As reminders…

Alpha–Variant first identified in the UK

Beta–Variant first identified in South Africa

Gamma–Variant first identified in Brazil

Delta–Variant first identified in India

Also as a reminder:

–The Marburg update is a little complicated by events on the ground in Guinea. This past weekend, Guinea had a coup d’etat. That is going to leave official reporting about Marburg a little suspect until they figure out who, exactly, is running the country. So far, though, no reports of new cases of Marburg.

–Nipah virus has been found again in Kerala, India. Kerala has had outbreaks of this virus a couple times in the last 3 years. This time, a 12 year old boy died of disease over the weekend. India believes it has all known contacts traced already, and is following.

Nipah virus, in brief, is typically acquired from animals, with outbreaks traced to contact with infected bats, horses and pigs. The primary reservoir appears to be bats, and thus far, has only been found in Southeast Asia, ranging from India through Malaysia and the Philippines. The virus can be spread person to person, and is respiratory. In fact, the more and more severe the respiratory symptoms are, the greater the chance of spreading it to someone else. Fortunately, it is nowhere near the efficiency of coronavirus in its ability to spread by the respiratory route. The bad news is the high mortality rate. Once in the lungs, the virus spreads to the brain, where most of the damage is done by attacking blood vessels inside the brain itself (although it can, and does, replicate in brain cells). Mortality in previous outbreaks has ranged from 30-91%, and there is no known effective treatment, although ribivirin, in small case numbers in the small previous outbreaks has hinted it might reduce the mortality rate some.

We’ll continue to follow just because of the sheer lethality of the virus, but so far, only one case and a limited, and known, contact chain in India.

–In coronavirus news, still a lot to cover.

–The most important update is a paper in JAMA published after we went to “press” last Thursday. You can find it here. The long story made short is that they went back to blood donation samples and tested for COVID antibodies. This is useful, now that we have pretty good kits for those antibodies available. In July of 2020, only 3.5% of the US population (give or take a bit) had antibodies to SARS-CoV-2. This was the prevaccine days, as you’ll recall. By May of 2021, 20.2% of the population had antibodies consistent with catching, and recovering from, SARS-CoV-2 (so more than just the spike protein antibody is present).

Yes, that means 1 in every 5 people, on average, in America, has already been exposed to SARS-CoV-2. Yet, there are only ~40 million confirmed positive cases in the US–or about 1 in 9 Americans.

This suggests asymptomatic, or at least so-mild-they-didn’t-get-tested-COVID, is running approximately 1:1 with confirmed cases. That is consistent with our estimates from about 14-18 months ago.

–Yes, that means the case fatality rate for COVID overall (the CFR) is about that of a bad flu, once you adjust for this new data.

That’s overall, though.

Again, the elderly, the immunocompromised, and those with particular risk factors (obesity especially, but underlying heart/lung disease, and pregnancy is actually starting to climb a bit too), the CFR is higher.

–The main public health threat is NOT the CFR–it’s ability to hospitalize people quickly, take up beds, and increase overall mortality.

–So how easily can SARS-CoV-2 do that now? Well, based on that JAMA article, 83.3% of the US population has effective antibodies to SARS-CoV-2, either from previous infection OR vaccination.

Unless a variant shows up that is truly unique enough to slip by those antibodies (and that is unlikely), SARS-CoV-2 is going to have a very tough time threatening the healthcare system in the US.

–Yes, I know you are reading about ICUs that are near or completely full. Hospitals that have delayed or halted elective surgeries again. This is a combination of persistent staffing issues and the delta wave case volume. And honestly, how many industries at this point cannot find enough people all of sudden? Where did everybody go?

Regardless, at 83.3% combined resistance in the US by May of this year, and climbing since, herd immunity is damn close.

–The other takeaway is that the UFC back-of-the-envelope calculations I made all last year projecting when the US would hit the approximate herd immunity point were off. This data suggest that from July 2020 to May 2021, I was over-estimating the rate of spread among the general population. Not a huge surprise, since we were relying heavily on numbers from sports organizations doing screening tests of participants and coaches–who were in much closer and more frequent indoor contact than most of the general population. So their positive rate was probably the high end versus the rest of the country, which was, on broad, nation-wide average, a little more isolated.

–Exciting news–we will get a real world test of how close the US is to herd immunity by the end of this week, early next at the latest!

Multiple independent experiments of (mostly) outdoor congregations of tens to hundreds of thousands of people, in close contact, for hours at a time, took place all through the Labor Day weekend. You can see one of them as it was in progress here.

Yeah, if -that- doesn’t stabilize or lift case numbers in the US, delta is conclusively on the retreat and chances of herd immunity being reached very, very soon are high.

–In other news, back down unda’ in Australia, they are testing out a shockingly authoritarian app to enforce mandatory quarantines. Citizens must by mandate load a government app on their phone. If the app pings them, they have to show the app (and thus the police) they are quarantined where they are supposed to be. If they are not, the police will be dispatched to their location. I am not making this up–you can find reporting on it here.

–Meanwhile, back in the US.

—“So if we hit herd immunity, even though they keep trying to adjust the metric, we can go back to normal, right?” I hear you ask, Hypothetical Reader.

To which I say:

That is a fundamentally political question, and I am less able to predict that. Just looking around the world, China is still shutting down entire cities for a handful of reported cases. Australia has clearly found China’s approach inspirational. Meanwhile, Sweden announced that they plan on ending what few restrictions they actually have pretty soon. We mentioned last year that it will be hard for some to come back from the war. Hence, every new variant of SARS-CoV-2 gets breathless headlines before the petri dish testing is even complete to suggest how worried we might be, let alone any real world data we have on it. One case of Nipah got immediate headline comparisons to coronavirus.

You have a wide range of responses and attitudes just in the US, with opposing archetypes of Florida and New York/New Jersey as an example.

Even at effective herd immunity, a level of resistance in the population where hospitalization from COVID becomes, oh, we’ll say flu-like or less, there will be places that keep calm and carry on in the presumption that it will not threaten hospital shutdowns and there will be other places that will likely react to that because it could get worse.

I can guess where those reactions will be more or less likely, but only guess.

I can guarantee that there will be some degree of angst for continued positive screening tests in asymptomatic patients that inflate “new cases” counts for at least a little while though. At least until you get a more clear separation of that from hospitalizations, which should start to happen when herd immunity hits.

–And yes, even with herd immunity close, because of their higher individual risk and previous data we discussed, I would consider a booster if over 65, immunocompromised, or otherwise at very high risk from COVID.

–The ivermectin saga continues, and thanks to a reader over the weekend who was concerned by an interview of an Oklahoma doctor, AND about the truth of the reporting of that interview. The report from the local Oklahoma station implied some Oklahoma ERs were being overwhelmed by ivermectin overdoses, and having to turn away gun shot victims. There was a similar story, although not picked up nearly as much as the Oklahoma one, of overdoses in Mississippi as well.

I did not think the Oklahoma report had been picked up by major news organizations when giving my take on the story to the reader.

I was wrong.

Rolling Stone picked it up, and prominently featured the story. So did Rachel Maddow and a number of medium sized news outlets. The Guardian and Daily Mail in the UK also covered the Oklahoma report.

Here’s the thing though–it’s hard to get access to ivermectin. No really. It’s not an over the counter drug. You need a prescription from a doctor, who, if they are competent, is going to give you a prescription for a human sized dose. As long as you take that dose correctly, and the pharmacy dispensed it correctly, an overdose is extremely unlikely.

The claim, which followed and yes, used the language of “horse dewormer,” was that the overdoses were happening because people were taking horse sized doses of ivermectin.

Even your vet, if you brought your dog to them, would not be prescribing a horse sized dose for a dog.

The only way to have a horse sized dose of ivermectin around is to have or work around livestock that at some point were prescribed ivermectin, which you could then divert. Even in Oklahoma and Mississippi, the number of Americans who have or work around livestock is not a very large number.

You would think that sense would be common, especially among journalists who have (or should have) an acutely tuned bullshit detector.

Sadly, it was not. It wasn’t until well after all of those mentioned outlets above took the story and credulously ran it that someone contacted the hospital system employing the interviewed physician and the Oklahoma and Mississippi poison control centers.

Lo and behold, the hospital system said that particular guy had not worked in the ER in the last two months and had not seen a single case of ivermectin overdose. Oklahoma, as an entire state, has had only 11 -suspected- cases of ivermectin overdose since May. Similarly small numbers for Mississippi.

A few phone calls could have saved a number of “journalists” some major embarrassment here.

–A few takeaways.

1. The physician interviewed was misquoted, but only slightly. He was a little bit over his skis, similar to the Mount Vernon physician arguing against mask mandates in schools we covered about a month ago. Physicians are people too, and just as prone to the same confirmation biases and tribal biases as anyone. I am sure both of them mean well, and were being vocal in defense of deeply held values and beliefs. I am also sure that they went farther than the facts in doing so.
2. It can happen to anyone. And I am willing to bet that these guys perceive themselves as being on different R and D teams. Willingness and ability to let your all too human cognitive biases get you over your skis is not unique to one side or the other.
3. The media is useless. Worse than useless. From “Plandemic” through failure to verify surprising claims with obvious and easily obtainable facts, media coverage has been, across the board, terrrrrrrrible through this pandemic. How many novels of these updates have I had to write because of it?
4. If they are this bad covering one of the most impactful events in our life times, how much else are they getting wrong? Think about your own area of expertise and when it gets reported on in the mainstream. Could you be doing your own update series on what they are getting wrong? I’m willing to bet, based on their performance here, you could.
5. So who are you really going to trust about your world and what is shaping it? Remember our modification of Ben Hunt’s rules. Why am I reading this? Why I am reading this now? How does this make me feel? Why might someone want me to feel this way? You’re still gonna get got sometimes. You can’t always have this shield up. But it will protect you, and keep you more balanced, the more you practice it. You will see just a little bit more truth, and react to it better. You’ll make better decisions, and whomever makes the best decisions wins.

–“The Intercept” obtained documents under FOIA that showed a grant application from EcoHealth Alliance for $3.1 million from 2014-2019 from the Dr. Fauci-led National Institute of Allergy and Infectious Disease. You can read about it here. This included a shade under $600,000 to create “chimera” coronaviruses crossing parts of bat and human coronaviruses to see if they could make the bat coronaviruses more infectious to human and mouse cells as part of the “Understanding the Risk of Bat Coronavirus Emergence.” The work was conducted in Wuhan.

Yes, that is absolutely gain of function research, and yes, certainly makes plausible the intermingling of human and bat coronavirus elements in SARS-CoV-2. This is NOT a smoking gun for a lab leak, but…man… certainly involves research that could easily have created SARS-CoV-2 and accidentally let it out in the right place in China.

In other remarkable coincidences, head of the EcoHealth Alliance Dr. Peter Daszak was emailing Dr. Fauci in April of 2020 to thank him for his “brave” stance in getting out early and definitively declaring that virus was of natural origin. You can read about it here. You’ll also note that the $600,000 grant to EcoHealth Alliance to study coronaviruses is mentioned–it was known. But the specific project and the details of what they were doing (creating crossovers of bat and human coronaviruses to make them more transmissible) took The Intercepts’ FOIA work.

That “thanks for not calling it a possible lab leak” email…is not a great look right now.

–Again, gun to my head, accidental lab leak is like 51% vs 49% more likely than not. But I also don’t expect definitive resolution within my lifetime given international relations at the moment.

–BUT… the FOIA work to reveal that gain of function research with highly contagious, pandemic possible viruses was occurring in Wuhan does let us talk more generally about the wisdom of such research. The benefits are often sold as identifying the major changes that the virus would need to become worse, so that we can proactively have drugs in the arsenal if that were to happen in the wild. Other arguments are to keep ahead of potential bioweapons, under the assumption that someone, somewhere, will be doing gain of function for nefarious purposes.

So you can easily talk yourself into the benefits of this, which is why EcoHealth Alliance proposed it, and undoubtedly why the NIAID funded it. Why not get out proactively in front of the most dangerous possible variants of potentially pandemic diseases by creating them in a controlled lab environment, and then studying how to stop them?

Yes, you have literally seen that movie before, when scientists used gene editing to gain of function their way to dinosaurs.

Just as Michael Crichton warned us, the hubris here is that you can control what you create, and that the lab will never have a leak. Because if you engineer a super bug, and accidentally let it out before you have found how to cure said super bug, you’re going to have a real bad time.

The risk of that leak is never 0. You can minimize it, and convince yourself that the chance that it would happen is so remote that it might as well be 0–but it’s still not 0. The problem of convincing yourself of the benefits and forging ahead anyways is the risk of ruin if that improbable event occurs. Some of you may be hearing echoes of Taleb in your heads, as he defined the now ubiquitous “black swan event” as a highly improbable, but highly significant, if it occurs, event.

The accidental release of a super bug you have created by gain of function research is a black swan event. The mistake that happens is looking at the odds of that escape as an ensemble probability, not the time probability it really has. For an explanation of this, and why it is significant, let’s go back to Taleb describing your cousin Theodorus Ibn Warqa’s experience in a casino on a single day versus many days at this link here. The entire chapter, and really the entire book “Skin in the Game”, is worth your time, but you can stop at the end of the casino analogy.

Or to put it another way, if the chance of your gain of function coronavirus escaping the lab is 0.001% on any given day, because so many containment failures would have to happen at once, you might think you’re safe. The problem is the virus has a 0.001% chance of escaping every single day. If you store it for 3 years, with a 0.001% chance of escaping per day, the odds it will breach containment are nearly 100%. Eventually, there will be one day when everything does go wrong.

Since the consequence of that is ruin, or…

Taleb would argue, and I agree, that you cannot safely do this kind of research. As a rule.

And it doesn’t just apply to biology. Remember “The Terminator”? The non-zero chance that a superintelligent AI, if we were to deliberately or accidentally create one, would kill us all is why there is serious ethical debate in tech circles over how close to that line to go. For an interesting story on AI applications of this probability concept, check out the novel “After On” (although the human characters are cliches and never really develop), for a plausible way a superintelligent AI could be created in a world like ours, and what that might be like. Or, more mind bendingly, why it may already exist… : )

That this is an obviously reckless thing to do may be why there has been the type of obfuscation that has required FOIAs to learn that, well, yes, they were modifying coronaviruses to see if they could make them worse. But totally so they could treat them better!

–Yes, the world is still apparently set to “maximum stupid.” Choose accordingly.

–Speaking of choices in a maximally stupid world, fun and short quiz here at the link…

–Lastly, before I get inundated with questions for reactions to the President’s vaccine mandate speech… remember a few things:

1. Vaccine mandates that do NOT account for the multiple publications showing natural immunity from recovered COVID patients are behind the state of the science. Antibody testing would pick up both vaccinated and natural resistance to SARS-CoV-2 if you really want to insist on it, and be consistent with the known biology.

3.

–The politicization of everything, including health and vaccines, makes me very sad.

–The chances of catching Nipah or Marburg this week are equivalent to the chances your cousin left Taleb’s casino a winner.

–The chances of catching coronavirus in many places in the world still is equivalent to the chances I’m about to blow your mind with some cool archeological engineering. Make sure you click this link and turn your volume up!

<Paladin>