Monkeypox

Surprise! Yeah, we’re going to mention this only to mention that cases are dwindling to almost nothing and we will soon be past the latest official WHO Global Health Emergency at this rate.

Ebola

Bad news is the outbreak continues, with at least one case in the capital city of Uganda. Good news is that contact tracing has caught up and then some, so big, big kudos to Uganda, who have responded with appropriate urgency. The new cases in the past couple weeks have now been traced to known contact chains. They cannot use this for ring vaccination (which would be ideal at this phase), since there is no approved vaccine yet and WHO stated they are likely still a few weeks from getting experimental vaccines in country. However, Uganda absolutely can quarantine off the known transmission chains, dramatically reducing if not ending the current spread. This also means that, despite spotting the virus a couple weeks of crucial head start, humanity has leapt back into the lead, thanks to the speed, diligence and competence of the Ugandan Ministry of Health. Now, they just have to enforce quarantines, continue to track, and wait. There are currently just shy of 1,000 known contacts.

Worth mentioning the saga of the case that reached the capital. Apparently, the young man became symptomatic and went to a traditional healer instead of a hospital. When they didn’t work, he went to a hospital and changed his name to avoid tracing. Finally, he skipped out on that to land and ultimately die within a hospital in the capital city, at least according to Ugandan reporting I could find. Uganda authorities are now urging citizens to maybe not go to traditional healers for Ebola symptoms.

Most up to date case numbers I can find are 54 confirmed infections, with either 19 or 20 deaths so far (obviously varied a little bit depending on the source). We’ll call it the Schrodinger’s Cat case.

Coronavirus

— China is seeing an uptick in large cities again, including new restrictive measures to combat newly detected cases in Shanghai. This will continue so long as China remains wedded to the “Zero COVID” policy, which it seems politically unable to escape, so long as that demonstrates that the Glorious Leader made a policy blunder on a major health and economic crisis. Highlighting again the weakness inherent in the Chinese political system and the folly of the CCP in pursuing this counterproductive policy, which is deeply unpopular with the citizenry it unjustly oppresses.

And thanks again to our CCP readership for dropping in the last couple weeks! Always good to have you guys. One more thought piece just for you:

“Criticism may not be agreeable, but it is necessary. It fulfills the same function as pain in the human body. It calls attention to an unhealthy state of things.” –Churchill

Elsewhere, you are seeing significant rises confirm in a good chunk of Europe, from Germany through Austria, Italy and Greece. There have been more “doom wave” headlines about this, as it is right on time for a fall wave, and past waves have started in Europe a few weeks before hitting the states. That said, most of the new cases are still BA.4 and BA.5, which are omicron cousins that have already been very active all year long in the US. There is reasonable expectation that herd immunity to these, to say nothing of more omicron specific boosters, may mute these waves, especially in terms of severe COVID. You may still see symptomatic breakthrough, but again, the pandemic threat is hospitalization. In Europe, there has been a slight uptick in those with risk factors, particularly over 65, but it’s unclear how many, if any, had an omicron booster and it’s also just a function of numbers at this point. At worst, you are looking at a smaller version of last year’s omicron wave, where everyone and their brother got symptoms, but severity in terms of hospitalization was down on a per case basis, and will likely be down even more on a per case basis given natural and vaccine derived omicron resistance in the US.

So far, in the US, early indicators are absolutely moribund and activity (also still mostly BA.4 and BA.5) is very low.

–First on the SARS-CoV-2 science beat, we have a nice little paper from The Lancet examining the real world performance of the Merck and Pfizer treatments for acute COVID. This is always useful to measure, as clinical trials are designed to show the safety and efficacy of a drug, but in a patient population that is focused for speed of recruitment and ability to follow easily and in detail to get the necessary data. Thus, the average risks, and average benefit, for the patients enrolled in the study can be calculated, and this average approximated to all other patients whom the drug might treat. Plus, all of the potential confounding variables are (theoretically) controlled, so you get as “pure” a look at safety and efficacy as you can on a clinical trial.

However, a point I have made privately to some of the readership before, your results can be expected to look like a clinical trial population ONLY to the degree that YOU look like that clinical trial population.

Or as Stephen Jay Gould put it in an essay long ago, “the median is not the message.” If you are significantly different from the clinical trial population for a drug, either healthier than their average, or perhaps worse than their average, your results can be expected to vary a bit. So the “real world” performance of a drug is a good thing to measure. The challenge with real world trials, though, is that it’s a better measure of how a drug will do against a condition against all possible patients who might receive it. The downside is the clinical data is MUCH harder to collect, and confounders are NOT controlled. And before you @ me for why we don’t just get real world evidence for every drug, you kind of want to know what the side effects and safety are, and if the benefits are worth those risks, LONG before you just send a new drug into the wild for everyone. You get that with a clinical trial.

So how did Pfizer and Merck’s drugs do in the “real world” in this Lancet study? Well, to make the long story short, both held up quite well, right where we expect them to. They both significantly reduced the risk of death and progression in hospital from SARS-CoV-2. However, the Merck drug did not show a significant difference from non use of an acute treatment agent in reducing the risks of hospitalization. Only the Pfizer drug reduced the risks of hospitalization. They cite a few other studies and measures in their discussion that suggest the Pfizer drug may be a little more effective, pound for pound, than the Merck agent.

However, it’s also important to notice (and the authors bring up in their discussion as well), that the patients who got the Merck drug in the “real world” in this study tended to be older with more comorbidities and were less likely to have been previously vaccinated than those getting the Pfizer drug. All of those could explain why the Merck drug failed to show significant protection from hospitalization while the Pfizer drug succeeded, as the Pfizer drug happened to be given to patients already likely to do a little better.

Regardless, main takeaway is the acute treatments are doing what we expect them to do–reduce the risk of severe COVID and death, and thus help keep the pandemic phase of the COVID experience behind us.

–Big write up this week on the complications of COVID around pregnancy. I want to be clear that this is different from effects on fertility, which, be it COVID or vaccination, have yet to be seen either anecdotally through the in vitro fertilization docs or in studies that have gone looking for them.

Issues during pregnancy on the other hand, definitely have some fire to that smoke.

I’m going to keep this part short and spare the Sciencepalooza for the most part. Pregnant women should be vaccinated against COVID, and for the following now known complications that can be seen in pregnant women who may happen to catch COVID:

1. Increased risk of death to the mother. The delta wave, in particular, was not kind to pregnant women. Despite being “low risk” by virtue of age, and often without the known comorbidities, there was a definite and detectable uptick in severe COVID and COVID mortality in pregnant women who got the delta variant, especially if unvaccinated. Again, this one hit home, as one of my homecoming dates from back in high school, per all the Facebook chatter, wound up with severe lung complications and was in the ICU for months after catching COVID, unvaccinated, while pregnant.
2. Increased risk of still birth. While it’s worth mentioning that after the 1918 flu pandemic, for example, there was a brief spike in the rate of still births attributed to increased pre-term delivery rates and increased maternal and fetal mortality. Interestingly, the cohort of babies born during the 1918 flu pandemic had a lifelong >20% increased risk of cardiac disease. While there are no contemporary case reports or series that I can find describing pathology of the increased rate of fetal loss, with COVID, at least, we have some characteristic findings. Again, not to go into too much gory scientific detail, but the placenta in a pregnancy lost during an acute bout of COVID shows clear and widespread evidence of loss either due to damage or clotting of the placental blood vessels. This is NOT a common complication–still birth with a COVID infection was still quite rare. And a little more common with delta. Overall, the rate of pregnancy loss was higher than pre-pandemic rates. I mention the flu papers here though because the pathology of these losses sounds like a combination of severe inflammatory insult, like a pandemic flu or COVID, plus SARS-CoV-2’s known ability to infect blood vessels directly AND initiate cross talk between the inflammatory system and clotting cascade. My guess is that the placental damage we seen in COVID is “COVID toes” of the placenta, with a bunch of micro-clots getting triggered as part of the massive immune system overreaction the virus provokes in some people taking the placenta out. This inflammatory burst may have consequences, if the lifetime cardiac risk data for the flu pandemic babies are any indication and not statistical noise. But that will take decades to learn.
3. Pre-eclampsia and eclampsia. These are pregnancy emergencies that already happen, COVID or not, in a small percentage of pregnancies, after week 20. With acute COVID, the risk for pre-eclampsia approximately doubles. Characteristically, pre-eclampsia and eclampsia are defined by dysfunction of the blood vessels, and sky high blood pressure is one of the presenting symptoms. Again, I suspect the increased risk for this in pregnancies complicated by acute COVID has to do with the immune reaction, direct infection of blood vessels by the virus, and cross talk to the clotting cascade triggered by SARS-CoV-2. Most likely, they tip a population of patients who was probably a little more predisposed to these conditions over the line into full blown clinical presentation. These conditions are treatable, but due require prompt recognition for best outcome.

To be clear, these risks are associated with virus infection during pregnancy, and have not been proven as a risk around vaccination. So pregnant women should definitely continue to be up on COVID vaccines, even though virus activity is muted at the moment, and the circulating strains continue to be high contagiousness, relatively less severe. Not worth the risk to Mom or baby.

–There has been growing local news of increased hospital admissions in kids with RSV and other seasonal viruses causing cold/flu symptoms. Ordinarily, there would not be so many hospitalizations from these, or at once. This was an unusual spike. I didn’t mention it because at the time, it was merely local coverage.

However, CDC is reporting that this uptick is much more broad, and we are seeing more kids in the hospital for RSV, non-SARS-CoV-2 coronaviruses and adenoviruses than is typical.

There is NO association, one way or another, to COVID vaccination status reported thus far. So if you see any headlines on that, they are fairly “Plandemic” at this point.

Nor is it proof of “weakened” immune systems–at least in terms of immunodeficiency, which is how that should be taken. Instead, what is most likely happening is that far more schools are in now in person and have lifted most if not all COVID social distancing restrictions. Just as mask use and social distancing hammered the flu during peak “lockdown” seasons the past couple years, they also hammered the plethora of other cold/flu viruses, like RSV, adenovirus, rhinovirus and non-SARS-CoV-2 coronaviruses.

You may recall from the long long ago, in the early epoch of the time of coronavirus, when we first observed that kids were not being affected nearly as often or nearly as badly as adults. We cited studies showing that many of them had T-cells from prior and recent cold infections (as kids get lots of colds, as all of us parents know) with non-SARS-CoV-2 coronaviruses that showed at least some cross-reactivity with SARS-CoV-2.

So what’s happening here is that kids have not been catching colds and spreading them at the usual rate these last couple years. But now everyone is together again, which is good times for these viruses once more. Before, you had recent enough infections that memory T-cells of close cousins of colds caught before could see through the clever disguises of these new circulating cold viruses and keep them mild colds.

Now, though, the memory T-cells are a little less frequent, and the genetic distance between the mutations causing “close cousin” viruses to colds they had in the past a little wider. So a few more than usual are slipping past kids immune systems to put a few extra in the hospital.

For the most part, the kids are there for a little breathing support, and then they are on their way. But it is putting some pressure on available children’s hospital beds.

I suspect this will last only through this fall and winter season, and then everyone’s T-cell immunity will be back to baseline from exposure to more the usual cold/flu suspects, and not some long term immune system disability that the most extreme headlines and articles are shrilly claiming for attention with this trend.

I know our family caught a nasty non-COVID cold within 2 weeks of school restarting. I suspect nearly everyone with kids in elementary/middle/high school did, let alone the usual months long slog of viral death that is pre-K daycare. I am also sure all the parents in the readership will nod sagely when I say that the highest risk of a cold/flu/strep throat racing through the family is within 2 weeks of going back to school, 2 weeks of back to school after any fall break and certainly around and within 2 weeks of back to school after Christmas/New Year’s.

This is because everyone has had time to travel during those breaks, catching new and exciting cold/flu viruses wherever they went, and now bring them back during the asymptomatic, or early symptomatic, parts of the incubation period by the time school starts back up. Which means they spread among the kids like wildfire, who then bring them home.

All the parents will also remember that when in pre-K daycare or early days of kindergarten, your little treasure caught a mild sniffle and an uncomfortable night time cough. A lot. You, and/or your spouse, on the other hand, got your ass kicked by a near fatal (it seemed) two week long death cold. From the same virus. Same effect as what is happening in the increased hospitalization rate of these kids to common viruses. As a parent of a really young kid, you have been in the adult world, where these viruses don’t transmit as often. But they have learned new tricks while you were in adult world, and these viruses spread easily amongst kids who have no idea what hand washing or other cold/flu precautions, like not drinking after each other or drooling over one anothers toys, even are. Their young, new immune systems are eager little killers, who are literally swimming in all of these similar viruses all day long. Meanwhile, yours is saying “Cold virus? Haven’t seen those much in years, but I remember cold viruses…”

And no, no your immune system does not remember these cold viruses. Although it thinks it does for a little bit too long. Because the viruses have picked up a few mutations from when you last had them, and it takes a hot minute for your immune system to get back up to speed. This approach leaves YOU far more symptomatic, and for longer, than them when your son/daugther coughs on you after daycare/kindergarten to give you a nice, big infectious dose.

So same thing going on now, but for these kids. And like what happens after you get out of the “post break vacation back to school period” or the “daycare/pre-K/K first 6 months to a year”, it will even out. The rate of hospitalization from non-COVID cold/flu viruses among kids will go quickly back to normal rates.

You heard it here first.

Socioeconomic

–Updating Nordstream discussion from last week, Sweden has done an investigation, but has not released the results. Russia has now been invited to complete their own investigation. One of the Nordstream 2 pipelines appears undamaged, and Putin has offered to run natural gas through it to Germany, but Ze Germans have said “nein.”

No, I am not sure how that factors into the “cui bono” calculus for whodunit, but does emphasize why all of the headlines and energy trying to guess last week was likely futile effort.

–Core inflation in the US hit the highest level in 40 years based on the data out just this week, which hopefully comes as no surprise to anyone who has been reading these sections all year. If there is a silver lining, food and fuel prices ex-US have come down a little bit in the last month or two, but that is A) unlikely to last and B) down from ridiculously high to slightly less ridiculously high and STILL higher than what caused the Arab Spring a few years back (and yes, I have seen the ongoing riots in Iran, speaking of that). In the US, official food inflation is running close to 11.4% annually. However, here’s a Twitter capture of someone’s local bakery whiteboarding why their prices have been going up, which looks like a slightly higher rate of inflation than that:

–The other (mostly) good news is that it’s the start of harvest season out here where the food grows, and the USDA reports are coming on in the US harvest. Corn and soybean yields are down slightly, although you have bumper crops in other legumes like lentils and peanuts (nitrogen fixers, which as we mentioned before were being planted more than usual this year as nitrogen based fertilizer prices went up). This appears to be a little in excess of the slight reduction in total acres planted of corn, and to some extent, soybeans–which passes the eye test this summer when we mentioned that a few more marginal fields than usual were lying fallow in farms we drove past.

Overall, the US yield is well within the average of the last 5 years for all major crops thus far. Down from the big years, but nowhere near catastrophe. What will be a globally critical winter wheat crop is starting to go in, and while the US cannot possibly make up for the volume of wheat from Ukraine and Russia, every little bit will help. It’s been a more challenging year, for sure, but so far, the American farmer appears to have gotten it done.

–That has not stopped the troubling news from elsewhere in the world. Pakistan was completely priced out of LNG, which it needs to run its power grid, with its latest offering literally going no bid.

Elsewhere, continued energy supply shortages and cost pressures continue to wreak havoc in Europe. In the early warning signs that widgets will be going missing by early next year, affecting supply chains around you, no matter where you are in the world, we have this:

And because the widget is missing…

I have anecdotally heard of pharmacies requesting longer lead times on refills because supply is slowing a bit.

It won’t stop with just pharmaceuticals though.

–More European food production is also shuttering due to energy costs. For example, the Dutch seed firm Plantise has had to close, and cited rising energy costs as the reason. Other big food companies with plants in Europe have been investing in onsite energy generation to keep the plants running (and Europe fed), while also lobbying to be sure that food production and distribution is prioritized for any rationing of energy off the grid this winter (and likely beyond). If that’s not a tell that there is a HIGH risk of such rationing, I don’t know what is. You can read all about this here.

Again, I cannot stress to our European readers, and others living abroad if your home nation is an importer of food and/or energy, you need to move NOW to ensure you have alternative, off grid supply of energy that you might need, and canned goods to last a bit. The down side risk is real, and arguably growing. Hedge against it now.

Another important, if underappreciated point from the Pakistan “no bid” article we posted above. What that shows is that even if your government tries, and makes the right moves to ensure that energy and food will be there, when the issue is absence of sufficient supply or supply in a critical time frame, there is nothing even good government can do. If the LNG or oil isn’t available, it flat out is. Not. Available.

–But yes, government policy choices can influence both availability of supply, as well as the cost of the available supply. Good break down here of a viral response by Valero to questions from the California government about price and cost of production of fuel in California, which, even though US prices have been falling, are significantly higher than every other state in the Union.

–Continue to plan for an interesting decade.

–Your chances of catching Ebola this week are equivalent to the chances this is real. And your chances of catching coronavirus are equivalent to the chances I can’t believe I didn’t know about that video until this week. Still hilarious though.

<Paladin>