to spin up behind it …

DOOOOM! Or not. Probably not. But it might, so give me clicks! Or just relax and check back Friday.

but … models don’t always do so great in this kind of situation. They are getting better, but 7-10 days just isn’t there yet for anything other than entertainment purposes. A couple of things to keep in mind – note there is no “X” on the NHC map, just a diffuse area where something might form. Second, no discrete model runs or INVEST area ID has been assigned yet. The Tropical Weather Outlook doesn’t have the majik words “interests in <name of some area> should monitor the progress of this system.” So unless you are a die hard weather junkie, you’ve got plenty of other stuff to worry about!

Like the debate tonight between the raging dumpster fire and the older well worn house that looks comforting from the outside but has bats in the attic, rats in the cellar, and an ax murderer living in the spare bedroom.

Or the continuing slow burn of the COVID-19 Pandemic. I posted on this yesterday, and nothing I’ve seen in the last month or so says there is any progress – or significant new threats. As I write this the talking head on the radio news said “we have hit 1 million deaths, one fifth of those in the US.” Which is total bullcrap for reasons I’ve discussed before (globally there is a huge undercount; the US is about 5% of global population and if you take in to account the horrible reporting in most of the world, is about 5% of deaths, not 20%). Guess he doesn’t read this blog. Sigh.

The economy continues to send up flares, red flags, warning lights, and Edvard Munch style screams. But Congress is deadlocked over the aforementioned election thingee, there is no coordinated plan to try to stabilize things, so the ongoing collapse of key aspects of the economy like small businesses continues. The wave of potential defaults is on the verge of becoming a tsunami, and when that hits the over-leveraged capital markets, Bad Things Will Happen.

In the geopolitical world, Donbass, Nagorno-Karabakh, Syria, Greece-Turkey, and Libya all continue to smolder. The situation in Nagorno-Karabakh is especially dangerous and tragic, given the involvement of Turkey in another potential attack on Armenians (which has a long and tragic history). It is one of many complex “frozen” conflict areas like Ukraine and the Balkans that were suppressed during Soviet times, but have flared up since. Why does this matter to you? The various tangle of alliances and obligations can rapidly drag outsiders in. Oh, did I mention oil? Because oil is involved as well … of course.

Oh, and Tampa Bay winning the Stanley Cup? Which sign of the apocalypse is that?

So we wait and see what happens. There’s always stuff to worry about, and it is best to be proactive when we can. But if you have a family emergency plan (always keep a week of emergency food, containers you can fill with water on short notice, and a contact plan), a weather radio, and are taking COVID precautions (masks when going to enclosed spaces, distance, good hand hygiene), you’ve got most of the bases covered, so enjoy life and don’t worry about all the might be’s until they become “probably”s …