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Member since: Sun Jun 4, 2017, 04:46 PM
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R0 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.


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...

What it feels like to survive COVID-19’s dreaded “cytokine storm”

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.
Posted by The_jackalope | Thu Apr 9, 2020, 04:29 PM (8 replies)

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.

The Earth Is Telling Us We Must Rethink Our Growth Society

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.
Posted by The_jackalope | Mon Apr 6, 2020, 12:09 PM (7 replies)

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.
Posted by The_jackalope | Sun Apr 5, 2020, 10:27 PM (19 replies)

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.

Posted by The_jackalope | Fri Apr 3, 2020, 12:01 PM (7 replies)
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