Monday, June 8, 2020

Surviving the Coronavirus: Part 12 (and final)

It's been 43 days since my last post. It's not the first time I've disappeared from this blog, and it won't be the last.

For the last six weeks I've been chasing the genetic basis for severe COVID-19 infections. I've documented the outcome of that effort in a lengthy technical paper I hope will lead to confirmation testing of my conclusion.

I offer the abstract of the paper immediately below.
Reportable COVID-19 infection rates vary radically from country to country. Remarkably, the reported rates in western Europe are more than an order of magnitude greater than in the tropics and sub-tropics. This suggests a common human genetic variant may be the primary culprit behind reportable COVID-19 infections.
Actual culprit identification will provide focus for efforts to identify prophylactics, treatments, and vaccines. Culprit identification will also identify pathways for relaxing the physical distancing measures that seriously constrain peoples’ lives and the world's economy.
Reportable COVID-19 infection rates show a definite male bias. This suggests that the culprit variant might be located on the X chromosome.
Reportable COVID-19 infections are associated with a remarkably low expression of type I and III interferons. This suggests that the culprit variant might be associated with the detection or signaling portion of the innate immune system.
By filtering gene variants based on their frequency, geographic distribution, chromosomal location, and function, one can substantially narrow the list of candidate culprit variants.
Of nearly 900,000 candidate culprit variants analyzed as part of the multi-layer screening effort described herein, only five survive frequency, geographic, chromosomal, and functional filtering. Those five candidate culprits belong to the HDAC6 and IRAK1 genes.
   The candidate variants are identified so that others may further evaluate them based on disproportional appearance among patients who have suffered serious COVID-19 infections.
The technical paper represents my best effort to ameliorate the suffering caused by the pandemic. I'll continue soliciting the attention of biomedical researchers who will hopefully be able to take advantage of my findings, presuming the findings are correct.

Other than that effort to circulate my paper, I will no longer be focusing my attention on the COVID-19 pandemic. Other significant tasks, too long ignored, beckon.

Friday, April 24, 2020

COVID-19 Prophylaxes: Face Mask Material, Breathability

In my first post of this mini-series within a series, I explained that the Prophylactic Index for widespread use of face masks (for those of us north of the tropics) is 12.7. I recommended that reasonable face mask requirements be part of any plan to relax social distancing rules. I said nothing about the efficacy of various types of face mask materials. I corrected that shortcoming, and then some, in my previous post.

While that previous post provided you with filtration information on nearly three dozen candidate materials for DIY face masks, it provided no insight into how easy of difficult it might be to breath through them.  I correct that shortcoming herein, and I make additional under-informed recommendations.

The fine folks at both the NIH and Smart Air tested the ease or difficulty of moving air through the various face mask materials that they tested for filtration efficiency. The NIH folks measured pressure drop across the material. The Smart Air folks measured the fan power required for a give flow rate through the material, and they provided their results as breathability scores ranging from 1 to 6.

Since most people don't relate particularly well to pressure drop, or have six fingers, I've converted both the NIH and Smart Air scores to a breathability score of 0 to 10, with the surgical mask at 5 and the most easy-to-breath-through material at 10. I provide a composite list of the results below, breathability winners on top.

Silk:  breathability score = 10
Pillowcase:  7
Scarf, 100% Cashmere:  6
Scarf, 100% Ramie:  6
T-shirt, 100% cotton: 6
Linen:  6
Cloth, floor cleaning, disposable, 3M: 6
Synthetic fiber, velvet: 6
T-shirt: quick-dry, 95% Polyester + 5% Spandex:  6
Bed sheet, brocade:  6
Scarf, wool, 100% merino: 6
HEPA Filter: 6
Polypropylene bag, non-woven: 6
Bandana, 100% cotton: 6
Neck warmer / snood, 100% microfiber polyester: 6
Cloth, dusting: 6
Paper towel, Scott’s blue shop towel: 6
Canvas, 0.45 mm thick:  6
Surgical mask:  5
T-shirt, 100% cotton (double layer): 5
Pillowcase (double layer):  5
Bra pad, muslin + sponge: 4
Nylon, 70D: 4
Dish towel / tea towel:  3
Pillowcase, antimicrobial:  3
Paper towel, brown, hand drying: 3
Bed sheet, 100% cotton, 120 thread:  3
Bed sheet, 100% cotton, 80 thread: 3
Denim, 10 oz, 0.7 mm thick:  3
3M N95 mask: 3
Coffee filter, CHEMEX: 2
Canvas, 0.75mm:  2
Nylon, 40D: 1
Coffee filter, HERO: 1
Canvas, 1.1 mm thick:  1
Dish towel, tea towel (double layer):  0
Vacuum cleaner bag:  0

So ...

All that you have to do to decide whether or not you should make your own masks, and settle on what material you should use (assuming you decide to go rogue), is look at two different sources of test data, for three different particle micron sizes, and somehow weigh those data against the breathability numbers provided above.

Or ...

You could just continue reading this august post, the one in which I have scored each of the candidate materials with another of my made up numbers, this time the soon to be famous Face Mask Index, or FMI. The Face Mask Index is merely the breathability score multiplied by the material filtration efficiency for 0.3 micron particles. (As an informative but boring aside, I had to adjust the NIH efficiencies for 1.0 and 0.02 micron particles based on 0.3 micron particle results for similar materials from the Smart Air data.)

The FMI results for each of the face mask designs / materials are presented below, in descending order of FMI. The winners are on the top; the losers are at the bottom. The list contains a few surprising results, but it is mostly populated with disappointing results.

Here we go.

HEPA Filter: FMI = 5.0
Surgical mask:  3.8
3M N95 mask: 2.9
T-shirt, 100% cotton (double layer):  1.5
Dish towel / tea towel:  1.4
Pillowcase:  1.4
Silk:  1.3
Linen:  1.2
Canvas, 0.45 mm thick:  1.1
Paper towel, Scott’s blue shop towel: 1.1
Pillowcase (double layer):  1.0
Coffee Filter, CHEMEX: 1.0
T-shirt, 100% cotton (double layer):  0.8
Synthetic fiber, velvet: 0.8
Pillowcase, antimicrobial:  0.7
Polypropylene bag, non-woven: 0.7
Bed sheet, 100% cotton, 120 thread:  0.7
Bed sheet, 100% cotton, 80 thread: 0.6
Canvas, 0.75mm:  0.6
Denim, 10 oz, 0.7 mm thick:  0.6
Bra pad, muslin + sponge: 0.6
Nylon, 70D: 0.5
Cloth, floor cleaning, disposable, 3M: 0.4
Cloth, dusting: 0.4
Bed sheet, brocade:  0.4
Scarf, wool, 100% Merino: 0.4
Scarf, 100% Cashmere:  0.4
T-shirt, quick-dry, 95% Polyester + 5% Spandex:  0.4
Scarf, 100% ramie:  0.2
T-shirt, 100% cotton:  0.2
Paper towel, brown, hand drying: 1.0
Bandana, 100% cotton: 0.1
Neck warmer / snood, 100% Microfiber Polyester: 0.1
Nylon, 40D: 0
Dish towel, tea towel (double layer):  0
Coffee filter, HERO: 0
Canvas, 1.1 mm thick:  0
Vacuum cleaner bag:  0

From a story-telling perspective, the most discouraging result is that I will not be recommending that people try to save themselves from the coronavirus by breathing through vacuum cleaner bags.

The most surprising result is the sequence of the top three items in the list. The HEPA filter wins because it has the best combination of filtration efficiency at 0.3 microns (83%) and breathability score (6). Though the N95 masks have the best filtration efficiency (96%), they get clobbered by their breathability score (3).

The disappointing result is that there are no great alternatives to the top three masks. All but the top three have such low filtration efficiencies that their breathability scores can't save them.

The most frightening result is that bandana score so low. I've seen many sites that mention bandanas as a viable face covering, and I fear those sites are doing more harm than good. Those poor people who take such bandana advice at face value might just as well wear their home made face mask around their neck, or put it in their back pocket. Either way, they will be taking it in the neck.

The bottom line is that you can't really do much better than just buying the reusable surgical masks, presuming you can get them. They have, after all, been working great for those 13 countries that began wide-spread use of face masks prior to 1 March 2020.

Not everyone will be able to acquire disposable surgical face masks, though. Given my ongoing efforts to free some of those wrongfully convicted, I'm particularly sensitive to those people we have behind bars, in close quarters, almost entirely reliant on others for potentially life-saving decisions regarding matters such as "which face mask, if any, should I wear?' In the one case consuming most of my wrongful conviction time and energy, I'm informed that the prisoners have been provided face masks, and that those face masks are seemingly made out of the same material as their bed sheets. That's pretty scary.

For those people who, for any reason, cannot get hold of N95 or surgical face masks, I recommend they somehow construct their own face mask using some combination of materials from the prioritized list below, using as much thickness as their breathing permits.

#1  HEPA filters
#2  coffee filters
#3  canvas
#4  paper towels
#5  denim
#6  bed sheets
#7  t-shirts

And my sincere best wishes to all those people in such dire straits.

Thursday, April 23, 2020

COVID-19 Prophylaxes: Face Mask Material, Filtration

In my previous post, I explained that the Prophylactic Index for widespread use of face masks (for those of us north of the tropics) is 12.7. I recommended that reasonable face mask requirements be part of any plan to relax social distancing rules. I said nothing about the efficacy of various types of face masks. I correct that shortcoming, and then some, in this post.

Clearly, some masks are better than others. I'll begin with the not-quite-a-party line. The N95 masks are the best, because they stop 95% of something or other that may or may not begin with the letter N. The N95 masks are generally cup-shaped, and they even have "N95" printed right smack dab on the nose. N95 masks, though, need to be properly fitted to be N95-worthy. Unfortunately, Mosts folks don't fit them properly, so the so-called N95 masks are actually N_something_less_than_95 masks, but that's neither as catchy nor as comforting.

Next apparently, in my under-informed opinion, are the so called surgical masks. They're the blue, pleated, nearly flat, paper (or paperish) masks so commonly seen among the people of the 13 countries that have such low infection rates. Good enough for a surgeon, I say, good enough for thee. Not according to the CDC, though. I attach their summary below. Click to enlarge.

The CDC helpfully advises that a surgical mask "Does NOT provide the wearer with a reliable level of protection from inhaling smaller airborne particles and is not considered respiratory protection."

The CDC should probably not share their wisdom with the non-N95-face-mask-wearing folks of Taiwan, since Taiwan's infection rate (as of 13 April 2020) was 17 per million while ours, here in the good ol' US of A, was a hundred times that, at 1,773 per million.

Instead, the CDC might want to consider several observational studies that show that surgical face masks provide the same level of protection against pathogens as do the N_not_quite_95 masks.

The earlier of the two studies was reported way, way, way back in 2009 in JAMA (Journal of the American Medical Association) as Surgical Mask vs N95 Respirator for Preventing Influenza Among Health Care Workers. The key points of that study read:
"Context: Data about the effectiveness of the surgical mask compared with the N95 respirator for protecting health care workers against influenza are sparse. Given the likelihood that N95 respirators will be in short supply during a pandemic and not available in many countries, knowing the effectiveness of the surgical mask is of public health importance. 
"Results: Between September 23, 2008, and December 8, 2008, 478 nurses were assessed for eligibility and 446 nurses were enrolled and randomly assigned the intervention; 225 were allocated to receive surgical masks and 221 to N95 respirators. […] 
"Conclusion: Among nurses in Ontario tertiary care hospitals, use of a surgical mask compared with an N95 respirator resulted in noninferior rates of laboratory-confirmed influenza."
Allow me to translate the somewhat muddled portion. The surgical masks were "noninferior," meaning that they were "just as good."

Ten years later on, in 2019, the same exact Journal published the results of another, significantly larger study, under the nearly identical, noninferior title of "N95 Respirators vs Medical Masks for Preventing Influenza Among Health Care Personnel." The key points of that study read:
"Question:  Is the use of N95 respirators or medical masks more effective in preventing influenza infection among outpatient health care personnel in close contact with patients with suspected respiratory illness? 
"Findings:  In this pragmatic, cluster randomized clinical trial involving 2862 health care personnel, there was no significant difference in the incidence of laboratory-confirmed influenza among health care personnel with the use of N95 respirators (8.2%) vs medical masks (7.2%). 
"Meaning:  As worn by health care personnel in this trial, use of N95 respirators, compared with medical masks, in the outpatient setting resulted in no significant difference in the rates of laboratory-confirmed influenza."
Imagine that!  Still no difference. The N95 masks were noninferior to the surgical masks!

So what about home-made masks? Given how much as the CDC is troubled by even surgical masks, I assume that the thought of an uninformed citizenry sporting about in home-made masks would cause the Center for Disease Controllers to suffer severe functional dyspepsia. Nonetheless, I have found two studies that actually tested various materials to see which, if any, might work for the construction of homemade masks. I combine the filtration results of those two studies in this post. In the next post, we will consider the rather important issue of being able to breath through the various materials. In the post after that, the third in this august sub-series within an august series, we will consider the issue of sealing the masks to the face.

The first study was reported online in a 22 May 2013 National Institute of Health technical paper, "Testing the Efficacy of Homemade Masks: Would They Protect in an Influenza Pandemic?"

The second study is more recent, less formal, and way more entertaining. It is presented in a blog post, not a technical paper. That august post is entitled The Ultimate Guide to Homemade Face Masks for Coronavirus." It is the fine work of the fine folks at Smart Air. Their mission statement follows.
"Smart Air is a social enterprise and B-corp that combats air pollution by delivering cost-effective air purifiers and providing open-source data on air pollution.”
The emphasis is mine. In my opinion, those folks are providing the most timely, most informative, most useful, most clear, and most entertaining information about face masks, bar none. You can do a lot worse than reading through their entire list of blog posts about the coronavirus.

The Smart Air folks focused their studies on particle diameters near 0.3 micron, which is three one-tenths of a millionth of a meter, which is really really really small, clearly smaller than a breadbox, and approximately three times the the size of the COVID-19 virus.

The NIH folks focused on two microorganisms, one of them being the Bacillus atrophaeus, a black stained bacterium frequently used in biomedical testing, having a diameter ten times that of the coronavirus. Their second microorganism was the Bacteriophage MS2, a single-stranded RNA virus (as is the coronavirus) but only 1/5 as large as the coronavirus. I'll provide the NIH results for both particle sizes below, sorting the items by decreasing order of filtering efficiency, winners near the top, losers near the bottom.

Surgical Mask:  96% for 1 micron,  88% for .02 micron
Dish towel / tea towel (double layer):  97%,  N/A
Vacuum cleaner bag:  94%,  86%
Dish towel / tea towel:  83%,  72%
Cotton mix:  75%,  70%
T-shirt, 100% Cotton (double layer):  70%,  N/A
T-shirt, 100% Cotton:  69%,  51%
Pillow case, antimicrobial:  66%,  67%
Scarf:  62%,  49%
Pillow case:  61%,  47%
Linen:  60%,  62%
Silk:  58%,  44%

Now for the lengthier, more innovative, more relevant Smart Air test results for 0.3 micron particles

3M N95 mask:  96%
HEPA filter:  83%
Surgical mask:  75%
Coffee filter, HERO:  62%
Coffee filter, CHEMEX:  49%
Nylon, 40D:  49%
Canvas, 1.1 mm thick:  49%
Dish towel / tea towel:  48%
Paper towel, brown, hand drying:  33%
Paper towel, kitchen (double layer):  33%
Canvas, 0.75 mm thick: 31%
Denim, 10 oz, 0.7 mm thick: 29%
Bed sheet, 100% cotton, 120 thread: 24%
Paper towel, kitchen:  23%
Bed sheet, 100% cotton, 80 thread:  21%
Canvas, 0.45 mm thick:  19%
Paper towel, Scott's blue shop towel:  19%
T-shirt, 100% cotton (double layer): 15%
Bra pad, muslin + sponge:  14%
Velvet synthetic fiber:  13%
Nylon, 70D:  12%
Polypropylene bag, non-woven:  11%
T-shirt, quick-dry, 95% polyester + 5% spandex:  7%
Bed sheet, synthetic brocade:  7%
Cleaning cloth, floor, disposable:  7%
Cloth, dusting:  7%
Scarf, wool, 100% cashmere:  6%
T-shirt, 100% cotton:  3%
Scarf, light, 100% ramie:  3%
Neck warmer / snood, 100% microfiber polyester:  2%
Bandana, 100% cotton:  2%

Once again, I congratulate the fine folks at Smart Air for doing all the testing and making the results available to all at no charge.

The results are quite interesting, as far as they go. Without considering one's ability to breath through something like a vacuum cleaner bag or silk tent material, it's a wee bit early to make even an under-informed recommendation. For that, hang tight until the next post.

[Mea culpa note in reduced font size: I initially published this post on 23 April 2020. On 24 April, I discovered that I had posted the Smart Air test results for 1 micron particles rather than for 0.3 micron particles. The filtration percentages were substantially worse and the order ranking order was somewhat different. I published this corrected version on 24 April.]

Tuesday, April 21, 2020

COVID-19 Prophylaxes: Face Masks

On 29 February 2020, the US Surgeon General spoke down to those of us among the general public who would deign to wear a face mask. "Seriously people," he tweeted, "STOP BUYING MASKS! They are NOT effective in preventing general public from catching #Coronavirus, but if healthcare providers can't get them, to take care for sick patients, it puts them and our communities at risk."

He put the important part in ALL CAPS, so I guess he is to be believed.

On 30 March 2020, the World Health Organization repeated their mantra that face masks don't work, at least for those of us among the masses. "There is no specific evidence to suggest that the wearing of masks by the mass population has any potential benefit. In fact, there's some evidence to suggest the opposite in the misuse of wearing a mask properly or fitting it properly,"

Using my magnum databasus, I have compared the infection rate of those countries with widespread use of face masks prior to 1 March 2020 to those countries who had no particular use of face masks prior to that same date. You can probably guess some of the countries, and you can probably guess the impending results.

Based on my prowling of the internet (a.k.a the source of all knowledge), I concluded that the following countries were taking widespread advantage of face masks prior to 1 March 2020. I present the 13 countries below in decreasing order of infections per million residents, that value being in parentheses, that value being current as of 13 April 2020. The grand prize winner will be at the bottom.

Keep in mind that the average infection rate for the good ol' USA, land of the free and home of the "Seriously people, STOP BUYING MASKS!" US Surgeon General, was 1,773 as of that same date.

Singapore (499)
South Korea (206)
Hong Kong (135)
Macao (89)
Japan (60)
China (57)
Thailand (37)
Phillippines (25)
Taiwan (17)
Indonesia (17)
Sri Lanka (10)
Vietnam (3)
Nepal (0)

We can use these data to calculate my world famous PI, which stands for prophylactic index. The average infection rate for the 13 countries in the face mask study group is 87 infections per million. The average infection rate for the 178 countries outside the face mask study group is 455 infections per million. The PI for face masks is 455 / 87 = 5.2.

On a worldwide basis, those countries that follow the advice of the US Surgeon General and the World Health Organization are 5 times more likely to become infected than those countries who tell those leaders to piss off.

In fairness to the US Surgeon General, in a public act of probably enforced contrition, he later posted a video, starring himself, advising that not only should people wear face masks, they can make their own at home. He even published instructions. Good for him for swallowing the bitter pill.

In fairness to the the World Health Organization, it has been considerably less contrite with respect to its indefensible face mask position. In its position paper of 6 April 2020, the WHO tried to cover its organizational ass as best it could. The emphasis is in the original.

“Wearing a medical mask is one of the prevention measures that can limit the spread of certain respiratory viral diseases, including COVID-19. However, the use of a mask alone is insufficient to provide an adequate level of protection, and other measures should also be adopted. Whether or not masks are used, maximum compliance with hand hygiene and other IPC measures is critical to prevent human-to-human transmission of COVID-19.”

Their new position, if I may be so bold as to state it clearly for them, is that face masks do work but only if you wash your hands.

Do we really need the WHO to tell us to wash our hands? Whose mother didn't tell him or her repeatedly to wash his or her hands?

In the same position paper, the motherly WHO immediately followed its new, brilliant "wash and wear" position with the following gobbledygook.

"Studies of influenza, influenza-like illness, and human coronaviruses provide evidence that the use of a medical mask can prevent the spread of infectious droplets from an infected person to someone else and potential contamination of the environment by these droplets. There is limited evidence that wearing a medical mask by healthy individuals in the households or among contacts of a sick patient, or among attendees of mass gatherings may be beneficial as a preventive measure. However, there is currently no evidence that wearing a mask (whether medical or other types) by healthy persons in the wider community setting, including universal community masking, can prevent them from infection with respiratory viruses, including COVID-19."

If I may be so bold, I'll try to clarify their gobbledygook for them. Here we go. Masks work if you are around people who are known to be sick, or if you are in a mass gathering of people not known to be sick, but they may not work when you are otherwise out in the public, rather or not everyone else is wearing a mask.

Sorry. That was the best I could do for them. It was like trying to put lipstick on the swine flu.

Here, back in the good ol' US of A, we are considering how soon and to what extent we should ease our semi-lockdown. Given the effectiveness of face masks in reducing the spread of the coronavirus, we should absolutely condition relaxation of the social distancing restrictions on adoption of appropriate face mask requirements.

To stress this point more fully, I'll end this post by recalculating the face mask PI based on just those countries north of the tropics. Recall that in my previous post, those countries north of the tropics have far, far higher infection rates than countries further south. Face masks, therefore, will likely provide those in the northern latitudes even greater relative benefit.

Here we go:

South Korea: 206 infections per million, as of 13 April 2020
China: 57
Japan: 60
Taiwan: 17
Nepal: 0

Average for northern latitude, face-mask-wearing countries: 68.1
Average for other northern latitude countries: 863.9
Increased safety factor for wearing face masks: PI = 12.7

As the contrite US Surgeon General might now tweet: ""Seriously people, START WEARING MASKS!" 

Sunday, April 19, 2020

COVID-9 Prophylaxes: Geographic Location

I provide my introduction to this COVID-9 Prophylaxes series in my magnum postus. Here I began detailing the results of my observational studies. Be aware that we are in search of one or more COVID-9 prophylaxes. In other, less suggestive words, were are in search of preventative measures to keep us from becoming infected.

Using my august magnum databasus, I analyzed the per capita infections of 191 countries. Though I have 208 countries in my database, I exclude from my analysis those 17 countries with fewer than 50,000 residents. Those small countries (in population, not necessarily in size) show extreme variations in per capita infection rates; some are extremely high and some extremely low. Rightly or wrongly, I attributed those extremes to the problem of small sample size, and I thereby excluded them without further study.

I obtained death and infection numbers for each country from the now world-O-famous worldOmeter site. I updated those numbers not long before writing this post. They are current as of 13 April 2020.

I obtained the population for each country from a different worldOmeter web site.

Since I'll be reporting infections per million people on a country by country basis, those two sets of data are all I need to get started. I will identify my other sources of data as appropriate.

I'll be reporting potential prophylaxes based on their Prophylactic Index, which I cleverly abbreviate as PI. The Prophylactic Index is a term I simply made up. It allows me to score potential prophylaxes by a single number. The PI is simply the ratio of two infection rates. More specifically:

PI = infections per million of control group / infections per million of potential prophylactic group.

The larger the PI, the more effective the potential prophylactic might be. As a hypothetical example, presume that one country with Possible Prophylactic #1 has 100 infections per million while every other country in the group has 1000 infections per million. In that hypothetical, PI = 100 / 10 = 10. In other words, the data suggests that Possible Prophylactic #1 residents will suffer 10 times fewer infections than everyone else, everything else being equal. Alternatively, those who do not (or cannot) take advantage of Potential Prophylactic #1 are 10 times more likely to contract the virus, everything else being equal.

With that dreadfully boring explanation now in hand, you get your first peek at the results of my observational study. It shows the prophylactic effect of living at various latitudes. Here we go:

Tropics (81): 6.1
South of Tropics (20): 5.3
North of Tropics (90): 0.1

Holy Cow!

To understand my feigned amazement, I offer the following, thrilling descriptive narrative. The number within the parentheses represents the number of countries in the potential prophylactic group. Using the Tropics as an example, the study compared the 81 tropical countries against the remaining 170 countries in the study. The non-weighted average infection rate for the 170 non-tropical countries was 6.1 times greater than the non-weighted average infection rate for the 170 tropical countries. The PI (prophylactic index) for living in the tropics is therefore 6.1.

With that shorthand in hand, we can move much more quickly.

Looking at the latitude results reveals that those of us living north of the tropics are 10 times more likely to become infected than are those living south of us. It's not immediately clear why that should be so, but that's what the data say.

One possibility, which we will consider carefully beginning with the next post, is that the apparent latitude effect is actually some sort of weather effect. Lots of smart people north of the tropics are arguing that the virus will abate when the summer arrives, due to increased temperature and humidity. Previous flu seasons, after all, tended to abate in the summer months. Why should the COVID-19 virus behave any differently?

If they be correct, those smart people living north of the tropics, then we can expect that the results will flip come northern hemisphere summer, which will also become southern hemisphere winter. Then the northern hemisphere folks will be only 1/10th as likely to contract the infection as their southern hemisphere antipodes.

I know what's coming in the next few posts though, and I fear that the smart NL folks might be in for a rude awakening.

I'll spend the remainder of this post summarizing the PI values for each geographic region on earth, excluding the arctic and antarctic. I'll allow you to begin speculating on what the results might mean.

Africa (55): 14.1
Oceania (6): 3.3
Latin America (20): 3.1
Asia (47): 2.6
Caribbean (17): 2.0
North America (4): 0.5
Europe (42): 0.1

Finally, Africa gets a break.

North America and Europe take it in the neck.

Friday, April 17, 2020

Surviving the Coronavirus: Part 11

Magnum Postus Edition

Magnum Opus is Latin for "Great Work." I'll allow you to guess at what I mean by Magnum Postus.

This is my 616th post for this august blog. The statistics page tells me that this blog is approaching nearly a million page views. That's chump change compared to the top blogs, but it's substantially more than most non-august blogs. I was going to write a post, seemingly within the next few months, bragging that this blog had just surpassed a million page views. Now it just doesn't matter. Who cares about such things? I don't.

I have usually written of freedom wrongfully denied and of needles wrongfully injected. I have been pretty much ineffective. After failing to prevent the execution of someone I believed absolutely innocent, I walked away from this blog. I returned, and I walked away again. Now I am back once again, considerably older and a tiny bit wiser, still grasping at some faint hope that I might help, in some faint way, to resolve a serious problem.

Based solely on the number of page views, my magnum opus is Johnny Frank Garrett and Bubbles the Clairvoyant. Some 37,000 pairs of eyes have zoomed across that article. It was certainly the title, much less certainly the contents, that attracted the viewers.

I sincerely hope that more eyes will soon fall on this post, and be amazed, and excited, and hopeful. Based on what I intend to relate herein, I consider this post to be my magnum postus. I urge you to stay tuned, to read to the last word, for new information on how we can get ourselves out of this deadly pandemic mess.

I am deadly serious.

As I have explained since the beginning of this coronavirus series, we will not be completely out of this deadly pandemic mess until we reach herd immunity. We will reach herd immunity only after a certain percentage of us are immune to the virus, either naturally (due to having survived the infection) or artificially (due to having been vaccinated).

The percentage required for herd immunity can be easily calculated from the starting reproduction number, a.k.a the Ro, R zero, R naught, whatever. The best estimate for the coronavirus Ro has, until recently, been somewhere between 2.28 and 2.5. That Ro range would indicate that we will be completely out of this deadly pandemic mess only after 56% to 60% of us have somehow gained immunity.

Unfortunately, the long term picture may be substantially bleaker than even a 60% threshold for herd immunity. The authors of High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2 argue, persuasively in my discouraged opinion, that the Ro is more likely 5.7. If they are correct, then 82% of us will need to somehow become immune before we cross the threshold to that herd immunity wonderland.

I have also argued from the beginning of this series that, until an effective vaccination is available and widely applied, we need to seriously distance ourselves from one another, also that we need an effective treatment, toot sweet. With a Case Fatality Ratio (CFR) of 0.66% (the current best estimate) and an R zero of 5.7 (the most recent best estimate), the virus, if left to its own devices, will take 82% x 0.66% = 0.54% of us. In the US alone, with our 330 million souls, the pandemic would claim 1.8 million.

Social distancing does delay the spread of the infection. It buys us time until vaccines can be developed, tested, and distributed. The vaccines will take a year or so, however, and the adverse effects of social distancing (on the economy and on our basic infrastructure) can be deadly in themselves. We need a means (oxymoron trigger warning!) to quickly ease back into a sustainable way of life while we await the vaccines. That is why I've stressed the need for a treatment, with chloroquine (or some variation thereof) being my unprofessional, not worth a nickel, top pick for most likely to succeed.

What I did not fully appreciate, however, is that there might be one or more prophylactic preventative measures that could act as a temporary pseudo-vaccine. Any such prophylactic preventative measure would be far better even than an effective treatment. Much better to avoid contracting the disease than to burden the system by suffering through an infection.

Social distancing is actually a prophylactic measure. It keeps us from infecting others or being infected ourselves. It does not, however, allow us to go about our lives as if we've been vaccinated. It is the non-disruptive pseudo-vaccination preventatives prophylaxes in which I have most recently become interested in, and in search of.

I believe that I have pseudo-stumbled across not just one, but three, effective prophylaxes that we can rapidly adopt, that will allow us to get back to work as a society, that will spare an untold number of lives. In this post I will present the evidence on which I base my outrageous claim. In this post, and many to follow, I will explain that each measure is being effectively used, either consciously or unconsciously, in multiple other countries. In this post, I will present what I believe to be a safe, low-cost approach for getting our lives back in order while, at the same time, saving more lives than we will thankfully ever count.

That is why I consider this post to be my magnum postus. Not because of its magnus writing, but because it reveals a simple, life-saving path forward.

To identify potential COVID-19 prophylaxes, I wrote my own database. It is an exceptionally simple database, at least for those accustomed to writing databases. Nonetheless, it has become my magnum databasus.

Because what I believe I have learned is too extensive for even one of my posts, which tend to be a bit on the lengthy side, I will use this post to summarize my conclusions. I will follow with a new series of posts to provide detail.

Focusing on countries north of the tropics, my results reveal:

Finding #1: Countries that began widespread use of face masks prior to 1 March 2020 have 11 times fewer infections from the COVID-19 virus compared to those countries that have delayed widespread use of face masks.

Finding #2: Countries suffering malaria at a rate in excess of 0.1% of their population have 66 times fewer infections from the COVID-19 virus compared to those countries with a lower rate of malaria.

Finding #3: Countries suffering tuberculosis at a rate in excess of 0.1% of their population have 83 times fewer infections from the COVID-19 virus compared to those countries with a lower rate of tuberculosis.

Based on the results just summarized, my conclusions are:

Conclusion #1: Widespread use of face masks provides society with a powerful prophylaxis against the COVID-9 virus.

Conclusion #2: There is at least one malaria medication, already in use prophylactically in some countries, either intentionally or unintentionally, that is an effective prophylaxis against the COVID-19 virus.

Conclusion #3: There is at least one tuberculosis medication, already in use prophylactically in some countries, either intentionally or unintentionally, that is an effective prophylaxis against the COVID-19 virus.

Based on my conclusions just summarized, I offer the following recommendations:

Recommendation #1: Face masks should be required for all people who venture out and may come near anyone else. If we adopt this recommendation, we can safely ease social distancing measures.

Recommendation #2: To identify specific medications that can act as safe, effective prophylaxes against the COVID-19 virus, we need quick-turnaround observational studies that are superior and more detailed than mine. If we identify and adopt even one such prophylactic medication, then we can safely eliminate nearly all social distancing measures.

Details to follow in subsequent posts.

Monday, April 6, 2020

Surviving the Coronavirus: Part 10

Time for Cautious Optimism Edition

This will be the shortest post of this august series so far. I'll provide a little extra white space to allow the cheering to die down.

I just checked the number of infections in the U.S. The curve seems to be noticeably rounding.  I checked the doubling period. It jumped to 9 days. I've updated my chart and I present the current version below.  Behold.

If the doubling period continues to increase, I will gladly miss my prediction that we will have a million infections by the end of the month. We will still go over a million infections, by a substantial amount, but perhaps not this month.

The one-day jump from 6 to 9 days might be a one day anomaly. Alternatively, it may be more evidence that we are indeed flattening the hell out of the curve. I'll check again tomorrow. Assuming that I'm not one of the one-in-a-thousand of us infected, I might provide another update.

Saturday, April 4, 2020

Surviving the Coronavirus: Part 9

Good News! Bad News! Good News! Edition

The good news is that I was wrong, oh so glad to be wrong, about when we would reach a quarter million infections in the good ol' USA.

In Part 6 of this august series, the Don't Die! Edition, I reported that the number of infections in the US was 53,478 as of Tuesday, 24 March 2020. As a pop quiz in exponential growth, I challenged readers to guess how many cases there would be in a week, as of Tuesday, 1 April 2020. I predicted somewhere between a quarter million and a half million.

The good news is that I was wrong, oh so glad to be wrong. According to the wonderfully named worldOmeter, the number of infections as of Tuesday, 1 April 2020 was "only" 215,003.

The bad news is that I was wrong by only two days. According to the now world-O-famous worldOmeter, as of Thursday, 3 April, there were 277,161 cases in the good ol' USA. As of today, this moment, as I write type this, at 1612 GMT, at 9:12 AM Pacific Daylight Savings Time, there are 291,545 cases.

Would anyone like to guess how long before we get to a million US infections? I predict we'll exceed that dramatic but no-more-meaningful-than-any-other number by the end of this month, with a few days to spare. I sincerely hope that I will once again be proved wrong, and this time by a wide margin.

The good news is that the doubling time is increasing. The doubling time is the number of days required for the number of cases to double. If there are 10 cases on day 3 and 20 cases on day 5, then the doubling time is 2 days. Similarly, if there are 100 cases on day 30 and 200 cases on day 32, then the doubling time is 2 days. Small doubling times are bad (for pandemics, not stock portfolios). Very small doubling times are very bad.

What we want to see are very large doubling times. When the doubling time reaches infinity, the number of infections has reached its peak, and the numbers will begin to drop.

We can, and I will, extract approximate doubling times from the daily infection numbers. Before I do that myself, I will present a quick mathematically based (don't tell anyone) summary on how you might do it yourself.

TRIGGER WARNING! Look away for a few lines if you are offended by math.

We'll call the doubling time Td.

We'll call the number of cases on a given day Nt (for Number today) and the number of cases on the previous day as Ny (for Number yesterday).

We'll call the rate at which infections are increasing Ri. We can approximate Ri by taking the average of two infection levels (one day after the other) then using that average as the divisor for the difference in infections between the two days. In other words:

     Ri =  (Nt - Ny) / [(Nt + Ny) / 2]

Now the easy part. For a good approximation of the doubling time, apply the incredibly simple equation below:

     Td = 0.7 / Ri

That's it. That's how I will use the worldOmeter data to calculate doubling times below.

If, in the extremely unlikely chance that you would like a more thorough discussion, see the Wikipedia article on doubling times.

TRIGGER WARNING CANCELLED!  You can now look back.

Below, I present the trend in doubling times for USA coronavirus infections in the good ol' USA on a daily basis, based on the good ol' worldOmeter data, in a handy dandy Excel chart.

On 13 March, the Feds declared the pandemic to be a national emergency. Governors began mandating social distancing practices, slowly at first, then more aggressively. Ten days later (or so) the doubling time for coronavirus infections began increasing from around 2.5 days up to nearly 6 days as I write type this sentence. The doubling time will continue to increase, but we have a long, long way to go.

There is no way that the coronavirus will not extract a heavy toll on our country, and on other countries. We need to be aggressive about social distancing, particularly the geezer community among us. We need to get masks and gloves and other protective gear to those who are most exposed: the medical personnel and other first responders, the grocers, those who work in Amazon warehouses, those who deliver our goods. We need to develop and distribute an effective treatment quickly, regs be damned, at least reasonably damned. An effective treatment will allow us to relax, but not remove, the social distancing measures until our society reaches herd immunity with a combination of infection survivors and vaccinated citizenry. That herd immunity, approximately 60% of the population, might be more than a year away.

This is not the time for us to squabble, to deny reality, or to blame others for our own national circumstance. There will be plenty of time to return to those well-worn comfy shoes after we have won this war.

This, instead, is the time for each of us to point at ourself and ask "How can I help rather than hinder?"

Sunday, March 29, 2020

Surviving the Coronavirus: Part 8

Evil China Government Edition

Those of you previously familiar with the august blog realize that American governments (at federal, state, and local levels) are far from being exceptions to my skeptical scorn. The Skeptical Juror blog has, until this coronavirus crisis, focused on the great harm our governments (at the federal, state, and local levels) have inflicted on some of our fellow citizens. Some of those who allegedly serve us, far too many of them, have carelessly, foolishly, and all too often intentionally used our legal system to bring down great harm, even death, on the innocent among us.

It should therefore come as no surprise to my ever dwindling list of followers that I will make no skeptical exception for those who govern the Chinese people. I do not trust the Chinese government any further than I can throw it. In this specific case, my metaphor server is not failing me. I cannot throw the Chinese government even an angstrom; I trust the Chinese government not even a whit, whatever the hell a whit is.

I'll waste just a bit of textual white space to make a lame effort to calm all the hair-trigger racist-labelers out there. I have no unique animus or dislike of the Chinese people. They are my fellow Earthlings. I feel a kindred spirit with them knowing that, in both absolute and percentage numbers, they suffer far greater harm (than we do) at the hands of those who allegedly serve us.

With that background, in that context, I herein discuss a report from China claiming that hydroxychloroquine is not effective as a treatment for the Wuhan coronavirus. The report is mostly in Chinese, and my skills in that regard are somewhat limited. The abstract, however, is in English. I'll therefore provide a condensed version of the abstract so that you can consider it yourself, kinda like a pop quiz, before I tell you why I am skeptical of it.

Sharpen your pencils, gather your wits about you, and prepare to focus. Here we go.
Objective: To evaluate the efficacy and safety of hydroxychloroquine (HCQ) in the treatment of patients with common coronavirus disease-19 (COVID-19). 
Methods: We prospectively enrolled 30 treatment-na├»ve patients with confirmed COVID-19 after informed consent at Shanghai Public Health Clinical Center. The patients were randomized 1:1 to HCQ group and the control group. Patients in HCQ group were given HCQ 400 mg per day for 5 days plus conventional treatments, while those in the control group were given conventional treatment only. [...] 
Results: One patient in HCQ group developed to severe during the treatment. On day 7, COVID-19 nucleic acid of throat swabs was negative in 13 cases in the HCQ group and 14 cases in the control group. The median duration from hospitalization to virus nucleic acid negative conservation was 4 days in HCQ group, which is comparable to that in the control group, 2 days. The median time for body temperature normalization in HCQ group was 1 day after hospitalization, which was also comparable to that in the control group. Radiological progression was shown on CT images in 5 cases of the HCQ group and 7 cases of the control group, and all patients showed improvement in follow-up examination. Four cases of the HCQ group and 3 cases of the control group had transient diarrhea and abnormal liver function. 
Conclusions: The prognosis of common COVID-19 patients is good. Larger sample size study are needed to investigate the effects of HCQ in the treatment of COVID-19. Subsequent research should determine better endpoint and fully consider the feasibility of experiments such as sample size.
Bonus points to those of you who were skeptical of the integrity of my condensed version of the report's abstract. Gold stars to those of you what actually compared my condensed version with the actual abstract. You were probably shocked when you realized that I removed some percentages, ranges, and statistical confidence levels without noting the omissions with bracketed ellipses. I did so [I lamely claim, after the fact] solely in a good faith effort to make my condensed version of the paper's abstract more readable and understandable to the reader and understander. Also, the delay provided you with time to consider your skepticism, presuming you have any.

Here are the issues that jumped out at me.

#1. Why only 30 patients? Wuhan alone has tens of thousands of cases that could be studied, and China has apparently been routinely using chloroquine in some form as part of their treatment. So why only 30 patients? Why not a huge observational study of documented cases across China?

#2. What were the demographics of the test and the control groups? I realize you said that you randomized them between the two groups, but you didn't give us the demographics of the starting pool of 30 patients. Did you take them all from a senior citizens center? That seems doubtful, since the fatality rate probably would have been higher. Did you take them all from a youth athletic club? Given that all but one of the patients responded well to whatever treatment was provided, I'm going to guess that the test population consisted largely of younger people.

#3. And just how many times did you randomize before you settled on your test and control groups?  Only once? More than once? Be honest with us. This issue relates back to issue #2. What was the demographics of your final test and control groups? How did they compare to one another? Was either group representative of the entire population?

#4. What the hell was the "conventional care" provided to the control group? You never mentioned that. Based on your own test results, I think we want whatever you were giving to them.

I became aware of this report a few days ago. Since I had written several times of some version of chloroquine as being a good candidate for a possible treatment, "my top pick" as I recall, I pondered about writing a post presenting contradictory evidence.

"Write the post," said the little devil on my right shoulder, accusing me of confirmation bias should I not."

"Ignore that bastard," said the little devil on my left shoulder, accusing me of carelessly spreading false information should I write of the report.

"You're tired of writing these posts," said the little devil in my left ear. "Do some of the other stuff you have to do. Do something you want to do. Take some time for yourself. You deserve it."

"You have an obligation," said the little devil in my right ear. "You didn't have to start this series, which you repeatedly refer to as an august series, even though most your readers have no idea what you mean by that. You can't just stop now, as things are getting worse, just before they will get real bad, just when you might make a difference, even if only an itsy bitsy, teeny weenie difference."

So I listened to the devil in my left ear, and I went and worked on my impending series of books about Louise Conan Doyle being the actual author of the Sherlock Holmes adventure. Yesterday was the most pleasant, least stressful day I've had in a while. I took some time for myself. I deserved it.

I have this nagging guilt problem though. I still have database design work I should be doing to generate an income, which I still need. I still have several tons of work to do on a specific wrongful conviction case that I've been trying to correct for over a decade. I still have responsibilities to help prepare and protect those close to me from the coronavirus onslaught that is rapidly approaching. And I still have this blog post to write, since the readership has increased slightly and must be waiting with baited breath with bated breath anxiously.

Also, and this is the factor that finally compelled me to write this post, I've come across an 80-page Norwegian paper that describes how broadly, persistently, and effectively China is using chloroquine as a treatment. In my quick summary of that lengthy paper, China not walking the talk. They are telling others that hydroxychloroquine is not worth using, but they are using it themselves, big time.

The paper is entitled "Essential Takeaways from China’s Response to COVID-19." It is authored by Yun Zhou (biomedical Researcher from Wuhan, living in Norway), Dr. Niels Chr. Danbolt (MD, professor, University of Oslo), and Stefan Krauss (MD, professor, University of Oslo). I present their key points, strategy, and additional point below. I excise some of their footnotes and parentheticals. Other than that, everything that follows, beneath the divider, is theirs, not mine. See the original if you prefer. Otherwise, continue reading this most august blog post to the end.

I congratulate the authors on their paper, their professionalism, and their effort to save lives.


Key points:

1. The morbidity and mortality rates are so high that the virus causes the healthcare systems to be overwhelmed. The virus must be contained, and that explains the massive Chinese response with extensive quarantine measures.

2. While an approved drug for COVID-19 treatment does not exist, some drugs appear to be effective in treating the disease. One of these is the malaria drug chloroquine (both the phosphate version, and the hydroxy-variant). Chloroquine appears to be most effective if given early in the disease when symptoms are mild. This was reported in Chinese newspapers and other state-controlled media as early as early February 3, 4. Chloroquine is the drug most often mentioned in Chinese newspapers. It simple and fast to produce in large quantities and its side effects are well known and controllable.

3. For patients not tolerating or responding to chloroquine, three other drugs have been tried: Remdesivir, Lopinavir/Ritonavir and Umifenovir (Arbidol). All of these have moderate to severe side-effects, they are less studied, and they are more expensive to produce.

4. Chinese authorities have, according to our open-source intelligence, placed large orders on chloroquine, and we have got the impression that they maybe using this drug on a vast scale. Guangzhou Baiyunshan Guanghua Pharma has resumed full production capacity and has a daily capacity of 2 million tablets, suggesting that the Chinese authorities believe that chloroquine is effective.

5. A key point is that Western publications have not caught up with the above information as it is only available in Chinese. The authors of this memo are concerned that Western authorities (e.g. CDC and WHO) are unaware of important information that can be used to effectively deal with the COVID-19 pandemic. Information on the potential benefits of chloroquine for treatment of COVID-19 mediated disease is beginning to appear in Western media.

6. To what extent chloroquine treatment has been a key factor in the apparent Chinese success in fighting COVID-19 is unknown, but the evidence for a key role of chloroquine in this epidemic is compelling and needs to be investigated.

7. Our sources indicate that chloroquine administered at a sufficiently early stage may lower the number of patients that will require hospitalization.  In fact, this is what the Chinese have tried to do. Early treatment of infected people in Wuhan City reduced the percentage of severe conditions from 38% to 18%. In contrast, when the disease has progressed into a serious condition requiring intensive care admission and artificial ventilation, the treatment is less effective and a significant number of patients will die.

To summarize:

a. There is an existing drug, well tested, well documented and with manageable side effects, which is neither exceptionally expensive nor difficult to produce and is fairly effective if administered at the correct time.

b. In order to maximize the effectiveness of chloroquine it will be necessary to identify infected patients as early as possible through extensive testing with a rapid turn-around time.

8. There are also rumors that chloroquine may prevent the development of the disease if given at smaller doses to asymptomatic individuals.  If this is correct, then prophylactic treatment of people at risk (e.g. health personnel and individuals with underlying conditions) may be possible.

9. A high percentage of infected people may be absent from work for months and the Chinese are becoming stricter with respect to declaring an infected patient disease-free. Effective March 6th, 2020, they only release infected patients from quarantine after they have developed COVID-19 neutralizing antibodies. Infected patients with no or minimal antibody response are kept in quarantine as there is increasing evidence that they continue to shed virus and therefore can infect others. We have also been told by friends in Wuhan that China is considering 4 weeks of quarantine rather than the current recommendation of 2 weeks.

10. There are speculations that some patients die from an uncontrolled immune response (a.k.a. “cytokine storm”) and the immune suppressing drug Tocilizumab is being tested to prevent or stop this serious complication.

11. There are discussions whether ADE (antibody-dependent enhancement) may complicate vaccine development and pose a significant risk if reinfection occurs with a mutated virus.

12. Because the disease originated in animals, it may be worthwhile to check whether domestic animals need protection.

Potential strategy implications based on the above findings:

1. More resources need to be allocated to learn more about what has actually happened in China and what the Chinese have learnt from it. Relevant agencies should search Chinese sources and also interview Chinese doctors and other relevant persons. This latter part may be somewhat challenging, for obvious reasons.

2. The capacity for early diagnosis need to be radically expanded and combined with a decentralized access to relevant drugs (including chloroquine phosphate and/or hydroxychloroquine). The majority of the infected may then be able to treat themselves at home under remote medical guidance. This could have major implications because the number of patients admitted to hospitals would decrease and fewer people would need long sick-leaves. This in turn would also reduce the infection rate among healthcare workers.

3. The production of chloroquine in sufficient amounts to cover the entire US population, and hopefully also those of US allies, should be contemplated. At present, we are dependent on the Chinese for production both of chloroquine and the central materials needed to make it.

4. The West should increase own production of a panel of anti-viral drugs and antibiotics. Anti-viral drugs reported by the Chinese and others to be effective, are not available in sufficient quantities.

An additional point:

It is currently speculated whether chloroquine is able, not only to cure, but also prevent the onset of a Corvid-19 infection. How can we get an indication if it can work prophylactically? Patients suffering from rheumatoid arthritis and patients with systemic lupus erythematosus are often receiving hydroxy-chloroquine to keep the disease in check. If these patients do not get infected (or have a reduced risk to get infected) with coronavirus, then a likely interpretation is that chloroquine may have a protective effect. We got the following information from a hospital in Wuhan: "In the early stage of the study group, through the clinical analysis of 178 patients with new coronavirus received by the hospital from December 2019, it was found that none of them has systemic lupus erythematosus. After that, in the consultation of 80 patients with systemic lupus erythematosus treated by dermatology department of the hospital, it was found that they were not infected with new coronavirus pneumonia."

This is at current only an indication. We therefore propose that the US authorities explores health registries to identify a potential connection between hydroxychloroquine treatment and Covid-19 prevalence. Information could be gained within days. Particular good sources may be European countries and South Korea, but also China. If hydroxychloroquine has a protective function, we may -in combination with traditional measures (quarantine etc.) – be able to bring the transmission rate below 1 (each infected will infect on average less than 1 other person) and the epidemic may be contained in short time.

Friday, March 27, 2020

Surviving the Coronavirus: Part 7

How Bad Could It Be? Edition

In Part 3 of this august series, the part that I have recently labeled as the Diamond Princess Edition, I respond to the claim of a Stanford epidemiologist that perhaps, maybe, kinda, the coronavirus is not so bad after all. In summary of that edition, the Stanford epidemiologist made a needlessly crappy assumption, ended up with a needlessly crappy result, and needlessly crappily misinformed his readership. I've since seen his needlessly crappy result quoted by others hoping that they can hope this problem away.

Today I see some similarly crappy analysis by John Lee, writing for The Spectator: "How Deadly is the Coronavirus? It's Still Far from Clear." John Lee doesn't claim to be a Stanford epidemiologist. Instead he claims to be "a recently retired pathologist and a former NHS [Britain's National Health Service] consultant pathologist." I guess I'll be punching up, again.

In my apparently-not-so-humble opinion, the former NHS consultant pathologist goes off the rails early in his article when he writes:
The simplest way to judge whether we have an exceptionally lethal disease is to look at the death rates. Are more people dying than we would expect to die anyway in a given week or month?
Apparently, woefully, the recently retired pathologist failed to read Part 1 of this august series, the part that I have recently labeled as the Deadly Peril Edition. Had he, he would have understood that the death rate, more properly the case fatality fate (CFR), is only one of two critically important pieces of information we need to make a first order assessment of how bad a pandemic might be. The recently retired pathologist made the same stupid mistake as did the Stanford epidemiologist. Both considered the CFR; neither reasonably quantified the eagerness with which the Wuhan coronavirus spreads.

Because I have higher regard for the intelligence and moxie of my readers than the former NHS pathologist apparently has for his, I'm not going to sugarcoat it. One can make a first order assessment of how bad a pandemic might be once one knows two characteristics of the bug: the CFR and Ro, also known as R zero or R naught, also known as the basic reproduction number, also known (by me) as the starting reproduction number.

The reproduction number tells us how many uninfected people an infected person will infect. The reproduction number varies over time depending on the number of people who are immunized (naturally or artificially) and on social behavior response. While the reproduction number is greater than 1, the number of infections will grow. When the reproduction equals 1, the number of infections will remain constant, as new cases exactly equal the number of cases resulting in cure or death. While the reproduction number is less than one but greater than zero, then the number of infections will fall. When the reproduction number equals zero, the bug can no longer spread.

If the bug can no longer spread because society has reached herd immunity (naturally and/or artificially) then the reproduction number will be permanently equal to zero. If the bug is no longer spreading because people are hiding in nooks and crannies (as they should until a decent treatment is available), then the reproduction number will be temporarily equal to zero. The bug is still out there, lurking, waiting for people to re-emerge, waiting for winter weather, waiting for people to stop wearing masks and stop washing hands. As long as the bug is out there, and as long as we don't have natural and/or artificial herd immunity, the reproduction number will increase, flatten, and decrease in waves as environmental and social conditions allow.

In terms of assessing the potential mortality of a virus or a bacteria, we are interested in a specific reproduction number. We are interested in Ro, the starting reproduction number, the value as it exists early on, when people don't recognize the disease as a pandemic in the making, before people begin to scrub up, mask up, hide in the nooks and crannies, before they become immunized, naturally or artificially. We can estimate Ro for an specific disease based on the experience of a specific population. Based on the unfortunate specific population of the Diamond Princess floating petri dish, the estimated Ro of the Wuhan coronavirus is 2.28. (See Diamond Princess Edition.) Based on the unfortunate specific population of Wuhan, where the coronavirus first struck with fury, the Ro is 2.28.

Once we have the starting reproduction number, we can determine the percentage of the population that will have to become immunized (either by surviving the infection or getting an effective vaccine) in order to created herd immunity and permanently drive the final reproduction number to zero. As I explained in the Deadly Peril Edition, the calculation is simple.
Herd Immunity Fraction = 1 - 1/Ro
Since I would somewhat rather be labeled a shipist than a racist, I'll use the Diamond Princess Ro for the calculation. If the Ro is indeed 2.28, then 56% of us must survive an infection or be effectively vaccinated so that we can all benefit from herd immunity.

Now that we have the starting reproduction number, which gives us the herd immunity fraction, can we begin to make sense of the case fatality rate. I'll use a CFR of 0.77%, based on the South Korea experience. (See Deadly Peril Edition.)

Assuming no vaccine, then 56% of a given population must get infected in order to create herd immunity, and 0.77% of those infected will die. To express this in the form of an equation (just this once, I can stop whenever I want, I swear) I'll introduce a new term that I will call the Potential Death Toll Fraction, to which I will assign the acronym PDTF.
PDTF=Herd Immunity Fraction x CFR = 0.56 x 0.0077 = 0.0043 = 43%
"Hello. I'm The Skeptical Juror and I'm an engineer. I haven't formulated an equation since my last post."

Without identifying the loopholes in the coronavirus, and without leaping through them, then the PDTF for any given population is 43%. Given that the population of the good ol' USA is around 325 million, the PDT is 1.4 million fellow Americans dead of the virus. Given that the population of the good ol' Earth (my favorite planet) is 7.5 billion, then the PDT is 32.2 million fellow Earthlings dead of the virus.

That's nothing to sneeze at, even though sneezing is not one of the symptoms of the disease.

Here's the good news. The PDT (potential death toll) need not equal the ADT (actual death toll), and it certainly won't. To fight back, and to save more than a million American lives (and tens of millions of our fellow Earthlings), we need to:

1. Flatten the hell out of the curve. Those of us most likely to succumb to the disease and those of us most likely to spread it to others must head for, and remain in, our nooks and crannies.

2. Make available an effective treatment / cure. There are some candidate treatments out there. We need to test the most likely of them quickly. If they fail, we need to be ready with more to quickly test and distribute.

3. Develop an effective vaccine. All the smart people say this is a year to 18 months off. We can't wait that long. That's why we need the effective treatment quickly, conventional protocols be damned, full speed ahead.

If someone sees a better path forward, please let me know. Do not, however, be like the Stanford epidemiologist or the former NHS pathologist. Do not talk to me about just the death rate. I'm sick and tired of hearing about just the death rate. Talk to me about both the CFR and the R, and how we can reduce both of those deadly numbers.

Wednesday, March 25, 2020

Surviving the Coronavirus: Part 6

Don't Die! Edition

There are now various geezers senior citizens out there talking about how they are willing to risk death if it means saving other lives by saving the economy. In other words, more specially in my words, they are willing to take a bullet for the team by stupidly not flattening the curve as much as they could. Glen Beck has just recently volunteered for the heroically-foolish geezer ranks, though he admits to not quite yet being a geezer.
I mean, I'm in the danger zone. I'm right at the edge, I'm 56. In Italy they're saying if you're sick and you're 60, don't even come in. So, I'm in the danger zone. I would rather have my children stay home and all of us who are over 50 go in and keep this economy going and working, even if we all get sick, I would rather die than kill the country. 'Cause it's not the economy that's dying, it's the country. 
It's a noble thought, but it's stupid. It's exactly the wrong thing to do. And if only not-quite-a-geezer Beck had been reading this august blog, he would have known better.

Consider, for example, my sister. She is not "right at the edge" of the danger zone; she's 70; she can see the edge of the danger zone only if she squints. She's been insulin-needles-several-times-a-day since she was a teenager. She is now battling a theoretically controllable form of leukemia, one that was diagnosed on the anniversary of the day her husband died of cancer, at home hospice. Her battle with leukemia, coupled with some mistakes at a hospital, has left her with reduced liver, kidney, and lung function. She could, in a foolish act of heroism, not isolate herself. She could Glen Beck it, go out and about, economic guns ablazing, trying like hell to stimulate the economy, trying to save it, trying to save the country.

But she shouldn't, and she doesn't, and I love her for it.

Instead, she isolates herself so that she doesn't catch the disease, so that she doesn't infect others, so that she doesn't get transported to the hospital, so that she doesn't add to the burden that most hospitals will soon be facing, so that she doesn't deprive someone else of the medical care that might save their life. She flattens the curve as much as she can so that we can hang on until we have an effective treatment, so that we can save a million lives.

Glen Beck, apparently, doesn't believe in exponential growth. Things aren't so bad today, he seems to reason, and they might be worse tomorrow, but that still won't be so bad. He's dead wrong if he thinks anything like those thoughts I have improperly attributed to him.

People simply can't think in terms of exponential growth. To see exponential growth in effect as it pertains to the the coronavirus, take a peek at the following numbers, if you dare. They show the total confirmed cases in the U.S. at the end of each Tuesday.

Jan. 14  — 0
Jan. 21  — 1
Jan. 28 — 5
Feb. 4   — 11
Feb. 11  — 14
Feb. 18 — 25
Feb. 25 — 59
Mar. 3   — 125
Mar. 10  — 1,004
Mar. 17  — 5,902
Mar. 24 — 53,478

Do you want to make a guess at how many cases there will be next week? I'm going to guess that there will be somewhere between and quarter and a half million, and still accelerating. Do you want to make a guess at how many will be out there the week after next? How about the week after that?

We're starting to hear of infections among celebrities and politicians. Soon we'll be hearing of infections closer to home, among people we know. Soon thereafter, we may begin hearing of deaths among people we know, and love.

We're certainly going to be hearing of hospitals struggling to get through this. If we're not careful, we're going to hear horror stories of people dying in hospital hallways and waiting rooms, or in tents or makeshift triage shelters.

So, Glen Beck, don't go out and about. Recognize that the most vulnerable of us out there are the ones who must most thoroughly isolate, since we are the ones most likely to overburden our health care system, since we are the ones most likely to take others with us to the grave.

So, kind and gentle geezer readers, do not model your behavior after Glen Beck, who can sit behind a microphone in a home studio if he so chooses. Model yourself after my sister, who sits alone, heroically, with a smile and a sense of humor.

Stimulate the economy as she does. Purchase things, but purchase them from home. And leave a really nice tip for the younger, less-at-risk, less-likely-to-need-the-hospital generation. And thank them, sincerely, for their service.

Stimulate the economy as The Skeptical Spouse and I do, because we can still afford it. We are paying for routine services even when those services cannot being supplied. Today, we will be sending checks to the two small business people who routinely cut our hair. The checks are in the guise of informal, unwritten (probably-won't-be-strictly-enforced) gift cards for future redemption.

Stimulate the economy as best you can, given your unique set of circumstances. But, if you are a geezer, particularly if you are even more of a geezer than Glen Beck, don't be foolishly heroic by rushing headlong into a viral machine gun nest when an Abrams tank could do it more safely.

Be like my sister.

Sunday, March 22, 2020

Surviving the Coronavirus: Part 5

Chloroquine Edition

Yes, it's all over the news now. Apparently someone read Part 2 and/or Part 4 of this august series, acted on it/them, and now the world is saved.

Perhaps I overstate the matter in one or two tiny aspects, but there is certainly good news afoot.

150 million or so doses of chloroquine (or some variant thereof) are being promised by various manufacturers. China's protocol calls for 2 tablets per day for 10 days. The 150 million doses would be good for 7.5 million cases. South Korea's protocol calls for 1 tablet per day for 10 days. The 150 million doses would be good for 15 million cases.

I've come across a nice looking site out there called Spin, Strangeness, and Charm. It's not a site about sub-atomic physics, as most of you immediately presumed. It is instead about media and political spin, the strangeness of the world around us, with a sprinkling of charm to keep everything in perspective. It's running frequent updates regarding the coronavirus, the updates seem to be rational and well informed, and everything there is free, so good on the fine folks at Spin, Strangeness, and Charm.

In a very recent post, "COVID19 update: a brief look at three possible drugs," TFF at SSC embedded a video from the questionably-named medical site Personally, I don't like combining thoughts of medical treatment with the word cram. The fine folks at Medcram, though, were apparently using "cram" in the sense of "cramming for a test." The site's banner reads "Medical Videos and Lectures Explained Clearly." Their underline, unlike mine, is hand-drawn, bold, colorful, and eye-catching. But I digress.

The video was quite well done. 17 minutes or so long, as I recall. When I attempted to play it a second time, it wouldn't play. I received an error message. When I tried to play it a third time, I got an error message. When I tried to play it a fourth time (and I really did do that), I got an error message. My guess is that Part 2 and/or 4 of this august series indirectly but eventually led to so many Google hits for "chloroquine" that the Medcram server was overwhelmed.

Somehow, astoundingly, blessedly, the server serving this site has been able to withstand the traffic. But I digress.

As a public service, I'll try to summarize the Medcram video, since you can't watch it yourself. (I just tried to view it again. Same result. Perhaps I'm part of the problem.) Since I'm not a doctor, physician, epidemiologist, biomedical researcher, or involved in any fashion whatsoever in the medical field, I may get things a bit wrong here and there.

Hang on. Buckle up. Here we go.

A virus is a strange creature, not at all like a human, or even a human cell. Instead of multiplying through dividing, as do our cells, it replicates itself inside our cells only after creating something that scientists cleverly call replicase. Wikipedia, which I can still get to, describes replicase in simple, understandable fashion.
RNA-dependent RNA polymerase (RdRP, RDR) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. This is in contrast to a typical DNA-dependent RNA polymerase, which catalyzes the transcription of RNA from a DNA template.
The coronavirus, and others of its evil ilk, have a loophole that we might be able to jump through. Coronavirus replicase hates zinc, because zinc kills coronavirus replicase. Good for us, bad for them. Don't go rushing to your store for zinc tablets, though, because our cell walls will not allow zinc to pass through without an appropriate escort. (The clever among you can now see where this is going.) Our cell walls, however, allow zinc to pass IF the zinc is escorted by Chloroquine!!!!!

If this works in practice as well as it works in the video, which is not working at the moment, then here's how you can survive the coronavirus. Have a medical profession administer chloroquine, or one of it's even better variants, make sure your cells are smart enough to allow the zinc to enter if escorted by chloroquine, watch the coronavirus already in your cells wither on the vine (my metaphor server is obviously down), get better.

But wait, there's more. The fine doctor in the fine video pointed out some very interesting comparisons between the outbreak in South Korea and the outbreak in Italy. Both countries have similar populations, 51 and 60 million respectively. Both countries have similar infections per million people. HOWEVER, the South Koreans have an order of magnitude fewer deaths AND more than an order of magnitude fewer instances of critical cases per infection.

Though the video doctor did not say so directly, it seems to me that the differential rates of critical cases per infection rules out the primary reason being differences in age distribution, testing, social distancing, wearing face masks, etc. There seems to be some difference in how the patients are treated after they have been infected. One difference is that the South Koreans have apparently been treating their patients with chloroquine while the Italians apparently have not.

The video doctor actually expressed cautious optimism that chloroquine will prove in practice to be an effective treatment. He did caution that we have been fooled before by early promising results, and that is all we have now for chloroquine. I already pointed out (in Part 4 of this august series) that the HIV drug that was once thought promising, and was being used in China, has since been shown in better controlled testing to have no effect.

As far as I am concerned, the best strategy for surviving the coronavirus, both as an individual and as a nation, is to flatten the hell out of the curve while quickly identifying and making widely available an effective cure. The chloroquine may be that effective cure. If not, we need to quickly move on to the next best candidate in the long list.

We need to save both our lives and our economy. To save us and it, we absolutely must quickly discover and widely distribute an effective cure. There is no other good option.