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

Omicron–Variant first identified in South Africa

Updating the chart above:

Ancestral: B.1.1.529 Omicron (and pretty much all the BA.X cousins)

Transmissibility: All the +

Immune Evasiveness: All the +

Vaccine Effectiveness: Check (for hospitalization)

Also as a reminder:

Marburg

–Details are sparse and difficult to come by. A very short report from Reuters quotes WHO officials with 2 new Marburg cases in Ghana this past week, bringing us up to 4 confirmed positive cases. The same Reuters report suggests that at least one more health area is now involved with at least one of these new cases. Ghana news reports that I can find suggest that one of the 2 new cases has also died, and was a family member of one of the first two cases–but also that this person did not show symptoms until AFTER the 21 day incubation period. Either this strain of Marburg is a little slower burn, and thus the observation and quarantine windows may be too short, or they got infected by whatever or wherever their deceased “Patient Zero” relative got it. Either way, the WHO and Ghana health officials appear to be doing their best to trace contacts and quarantine close contacts of the new cases. We’ll continue to watch this one, but pandemic risk remains quite low.

Monkeypox

–Yes, I saw that the WHO has moved the monkeypox outbreak to be an official global health emergency. You may recognize an official WHO global health emergency from other global health emergencies like Zika virus in 2016, the West Africa Ebola outbreak of 2014, and, of course, the coronavirus pandemic.

This current declaration was not without controversy. The WHO’s own expert panel could not reach consensus about calling the monkeypox outbreak a “global health emergency”, so the Director General of the WHO made himself the tiebreaker and issued the declaration. The debate on the expert panel has been similar to the debate on these pages–monkeypox, especially the strain that has gone global, is not that medically dangerous. There is no chance of overwhelming hospitals with a deluge of coronavirus hospitalizations, which was the main pandemic threat of SARS-CoV-2. Ebola, of course, has a 60-80% mortality rate. Zika was causing a number of severe, debilitating birth defects. Monkeypox runs its course in 2-4 weeks with fever and malaise, plus a rash which can become painful skin lesions, but the vast majority of patients recovering, typically without any specific treatment. The Director General cited as reasons for his vote a jump in global cases from ~3000 last month (when the same WHO expert panel declined to call the outbreak a global health emergency) to ~16,000 cases in 70 countries, especially in a virus not previously known to circulate to quite this degree.

Mostly, this seems aimed at providing additional resources for vaccines and contact tracing, especially in developing nations. The vaccine manufacturer is already struggling to keep up with demand, and some places in the US, like San Francisco, are having trouble getting enough shots for those who want and need one, despite 370,000 vaccines distributed to the states.

In fairness, concerns that monkeypox may entrench itself as a sexually transmitted disease in the US may be warranted. On the other hand, there is still time to contact trace and ring vaccinate it to death, or, lower probability, it simply extinguishes itself since monkeypox typically does not spread well past the 3rd or 4th round of infections in previous outbreaks. Tough to say.

Also worth mentioning that your condoms will be all but useless against monkeypox, unlike most other sexually transmitted diseases. The reason for that is the lesions which are particularly infectious can look like pimples all the way to the blisters you are seeing in monkeypox photos, and are not confined to the genitals (only a minority of cases thus far in the US have reported anogenital lesions). Any intimate contact with the rash can be quite infectious, and patients are symptomatic from the time symptoms first start until the rash has fully healed. Contact with items touched by a rash-ing person can also be infectious. For your classic STDs like HIV, gonorrhea, syphilis, and the herp, intimate body fluids are the main cause or the infectious lesion is on the genitals–thus, condoms can help there. Monkeypox, well, I wouldn’t count on it. Unless it’s like a full body condom.

Wait, are full body condoms even a thing?

Huh…

Pray for me, brothers and sisters, for I am about to search for “full body condom” on Google…

Yes.

Yes, they are a thing. Not a thing I would recommend, but they are a thing.

Instead, the WHO recommended this week that gay and bisexual men (98% of current cases, with 95% of cases spread by sexual transmission) reduce the number of sexual partners, “reconsider considering sex with new partners” and “exchange contact details with any new partners to enable follow up if needed.”

Yes, I know. The quotes, especially, call for all the jokes. But we aim for second lowest common denominator on these pages, and by Gawd, we’re going to hit it!

…and then apparently exchange contact details with it, because tracing wasn’t the only contact we were having…

DAMMIT! We were so <close> to the high road…

So close…

At any rate, the US is currently at juuuust around 4,000 cases of monkeypox (leading the world, but likely because of more available and aggressive testing right now), with most states having at least one confirmed case. You are starting to see a little bit of lift off, which is why contact tracing will be important. But despite the global health emergency, this is NOT likely to be a pandemic anywhere close to COVID. The main risk right now is that it grows into a persistent nuisance, especially as an STD, and currently the highest risk remains with men having sex with men–although anyone in close contact with an infected person is at risk, and you are starting to see at least a little spread outside of this demographic.

Coronavirus

–Mostly slow week in the ‘rona. Headlines that came my way weren’t even all that risible, and mostly seemed to be the futile re-litigating of escaped lab origin versus natural origin, or just usual political nonsense.

Around the horn, cases remain sky high in Japan and other parts of southeast Asia. Wuhan picked up a few new cases. India is showing just a low, sustained rise–no exponential take off yet for all the angst about the latest, greatest DOOOOOOOOOOM variant headlines were reporting there. New Zealand, in terms of death rate, is actually getting hit relatively hard these past several months–however, the fact that they are a small island that can actually enforce prolonged travel quarantines had spared them most of the previous waves. Their senior citizens and other high risk patients are unfortunately catching up a bit as the omicron cousins have inevitably broken through there, despite vaccines. It’s not immediately obvious to me how much access there is in New Zealand to the acute SARS-CoV-19 treatments like the antiviral pills or monoclonal antibodies, especially versus likely demand given their relatively high case volumes these past couple months though. Parts of central and south America are still riding BA.4/BA.5 waves, and cases are still quite active across a good part of Europe. In the US, cases continue to remain level to possibly trending down. Leading indicators in the US are trending down as well. Also saw a headline this week that labs which had opened up, or expanding testing for coronavirus, are starting to lay off coronavirus testing personnel as test request volumes continue to fall.

–Activity in South Africa remains minimal.

–There is a reasonable chance that BA.4/BA.5 was the fall wave come early. If there is no real uptick in cases, to say nothing of variant severity, by this fall, we may be formally starting to shut these updates down.

Pending the next serious pandemic, or outbreak of exotic high mortality ways to die, like Ebola/Marburg, of course.

–Speaking of which, regarding flu, Australia’s season appears to have peaked in recent weeks. Reported cases were higher than the 5 year average, but that may be a little skewed by the crushing fall flu had during peak corona mask and lockdown policies. Raw mortality appears to be ~0.09% with a hospitalization rate of ~1 in 200, but of course, total cases likely exceed reported cases, as not everyone gets their flu confirmed by testing, and thus reported. So those are best viewed as max mortality rate and hospitalization rate, and actual is likely less. Maybe an average-ish flu season headed the US way?

–Some articles floating around this week like this one, where “scientists are close to figuring out why some people haven’t caught COVID yet.” Be wary of these, because the work they so breezily describe are either cohort studies (and likely retrospective) or massive gene/other lab test association studies. In a cohort study, you have a group of patients who have a condition (in this case “caught COVID”) and those who don’t (in this case, “have not caught COVID yet that anyone can tell”). In a retrospective study, the cohorts usually start with the disease (or without it, depending on the cohort), and then work back through their risk factors and behaviors to find an association with the disease. Then you look for other things, risk factors, that are common in one group, but not the other. So, for example, if you took a group of patients who already had emphysema and matched them to a similar group of patients who did not have emphysema, and then looked through their history for risk factors, you might find that the emphysema group all smoked, while there were hardly any smokers in the group without emphysema.

This can be a useful hypothesis generator, but has significant limitations. First off, you may not even know what you -should- be looking for (if it’s something surprising), and thus never evaluate what the real risk factor turns out to be in your study. Second, if the cohorts are not well matched for all of the things that do matter, you can wind up with a confounding variable problem. Lastly, even if you have a good handle on the risk factors that should matter and match the cohorts well, all you prove is association. Causation will require an entirely study design.

You can also do a prospective cohort study, where you follow two groups of patients, one with a risk factor or behavior and other without, over a long time and see which group develops the disease you are interested in at a higher rate. So again, we might have a group of young smokers and a group of similar young people who don’t smoke and follow them for 20 years. If the smokers have a higher rate of emphysema, we can reasonably conclude that smoking might have something to do with that. Again, though, it proves correlation, not causation, and there could still be confounding variables, since you are not randomizing the groups and risk factor among them. It would also have been difficult, mid-pandemic, to set up a prospective cohort study for COVID. Most of these are retrospective.

The other kind of study, where they mention specific genes in that article, for example, which may be associated with lower rates of successful COVID infection, are from massive gene association studies. These invariably suffer from not having nearly enough samples for the sheer number of variables they are testing. To try to put this simply, if you get blood work done by your doctor at a lab, and you are truly perfectly healthy, the reference interval for one of those routine lab tests is usually set at two standard deviations around the mean (average) value of that lab test in a normal group of people. This means, by definition, 95% of normal people will test normal–but 5% will have a value considered “out of range” even though they are normal. Or to put that another way, if I give that same lab test to 20 people, by chance alone, we would expect one of them to have a value for that test that is out of range.

(and by the way, the normal population used to set the range is usually volunteer blood donors from the lab staff itself)

By the same math, if I do 20 different lab tests on you on the same day, where the positive/negative range for them is that same +/- two standard deviations around the average of a normal population, one of those lab tests will likely flag as abnormal–by chance alone. This is why when you get a large panel done, there always seems to be one or two out of whack. Your doctor will ask a couple questions about those to see if you have signs/symptoms suggesting the out of whack result is real, but when it’s not, your doctor doesn’t freak out too much about one odd lab result. They’ll usually just repeat it in a bit and when it comes back normal, no worries, right?

Okay. So in these gene association studies, they are testing thousands of genes at once, to see if any of them associate with people who have not caught COVID yet, in the assumption that those genes might be protective against COVID. By chance alone, you’ll get a bunch of genes that will LOOK like they are associated, but are not. Although there is fancy stats that claim to be able to correct for this, none of them do, not completely. Gene association studies are good for a hypothesis only, but are notorious for having the gene that looks associated not pan out on repeat testing. For a more complete explanation of this, see Box 1 in this paper.

By the way, remember that hot minute that type 0 blood was protective against COVID, early in the pandemic, from a similar massive association study? And how subsequent studies looking at blood type more specifically did not confirm that? Odds of the same happening to all those named genes in the MSNBC article are quite high.

Socioeconomic

–Last weekend, there was good news on the global food shortage front, as Ukraine and Russia struck an export deal detailing a corridor, policy and procedure that would allow Ukrainian wheat shipments to leave through the port city of Odessa. This would, in theory, relieve some of the price pressure to say nothing of the prospect of actual shortages, especially in the parts of the world which import a lot of that grain.

Ask yourself though.

If you were this guy…

engaged in a war of naked aggression, which has not been going according to plan, against an enemy you harangued as degenerate, amoral, actual Nazis (no really–go read his ranting justifications for all of the misery he has brought on Russia and Ukraine), and you had the opportunity to first show what a misunderstood good humanitarian you are by permitting grain shipments, even in the midst of shooting war against this mortal and deadly …threat… to your larger and better armed country…

…and then perhaps confirm the other guy as the dangerous degenerates sociopaths intent on wreaking human misery everywhere, who must be stopped, that you claimed they were when you launched your war…

…”confirm” them as that, if, perhaps, some weapons were to be “found” in one of those ships or those shipments or the port were to be attacked by desperados that you could claim was your enemies, intent on disrupting this needed humanitarian relief…

…which might just help convince your own people, or maybe even some of the world now convinced you are a dirtbag and sanctioning the hell out of you, that hey, maybe you ARE the good guy after all…

Well, if you’re the guy pictured, how long do you think that treaty will last?

–Approximately less than 24 hours after the agreement was announced in international headlines, Odessa was hit by missiles. Although Russia initially denied involvement, they later confirmed it was, in fact, their missiles. Totes accident, you guys. Totes.

So I guess the answer to my question is “approximately less than 24 hours?”

–Elsewhere, against the recommendations of the ministers of agriculture of the regions of Canada that are their “breadbasket” (all of whom are former farmers and ranchers themselves), Justin Trudeau announced a measure nearly identical to the one that has caused farmers in the Netherlands to protest nearly indefinitely at this point. In the name of fighting climate change, Justin from Canada has announced policy for a 30% reduction in nitrogen emissions by reducing fertilizer use specifically.

How is that expected to work out?

“Total Emission Reduction puts a cap on the total emissions allowable from fertilizer at 30% below 2020 levels. As the yield of Canadian crops is directly linked to proper fertilizer application this creates a ceiling on Canadian agricultural productivity well below 2020 levels.” –Fertilizer Canada

In the “hold my beer” extreme of this kind of policy, in April of 2021, the President of Sri Lanka completely banned the import and use of synthetic (read: nitrogen) fertilizers. Yes, that would be the same President of Sri Lanka last seen on a military airplane fleeing the country as protestors burned his house. In June of 2021, a group of agriculture scientists in Sri Lanka tried to point out the obvious and predictable effect of this policy to the President:

As it turns out, the scientists were right. Coupled with significant mismanagement elsewhere in the economy, the usual rumors of corruption, and ultimately, Sri Lanka running out of currency reserves to be able to afford the food it now has to import after those kinds of crop production losses PLUS rising fuel costs, and you get the headlines we have been tracking in Sri Lanka.

Now, is Canadian agriculture going to implode and the Canadians (and Dutch) going to to starve from these policies?

No. But you will take net food exporting countries like the Netherlands and Canada, and at best reduce their exports significantly. With less food available overall because of these shifts, the price of food will get a bid. Inflation in foodstuffs will remain, and the world’s poor, many of whom live in countries without the blessings of arable land that Canada and the Netherlands have, will quite literally starve.

–Of course, even if they didn’t voluntarily reduce nitrogen fertilizer use in Europe and Canada this past month, involuntary reductions may be coming worldwide. BASF, a major German producer of many chemicals, including nitrogen fertilizers we covered recently, announced it is having to reduce production of fertilizer specifically. The production process used globally for a lot of nitrogen fertilizers relies on natural gas; the man in the photo above (not “The Exorcist” poster, the other photo) may or may not have something to do with the continuing maintenance and paperwork issues that have seen Russian deliveries of natural gas to Germany drop to about 20% of what they should be.

–As for how Germany plans on making up that shortfall, Germany announced that it will increase the import and burning of wood pellets for energy, rather than turn to (even more) coal or delay shuttering nuclear plants. This has drawn predictable howls of hypocrisy as Ze Germans continue to insist that developing nations also feeling considerable squeeze from energy prices and generally insecure and insufficient global supplies of energy right now stick to their clean energy commitments, even as Ze Germans turn to coal and wood.

Why is wood an especially puzzling choice for a “green” alternative to Germany’s energy insecurity?

• When burned, trees generate more CO₂ emissions per unit of energy generated than fossil fuels. An oft overlooked fact is that burning wood emits more CO₂ than fossil fuels per megawatt-hour (MWh) of electricity generated or per unit of heat generated. For example, per data from Laganière et al. (2017), smokestack CO₂ emissions from combusting wood for heat can be 2.5 times higher than those of natural gas and 30 percent higher than those of coal per unit of generated energy. In terms of electricity generation, smokestack emissions from combusting wood can be more than three times higher than those of natural gas, and 1.5 times those of coal per MWh.
• There is a carbon sequestration opportunity cost. Harvesting trees for energy releases carbon that would otherwise have remained stored in the forest. It also forgoes future carbon sequestration that otherwise would have occurred had the trees been allowed to continue growing.

— World Resources Institute, https://www.wri.org/insights/insider-why-burning-trees-energy-harms-climate, last accessed 27 Jul 2022

–So again, if the aliens came today, who is the leader you take them to meet? Who strikes you as serious, thoughtful, and managing the present moment well?

–Oh, and lest we forget, plenty of looming or active strikes among huge numbers of workers critical to the supply chain. Worldwide. Article here.

—Think piece well worth your time, especially as we move into another election cycle.

–Finally, yes, we all saw the reports. The all too familiar reports from these last several years. An entire city. Apparently under siege, with authorities struggling to contain a force of nature over which they had little control, and less hope of stopping. A populace confused, bewildered, and staggering, locked down inside their own homes, for some semblance of safety.

“Homes,” indeed.

Poor bastards.

Home was safety. Security. Certainty. Home is your favorite meal, in peace. Home is family, and the memories of holidays and laughter and the good times. Home is your own bed, your own bespoke spot in it, honed through the years to throw its arms around you and keep you through the night. Where the other side of the pillow is always cool.

Yes, “home,” that last bastion of familiar, the one constant left in a world seemingly spinning off its axis. “Home” is, should be, sabbath, and every bit as sacred. The long for rest at the end of day spent out there, contributing your portion to the creation of the wider world.

No more.

“Home.”

Not for these poor, poor bastards.

“Home” had been cruelly twisted. Now, it was a fortress, and one known, expected to fail. Security? Safety? There was none. Certainty? Only of a twisted, degenerate kind. For the only certainty left these poor, poor bastards is the knowledge that their most personal and sacred space was gone. Certainty was now knowing the last refuge of normalcy at this moment in the world, this extended, eternal pause that halted time these past two years, would be taken from you, forcibly, in all the expected horror.

In an instant.

To the sound of whispering rustles of the paper in the door frame…

Confident, terribly purposeful, and oh so quiet footsteps on the mats…

The distinct, unmistakable shadow on the shoji, framed by the moon behind it. Almost human, yet somehow not. If it had been some common burglar, even though a criminal with the same base intent, well, the humanity of the criminal’s shadow would have been relief compared to this. The shape of some distant ape cousin.

A feral, bestial shadow.

Now the shadow stops…

Now the low, dark squat head raises towards the moon, and unmistakably sniffs the air….

The family cowering on the wall opposite the shoji can only huddle silent, transfixed, at the horror of inevitability before them.

It has their scent.

And now the shadow stretches forth its arm.

And now the soft hiss of the shoji along its runners, opening slow, and moonlight spilling through the breach to grimly alight on the family inside, locked in one last desperate embrace…

Yes, my friends, you know too well that this is the reality behind the headlines, kept benign lest the truth you have come to see and know gets out. And the true terror… the true horror… the true threat be known.

You don’t need to read the article to know the details, but still you do. Roving bands of macau monkeys, breaking into homes, injuring 42 in Japan. Or is it just one monkey? No one knows. No trap, however cleverly set, ambushes them. Investigations turn up little. They leave scant trace, no evidence.

They own the night.

But you know this, reader. You know without being told. You know how it began before the article tells you, targeting only women and children at first. Then elderly men. And now, hale, young adult men. A carefully executed escalation of terror, to prove to the populace that no one was safe, that none would be spared.

No quarter. No prisoners.

The Army of the Bioterrorist Monkeys.

Your chances of catching Marburg this week are equivalent to the chances that the Army of the Bioterrorist monkeys will show mercy…

Your chances of catching coronarvirus are equivalent to the chances that speaking of the Army of Bioterrorist Monkeys, shirts are under way, but moving a little slow with supply chains/personnel etc. More to follow as things progress.

<Paladin>