Spirit, Speak Comfort To Me!

OK, before someone gets upset I’m not taking the current crisis seriously, don’t misunderstand: this is a serious situation. But there is no cause to lose our sense of humor or be grim. Yes, we must take action, but no, it’s not the end of the world (unless you’re a nurse or doctor, then it might feel like it for a couple of weeks).  I’ll crunch the numbers downthread and it’s not as bad as you might think if you keep perspective.  But do not doubt the sad fact that the US health care system can’t really keep up with a normal flu season; there is no way it can handle a rapid influx of respiratory patients. That is why COVID19 is so dangerous, and why everyone needs to take it seriously, following the CDC guidelines, limit interactions outside your immediate household (aka social distancing), keep strict hygiene protocols, and otherwise doing everything you can to try to slow down the rate of spread. It’s more than likely not about you. It’s about that 1% of so of the population who will get very sick, and may not get enough care because the system will be overloaded.

Here’s the latest analysis.  First, please, please, please, stop obsessing on every blip in the numbers!  They are not “skyrocketing” or whatever inflammatory phrase the media is using at the moment. Second, the absolute numbers don’t matter.  Yes, each and every one is a life, and a tragedy.  But what matters in terms of risk is the denominator: how many people are getting sick and passing away in terms of what size group?  Losing 100 people in Chatham County (pop about 290,000) is very different from losing 100 people in New York City (pop 8.6 million).  Don’t compare them.  It’s mortality per unit population that matters – and how fast that mortality happens.  Please stop feeding the beast by quoting and hyping how many deaths per day without context.  It’s not helpful, and causing people far more stress than is appropriate.

Time for some math: deaths from the virus are progressing along what is known as a logistic function.  This type of function was originally developed for use in population growth, but has found it’s way in to many other fields.  In biology, this is sometimes called a carrying capacity curve.  We are entering the scary part of that curve.  Here’s what the curve looks like with data for several areas as of 24 March 2020.  The black line is a theoretical curve that represents an estimate of how things might progress.  The grey line is for comparison, the 2017 H3N2 flu progression speeded up by a factor of 5.  The dots represent actual data as of the totals for yesterday as reported this morning.  Click to embiggen …


Of these, China (grey +) and Iran (blue o)  look weird.  I suspect those numbers are “munged.”  But Spain (red dots) and Italy (green dots), which are the farthest along of societies that might resemble the US, seem ok.  (South Korea is even further down the curve, but they took very early intervention, and have more hospital surge capacity than the US, so may not be a good analog).  New York is the cyan triangles that are hard to see because  it’s just starting to creep along the curve – about day 25 or so.  The next 20 days will be very scary – you can see that is the steepest part of the curve, and people will talk about doubling times, and extrapolation the daily rates far beyond the point where they will start to  settle down.

Where will it end?  The latest projections are that the US will see between 50 and 90 thousand deaths.  (2017 saw 61 thousand H3N2 influenza deaths – but over 6 months, not 6 weeks!).  New York will likely see upwards of 5 thousand (currently 200 or so).  Smaller communities will also see a rapid rise in deaths that, without context, will seem terrifying. Expect the health care system to be in crisis, and please do what you can to support the medical community.  This will be horrific for them.  Chatham County, Georgia hospitals, which serve about 400,000 people, will likely see nearly 1,000 respiratory cases, of which 100 may die, all in the next three weeks.  But again, by the end of April, most parts of the country should be at the upper end of the curve, with the deaths per day decreasing.

How soon will we know if that is our future, or something worse?  Italy should be at near their peak.  I expect that by early next week we will see a downward trend in their numbers, followed by Spain 4-5 days later.  If by the 1st of April Italy is still recording 700 or more per day, that will be a source of concern.  Will update the graph this weekend … meanwhile, don’t hoard TP like this guy.

How bad is Italy (ok, one more COVID post this week).

As of the final totals from yesterday, 22 March 2020, there have been 5476 deaths from SARS-COV-2 in Italy. To put that in perspective, in the 2013/14 influenza season, there were 7027 excess deaths due to influenza recorded. In 2014/15, a  20,259 deaths were attributed to that outbreak, while in the worse recent year, 2016/17, 24,981 died from influenza. (from Rosano et al, Int. J. Infections Diseases, Vol 88, Nov 2019, pp 127-134).

Yes, COVID19 is different in how fast cases are coming, but not in whole population mortality. The speed of progression seems to be about 4 and 6 times that of influenza, and that is producing a HUGE strain on the system. But the outcomes have yet to approach a bad influenza outbreak. The present rate of the last three days of 690/day will have to continue for another 28 days to reach the 2016/17 flu season toll. I’d be very surprised if the rates don’t start to drop soon. If they haven’t dropped in Italy in two weeks, maybe then it’s time to worry, but for now, things seem on track for this to be a “flu season in 6 weeks” virus. Catastrophic for the health care system, but not a big deal in whole population terms. In economic terms, that’s a whole different question …

To repeat from yesterday: The US health care system can’t really keep up with a normal flu season; there is no way it can handle a rapid influx. That is why COVID19 is so dangerous, and why everyone needs to take it seriously, following the CDC guidelines, exercising social distancing and hygiene protocols, and otherwise doing everything you can to try to slow down the rate of spread. It’s more than likely not about you. It’s about that 1% of so of the population who will get very sick, and may not get enough care because the system will be overloaded.  Fixating on every up or down tick in the numbers, and chasing down every wild number or wild theory making the rounds is just not sensible or conducive to sanity.  My advice is to be careful, keep watch over those around you, take advantage of the time off as you can, check the news maybe once a day to see if anything has really changed as to what you should do, but don’t drive yourself crazy hitting refresh; this is a slow motion disaster. April will be the cruelest month – but by the last week things should be looking up.

What a fashionable Italian Cat might look like.

COVID19 vs Influenza: why it’s worse, why it’s not.

OOPS: these are per 10,000, not 1000.  

You’re seeing lots of graphs and tables on COVID 19.  In a disgusting display of fear mongering, networks are now keeping running counts of the cases and deaths on screen as if tracking stocks or something.  But all of that lacks context.  How does COVID19 compare with a bad influenza outbreak? We’re starting to get enough data to seriously answer that question. I’m using the 2017 H3N2 outbreak for reference, which was a bit worse than an average season, and the data from three areas that are relatively farther along in the process: Hubei, China, Daegu, ROK, and Lobmardy, Italy.  Influenza is in blue; Hubei is orange, Daegu yellow, and Italy in green.  We start the clock on our graphs at the first known case and plot cases per 10,000 population by week:

Oh.  That’s not very interesting.  The COVID19 cases barely show up!  What is going on?  Well, to start with, we are probably only detecting/reporting a fraction of cases.  Lets scale H3N2 flu to assume we are only detecting 5% of COVID-19 cases (which seems to be the range in the literature at the moment):

That’s a lot more interesting – and really illustrates how COVID19 is both different from and more stressful for the health care system, and not as bad for the general population, as influenza.  Notice how rapidly the cases explode for COVID19.  This is why the outbreak is so stressful for hospitals: the cases flood in over 3-4 weeks, as opposed to 20 weeks for a flu outbreak.

There is a lot to learn from these numbers and graphs.  Notice the sharp break in the Hubei China curve.  There are likely two reasons for that. First, they instituted rather draconian travel restrictions.  Second, they are likely not being entirely honest about their reporting, either internally or externally.  From the Korea curve. which is probably pretty reliable, it looks like COVID19 cases will level off between 1.5 and 2 cases per 10000.  H3N2 leveled off at over 60 per thousand, but if we scale it to the same detection rate we suspect we are seeing for COVID19, then 3 to 3.5 is the range, and therefore COVID will have maybe 2/3 the impact of a bad flu season in terms of total number of cases, and mortality.  Italy is in the steep part of the curve.  We should see their case rate slow over the next week and level off, probably in the 2.0 to 3.0 /10,000 range (a bit higher than Korea due to the older population and later implementation of control measures).

What about the US?  We are just entering the steep part of the curve.  It will be very scary as cases explode – but keep it all in context.  If these trends hold, the US can expect about 30 to 35 million people to be “symptomatic” (most mild), 400,000 to 500,000 need hospitalization, and 30-40 thousand deaths.  Compare to the 2017 influenza season: 45 million symptomatic, 810,000 hospitalized, 61,000 died.  HOWEVER, rather than coming over 20 weeks or so, those cases will come over maybe 4 weeks -five times faster.  The US health care system can’t really keep up with a normal flu season; there is no way it can handle this flood.  That is why COVID19 is so dangerous, and why everyone needs to take this seriously, following the CDC guidelines, exercising social distancing and hygiene protocols, and otherwise doing everything you can to try to slow down the spread.  It’s more than likely not about you.  It’s about that 1% of so of the population who will get very sick, and may not get enough care because the system will be overloaded.  The state of the US system is a disgrace, and its inability to handle this outbreak is the result of health care policy decisions going back decades.  That will likely be the subject of an upcoming vehement rant …

Data sources:
Influenza Hospitalization Surveillance Network (FluSurv-NET), US Centers for Disease Control.
2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE

The difference between data and information (19 March COVID Notes)

When looking at articles about any subject, but especially science topics, you have to appreciate the difference between data and information.  For example, people are freaking out about articles like this one that are saying the SARS-COV-2 virus (the beast that causes COVID19) can survive “for hours or days” in the air or on surfaces.  That is “data”.  But what does in mean to you, practically?  How is this different from other virus like influenza? That would be information. So let’s convert that data point into information …

To start with, let’s be clear it doesn’t mean anything different from the standpoint of guidelines:  your best bet as to what to do is  the CDC COVID-19 web site. For other preparation tips, try the DHS/FEMA site. By now you should know the drill: wash your hands, don’t touch your face, social distancing, just stay home and isolate if you don’t feel good. Help those around you as needed.

OK, so SARS-COV-2 can survive in airborne droplets for a few hours, and on surfaces for a few days in a controlled environment.  How is that different from the cold or flu?  Well … it isn’t.  The influenza virus can remain infectious for several days on things like doorknobs. The viruses that cause the common cold (and recall 20% of them are in the coronavirus family) can be viable for over a week, even longer.  To quote from NIH (who funded the study):

The findings affirm the guidance from public health professionals to use precautions similar to those for influenza and other respiratory viruses to prevent the spread of SARS-CoV-2 …

These kinds of studies are important for practitioners to assess the guidelines and see if anything needs to be changed. However, reporters have a responsibility to put that data into context so it becomes information.  Sadly, they often don’t, or do it “below the fold” so they grab the attention of readers (ZOMG! Its Lives!) but people don’t see the context (oh, it’s just like other viruses).

In summary, for cold and flu and, now, COVID19 season, just follow Sgt Apone’s advice and you’ll be ok …

Not enough crayons …

Between the sheer magnitude of the misreporting going on in the major news media, and the monumental incompetence and feckless positioning to take advantage or avoid blame for the COVID19 crisis among US political leaders, it’s hard to know where to start.  The second biggest thing that bugs me is the assumption that people are stupid and have to be manipulated.  The biggest thing that bugs me is that the people doing the manipulating (media, leaders) think they are knowledgeable and smart enough to know what is best and that manipulation is required.  So for today a “short” post pointing out one small element of the madness.

Imperial College, London, released a report on modeling the potential impact of the virus.  It’s an interesting study, properly interpreted it’s good, valuable work.  But that’s certainly not what is happening.  One example is the New York Times article on the study.  They plucked out a graphic showing 2.2 Million US deaths, labeling it in the fine print as showing the number of deaths “in the absence of actions.”  What they don’t say is what the report itself said: that this scenario was unlikely.  That upper bound assumes that people would do nothing even as others around them fell sick.  Worse, this scenario is now in fact impossible: actions already taken will have a profound reduction on this total, even if the assumptions in the model (which are very bad case assumptions) are correct.  There are also reasons to believe that many of the assumptions in the paper are extreme, based on data that has become available later – this is a rapidly moving situation, and it is hard for peer reviewed research to keep up.  But it is valuable document showing the potential impact of various mitigation actions.


As I have ranted previously, there are always a huge range and variation of scenarios for any disaster.  Which scenario you use for a given purpose varies depending on the application.  There is no “right” number.  But there are a lot of wrong numbers, especially for what is most likely to happen.  I think most people understand that you sometimes have to plan and take action based on what could happen, even if though what is likely to happen is something more benign.  The problem is, by always emphasizing what might happen (much less the most extreme version of that) just causes a lot of fear, anxiety, and panic.  I just don’t buy it you have to scare people: most people, most of the time, will do the right thing if you just take the time to explain it to them.

As I have been saying all along, your best bet as to what to do is still the CDC COVID-19 web site.  For other preparation tips, try the DHS/FEMA site.  By now you should know the drill: wash your hands, don’t touch your face, social distancing as needed, stay home if you don’t feel good.  Help those around you as needed.  And try not to stress too much over the numbers, the drama, and the politics.  Most of the numbers (and the rhetorical extremes) are bogus anyway.

The Worst Case Scenario (15 March 2020)

OK, here it is: SARS-COV2 continues to mutate and the mortality rate increases for younger demographics, with the whole population mortality exceeding 10%.  The economic spiral rapidly accelerates into a financial system collapse, and a global depression results.  As social unrest spreads, various state and non-state actors seek to exploit the situation, and a peer-on-peer nuclear exchange is ultimately triggered.  The surviving fraction of humanity is reduced to a mad-max style existence. This is not a joke or exaggeration, this is what some of the models and associated analyses are currently forecasting as our near term future.  However …

Mad Max Fury Road promo shot. Or Abercorn Street in Savannah on word that WalMart has toilet paper. Could go either way.

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You’re Doomed, Friday the 13th Special Edition

Some argue COVID19 is like the flu.  Others scream in outrage that it isn’t at the slightest implication that it is.  Both are right, yet dangerously wrong.

Those who say it’s nothing like the flu are right.  In many ways the SARS-COV-2 virus that causes COVID-19 is potentially much more dangerous, especially to certain segments of society.   It is especially devastating to the health care system for two key reasons: it spreads quickly, and while the total numbers becoming seriously sick appear smaller than influenza it has a much higher complication rate for those who do get sick with it.  If we don’t take action, the US we will run out of respiratory support equipment (and people trained to use it) quickly, and it’s going to get ugly. South Korea has four times the hospital beds per capita than Italy – 12.4/1000 vs 3.4/1000.  Most areas of the US are under 3 per 1000. South Korea is farther along the progression than Italy, yet has a hospitalized/identified mortality rate of less than 1%. Italy is currently at 6.6%.

But those who say “worse than the flu!” are also wrong in a very dangerous way.  In societal terms, the hospitalization and mortality rates are comparable to influenza.  As of yesterday evening, those numbers in the outbreak areas in China and South Korea are still converging to the same range as influenza.  In areas that are still in the “exponential” part of the curve, Italy, Iran, and now Seattle, the day to day increases are scary, but are progressing in about the same way.  (As an aside, beware mathematicians who extrapolate the exponential expansion numbers: that is only one phase of the progression and doesn’t last forever …)  This is manageable with some common sense: concern is justified, appropriate and measured action is justified, fear and over reaction is not. The societal and economic impacts of fear are significant, and our economy in particular has a number of fault lines (especially in the areas of liquidity) that this has the potential to cause a major recession or worse.

Those who say it is similar to influenza also have a point, in general terms.  As noted above, the overall number of people who are getting sick, dying, etc. are about like bad influenza year.  In total number terms, based on what we saw in China and are seeing in Italy, about 400 thousand Americans will need hospitalization, and sadly about 30,000 will die.  But, again, the H3N2 influenza out break of 2017, against which the vaccine was only partially effective (and only 37% got anyway), hospitalized 810,000 and killed 61,000.  But, saying “it’s just the flu” misses the point just as badly as saying “it’s a bazillion times worse than the flu!” for the reasons noted above: it’s moving faster, and a greater strain on the health care system that doesn’t handle the annual flu outbreaks well.

This is a fascinating exercise in how people deal with risk.  It is also yet again a depressing example of a major societal threat we knew was coming, that experts warned about for many years, and recommended plans be made to deal with it.  But the short-sighted leadership class (of all political stripes) utterly failed in their responsibilities to get ready for it, and are now failing to react appropriately.  And it’s the average person who pays the price for that failure.  Sigh.

Get Away From Me! What part of “social distance” do you not understand?

Usual reminder that the CDC web site has consolidated information and links on the current situation, and as to what actions various at-risk groups should do, as well as what the general public can do to help stop the spread to those groups.


Dualistic Thinking and Prophecy (COVID update, 12 March 2020)

Before the numbers, a question: Is the COVID19 pandemic a crisis, or not?  In the US how you answer that seems to break along political lines.  But the answer isn’t really a simple “yes” or “no,” and that is a source of conflict and confusion in a society that demands simple, sound bite style answers that hopefully break down along party lines.  In many instances, the question “is or is not” (“to be or not to be” as some English dude wrote) is the wrong question.  The Buddhists call this “dualistic thinking”.  In the COVID crisis, the answer to the question above is a firm “it depends.”

The short version (and you know the longer version is below!) is that this is not a crisis for the vast majority of people.  Even if you get it, it’s not as bad as many of the influenza strains going around.  HOWEVER: if you are in a vulnerable population, it is as much as 10 times deadlier than the flu.  In addition, because of the rapid progression, lack of immunity, and severe respiratory distress of patients who present for treatment, it is a potential catastrophe for our health care system, which does not have the capacity to deal with this.  Thus the contradiction and conflict: for most people it’s not a big deal, but for the health care system it risks overload, and for vulnerable populations, it’s deadly.  So how do you balance all that, prepare, but not scare people and wreck the economy?  Clearly, not how we’re doing things at the moment …

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The Decision To Cancel … (10 March 2020 Notes)

The US is now well in to the mode where state and local leaders are having to take key decisions on COVID-19 with respect  to closures.  It’s a difficult situation.  The dilemma is that the available data indicates this has no more implications for the general population than a bad influenza strain. That’s not to minimize COVID19; the problem is we don’t take influenza as seriously as we probably should. The 2017 H3N2 strain hospitalized 810,000 people and killed about 61,000.  The current modeling indicates that COVID19 will hospitalize 378 thousand, and kill about 20,000.  Big numbers, but smaller than the flu.  However …

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ZOMG! The COVID Numbers Changed! (Or did they?)

One of my major frustrations with the “news” media is how they treat numbers. In a situation like we are facing with the COVID-19 outbreak, the data is very fuzzy, and we are apparently seeing wild swings in the numbers.  Headlines like this one in the New York Times are facing folks as they wake up this morning: Cases and deaths surge in Italy as its north is locked down.  So we should panic, right?  Maybe not.  

As previously noted, I’m using data from the nCoV-2019 Data Working Group data base, Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data as well as the current (9 March 2020) World Health Organization database. I’m also indirectly using other sources of information to cross check these data.

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