The_jackalope
The_jackalope's JournalR0 and cytokine storms revisited
CDC has published a paper establishing the median R0 (reproductive number) of the novel coronavirus at 5.7, with a 95% confidence interval of 3.8 to 8.9. This is far above the initial estimates of 2.2 to 2.7, and helps to explain the explosive spread of the disease.
https://wwwnc.cdc.gov/eid/article/26/7/20-0282_article
A couple of weeks ago, someone started a thread here about the probability that cytokine storms were involved in Covid-19. The poster was roundly criticized and soundly spanked. Weeeelllll...
A doctor and coronavirus patient in recovery describes his experience surviving COVID-19's worst side effect
The cytokine storm affects a substantial number of severe COVID-19 patients, enough that it has become the subject of a subset of medical research into COVID-19. Those unlucky enough to experience cytokine storm will have their bodies and especially lungs flooded with cytokines, immune system helper molecules, as their immune system struggles to fight off the invading virus and the dead lung cells it produces en masse. The overreaction results in the immune system building up too many of these kinds of cells, which can lead to respiratory distress or bacterial pneumonia and, ultimately, death.
Not everyone who experiences a cytokine storm will die, fortunately. Such is the case of Jonathan Raskin, a 69-year-old pulmonologist who practices medicine in New York City, and who contracted coronavirus a few weeks ago and is currently in recovery. After self-isolating at home, Dr. Raskin's temperature swelled to 102.8°; he spent several days in the hospital in a very bad state (by his own admission) before slowly recovering. As a pulmonologist, Dr. Raskin's insights into what was happening to his own body are particularly keen, as he had a medical understanding of what was happening as it happened to him.
My lab work was stunningly bad. A normal white count might be between 4.5 and 10. My white cell count was at 2,000. My lymphocytes — which are the cells that fight in a virus, normally fall somewhere between 1000 and 1,500 — they were under 200. I don't know if you know the term but the early cells that fight infection are called "bands," and you don't have [them] normally — I had 20% bands. My platelet count was around 100,000, which is low, and I knew I was in trouble.
In the current context, we believe we have a biomarker of this condition, a serum level of a non-specific but is an acute phase reactant called serum ferritin. It looks like it may be to be one of the more reliable biomarkers of cytokine dysregulation. A serum ferritin is normally below 400 in our lab, mine was 18,000!
This is one seriously vicious disease, and it probably hasn't shown all its cards yet.
The Earth Is Telling Us We Must Rethink Our Growth Society
William E. Rees is professor emeritus of human ecology and ecological economics at the University of British Columbia.. Heiam Rees is one of the people responsible for developing Global Footprint Analysis.
This article invites us to taker a big step back to look at the coronavirus crisis.
As the pandemic builds, most people, led by government officials and policy wonks, perceive the threat solely in terms of human health and its impact on the national economy. Consistent with the prevailing vision, mainstream media call almost exclusively on physicians and epidemiologists, financiers and economists to assess the consequences of the viral outbreak.
However horrific the COVID-19 pandemic may seem, it is merely one symptom of gross human ecological dysfunction. The prospect of economic implosion is directly connected. The overarching reality is that the human enterprise is in a state of overshoot.
We are using nature’s goods and life-support services faster than ecosystems can regenerate. There are simply too many people consuming too much stuff. Even at current global average levels of consumption (about a third of the Canadian average) the human population far exceeds the long-term carrying capacity of Earth. We’d need almost five Earth-like planets to support just the present world population indefinitely at Canadian average material standards. Gaian theory tells us that life continuously creates the conditions necessary for life. Yet humanity has gone rogue, rapidly destroying those conditions.
When will the media call on systems ecologists to explain what’s really going on? If they did, we might learn the following:
* That the current pandemic is an inevitable consequence of human populations everywhere expanding into the habitats of other species with which we have had little previous contact (H. sapiens is the most invasive of “invasive species”).
* That the pandemic results from sometimes desperately impoverished people eating bushmeat, the flesh of wild species carrying potentially dangerous pathogens.
*That contagious disease is readily propagated because of densification and urbanization — think Wuhan or New York — but particularly (as we may soon see) because of the severe overcrowding of vulnerable people in the burgeoning slums and barrios of the developing world.
* That the coronavirus thrives because three billion people still lack basic hand-washing facilities and more than four billion lack adequate sanitation services.
A population ecologist might even dare explain that, even when it comes to human numbers, whatever goes up must come down.
All of which, while bluntly true, is cold comfort to those drowning in the Covid-19 tsunami.
Did anyone watch "Into the Red Zone" on MSNBC tonight?
What a harrowing experience.
Observe the 6-foot rule. Wear a mask. Stay the fuck home.
You don't want what's coming. It's not just curves on a graph.
Big numbers
I've been trying various ways to figure out, when all is said and done, how many people world-wide are likely to die from this COVID scourge. I've been hampered by the fact that statistics was my worst subject in university, even though I'm endlessly fascinated by the behaviour of datasets. That makes me just knowledgeable enough to be dangerous. I accept that my conclusions are endlessly debatable, but right now all such results are debatable, so I don't feel too bad.
Based on the global statistics, it looks to me like the eventual Case Fatality Rate for identified cases and deaths will be around 6%. I derived this from the published global case and death data going back to mid February. I calculated ten sets of ratios, one based on the each day's deaths divided by the same day's cases, all taken from worldometer. Then, based on the idea that one day's deaths may be better correlated with some previous day's cases (because it take a while for identified cases to die), I created 9 more series by dividing each day's deaths by the cases on each of the nine previous days.
I graphed all ten series of CFR percentages, and got a set of nested curves, all of which rose and then turned back down. I put a well-fitting trend line on each curve, extended it out about 2 weeks, and found something very interesting. The curves all crossed at the 6% point, except the one using same-day data. I'm not enough of a statistician to tell you why that intersection might have happened, but my pattern-recognition circuits all lit up when I saw it. The graph is below.
Ass a sort of cross-check, I extrapolated the global curves for identified cases and deaths out 14 days, and used the end-points of those two projections to calculate the projected CFR six weeks from now. Again, the answer was about 6%. (graphs below)
So, absent any more reliable estimate at this point in the pandemic, I've adopted 6% as my tentative CFR. I'll watch the behaviour of the data as time goes on, to see of the estimate changes.
Applying this to the future state of the world, assuming an identified infection rate of 10%, a CFR of 6% implies about 48 million deaths worldwide.
As far as the USA is concerned, a 10% infection rate and a 6% CFR projects 2 million deaths, which is within the range of the high-level projections revealed by Dr. Birx.
Obviously these are little more than wet-finger estimates because it's still early days. They will obviously change as time goes on and the results of social distancing and lockdowns are felt (or not) in different places. But it does hint at the death tolls we should be prepared for.
This so sucks.
Is anyone else putting together a DNR or Advance Care Directive?
I'm 69 years old. I have asthma, hypertension and heart failure. After reading a couple of doctors' descriptions of late stage Covid-19, I finally decided to set down my wishes for my partner and doctors. My directive specifies sedation instead of intubation, and includes an "Allow Natural Death" clause. I will also be adding a request for medical assistance in dying if I end up in that state, if that is possible. If not, sedation will have to suffice.
I've lived my life, and I'm quite satisfied with it. I don't want to suffer at the end, and I want to make sure I don't use medical supplies and attention that are needed more urgently by others.
Who else is making such preparations?
US cases have been increasing by 33%/day for the last 3 weeks.
That means the case count is doubling every 2.5 days. The behavior is remarkably consistent since at least March 2, when there were only 105 cases. If that exponential behavior remains in place for just another two weeks, there will be on the order of 2.5 million cases in the USA.
The global All Case Fatality Ratio (including cases that are still active) has gone up to 4.4%, and the Case Fatality Ratio for resolved cases (those who have recovered or died) has risen to 13.9% from 5.6% two weeks ago.
That last number scares the living shit out of me. Unless something really major happens to change the epidemiology of this thing, the USA is looking at an unavoidable human catastrophe that will make the argument over stimulus packages look like playground name-calling.
Keeping up with the numbers
Data comes from https://www.worldometers.info/coronavirus/ as of 4:00 pm March 18 and 11:30 pm March 21
Global data:
March 18: Cases are increasing by over 17,000 per day. Deaths are increasing by almost 1,000 per day.
March 23: Cases are increasing by over 32,000 per day. Deaths are increasing by almost 1,700 per day.
March 18:The "All Case" CFR (Total Cases/Deaths) is 4.1%. The "Closed Case" CFR ((Recoveries+Deaths)/Deaths) is 9.6%
March 23:The "All Case" CFR (Total Cases/Deaths) is 4.25%. The "Closed Case" CFR ((Recoveries+Deaths)/Deaths) is 11.9%
What I call the "All Case" CFR is what Wikipedia calls the preliminary CFR. The Closed Case CFR approximates what Wikipedia calls the "final CFR". The article contains this caution:
The global infection curve is showing no signs of decelerating into a sigmoid inflection. Simple, high-correlation quadratic projections show 9 million infections and 600,000 deaths world-wide in two months. These are increases of 30+ times today's numbers.
My concern, frankly, is that these projected numbers will prove to be too low.
Different nations will show different CFR values depending on their demographics, population density, the timing and urgency of the testing and distancing measures they undertake, and the quality of their health care system. National values currently vary from a "Closed Case" CFR of 3.5% in South Korea to about 40% for Italy and Spain. The USA isn't doing well yet, with a Closed Case CFR of 66%
The numbers are bad, getting worse fast, and there is no end in sight. If you're not an essential worker, stay home and wash your hands. If you are an essential worker, bless you and may you stay safe.
Tonight I'm feeling like
Mother Nature has sent us all to our rooms to think about what we've done.
My latest COVID-19 numbers and estimates
Data comes from https://www.worldometers.info/coronavirus/ as of 4:00 pm March 18, 2020.
Global data:
Cases are increasing by over 17,000 per day.
Deaths are increasing by almost 1,000 per day.
The "All Case" CFR, using the data for all cases and deaths is 4.1% It has been climbing continuously for the last month up from 2.8%.
The "Closed Case" CFR using the data for recoveries and deaths is 9.6%, and has been climbing steadily for a week and a half, up from 5.6%.
Projections based on quadratic fits to the month of global data since 19 February, and extended out to April 15 indicates 600,000 cases for a second-order fit (R^2=0.976), and 1.4 million for a tighter third order fit (R^2=0.998).
US Data:
American cases are rising by 1500 per day, but there really isn't enough data yet to be confident of the trends.
Based on data from 1 March, projections indicate between 70,000 and 225,000 cases by April 13.
Every fruit tree benefits from pruning
Dutch trends forecaster Li Edelkoort has a provocative outlook on Covid-19, the deadly coronavirus strain that has upended manufacturing cycles, travel plans, and conference schedules around the world. Speaking at Design Indaba, a conference in Cape Town last week, the celebrated 69-year old design industry advisor pictured Covid-19 as a sobering force that will temper our consumerist appetites and jet-setting habits.
“The virus will slow down everything,” Edelkoort notes. “We will see an arrest in the making of consumer goods. That is terrible and wonderful because we need to stop producing at such a pace. We need to change our behavior to save the environment. It’s almost as if the virus is an amazing grace for the planet.”
But after the coronavirus, utopia looms, Edelkoort suggests. Indeed, Covid-19 could open new avenues for innovation, akin to how the bubonic plague ushered in an era of labor reforms and improvements in medicine in the Middle Ages. Being confined to our own towns or cities could foster a revival of cottage industries and an appreciation for locally made goods, she says. “There are so many possibilities,” Edelkoort says. “I’m strangely looking forward to it.”
I think this is the perspective I was missing in my support for the virus.
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