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:

Will again be short and bullet pointy this week–was traveling for work again early this week, and just wrecked my writing windows.

Marburg

–No updates on case counts that I can find as of post time this week, so still at two official cases. A little more detail on them available though. One was a 51 year old farmer who denied contact with other sick people or the common presumed animal reservoirs of Ebola and Marburg in the past 3 weeks. The other was a 26 year old farm laborer/farmer who also denied contact with other sick people or common reservoirs in the previous 3 weeks before his death. It’s not clear if the two were contact with each other. They are from separate rural districts in Ghana, but those districts share a border, so there may be a common infection source. Handicapping comes down to if these guys knew each other and both got infected at the same time. If there is a single common source in this area, then contact tracing (which will be a challenge given the area and internal politics of Ghana at the moment) should help contain the outbreak. If, however, there are multiple infection chains already, the virus is more widespread than it would seem. Then it depends on how much of a head start Marburg has. To be clear, this would mostly be a “how far in Ghana” question right now, with some risk to neighboring states. Yes, there is a chance that it could hop on a plane at this point in the outbreak–there is always is–but that chance is pretty minimal. Don’t lose sleep over that. You have a far, far better chance at the ~$660 million Mega Millions this weekend.

And I’m already going to win that, so scale your estimates of running into Marburg in the flesh accordingly.

Leptospirosis

–Thanks to the UK reader who forwarded the investigation of a couple of bizarre deaths in Tanzania last week. We were waiting for more details from the investigation this week, as an uncommon presentation of a common thing is always the most likely bet, and the ways to die an infectious disease death in parts of Africa are legion. These cases made news reports across the pond mostly because the patients in question “died bleeding from the mouth and nose” after otherwise non-descript fever and GI symptoms. A fever that bleeds is always suggestive of a hemorrhagic virus, but other things can do that too as uncommon presentation of more common disease. They had ruled out the usual hemorrhagic viruses with testing in Tanzania; hence the investigation. Well, turns out it was just an odd presentation of leptospirosis, which is a bacterial infection commonly acquired through exposure to animals, particularly rodents. You can get this anywhere–the US will see ~150 cases a year, most in Puerto Rico and Hawaii, as the causative bacteria likes it a little warmer. When detected in time, antibiotics do the job. This is usually more of a risk when traveling, but even then, odds are good you will live your life having never contracted leptospirosis. Unless you travel to Tanzania and play with rats right now. If that’s your summer travel plans, well, you do you–just don’t say we didn’t warn you.

Regardless, this will end our coverage of leptospirosis outbreaks for the foreseeable future.

Coronavirus

–Around the horn, Europe, parts of South America, Oceania and definitely south east Asia are getting hammer timed by BA.4/BA.5. At least in terms of new reported cases. While everyone is reporting huge spikes in positive cases, outside of China, there has been little movement towards more restrictive policies in spite of climbing numbers, as the new cases are mostly bad colds. For example, Japan currently has a reported case spike at least as high as the omicron wave. In fact, in the current sumo tournament, 1 in every 5 wrestlers is now out of the tournament, even as it enters the championship days. The withdrawn wrestlers have tested either positive themselves or having teammates in close contact who tested positive. In some semi-comical moments, there have been junior level bouts that happened, only to have the junior guy who just wrestled withdrawn and his entire team removed for the rest of the day because someone on the team just tested positive. But his opponent, in theory just in visible close contact with a known contact, has been free and in the clear to wrestle again the following day. Earlier in the pandemic, similar to UFC fights, the tournaments were going on with massive in person attendance restrictions or empty stadiums. They have not reduced attendance, which is back to near normal (everyone still in masks though), and there is no longer enforcement of COVID bubbles for the wrestlers. This being sumo, ALL of them are high risk based on their BMI, but no reports of hospitalizations or severe COVID from this wave yet.

Elsewhere in Asia, China is considering lifting some restrictions in Macau this week if cases continue at their current level or lower by the weekend. However, other provinces are seeing increases in new cases, and high likelihood of “zero COVID” lockdowns and mandatory testing regimes. In Australia, government officials during a debate on lowering the mandatory isolation requirement of positive COVID tests from 7 to 5 days included mention that there are flu strains in Australia (it’s their winter, and hence flu season) that are “more severe than COVID right now” as part of the argument for re-thinking. However, most of the medical advisors appear to be in favor of keeping the 7 day isolation, perhaps considering that it would remove some people from flu’s path as well.

I bring it up only because those flu strains will be our flu strains shortly, and to clarify, those flu strains are worse relative to current COVID strains, which are mostly a bad cold right now. Not that this is some super pandemic flu starting to rear its head (despite that always being a possibility with flu).

–Cases in the US remain level to slightly falling, as one might expect. Some media sources are starting to throw up charts of rising hospitalization rates, although they are far quicker to caveat that it’s “unclear” how many of them are admissions to the hospital for other things, only turning positive on screening COVID tests.

The latter seems to be the case, and just so you know it’s not just me saying this, we have the following interview with LA area hospital officials and epidemiologists. You should watch the 8 minute video. But the money quotes are:

“The numbers of COVID positive tests have continued to go up, but this isn’t because we’re seeing a ton of people with symptomatic disease being admitted. We’re seeing a lot people with midl disease in urgent care and ER who go home and do not get admitted. Of those who are admitted, they’re 90% of the time not admitted due to COVID. Only 10% of our COVID-positive admissions are admitted due to COVID. Virtually none of them go to the ICU, and when they do go to the ICU, it is not for pneumonia. They are not intubated…

…We have not seen one of those [COVID case requiring ICU] since February. It’s been months.”

and

“Certainly, if the experience of our hospital is reflective of across the country, which I believe it is, we’re just seeing nobody with severe COVID disease. As of this morning, we have no one in the hospital who had pulmonary disease due to COVID. Nobody in the hospital. Nobody. Nobody who had COVID-19 disease as we would see in the past.”

–More contagious, less severe over time. That’s how pandemics go.

–Also, because obviously:

–On the plus side, this is also why I am not especially concerned about the news that the US President is COVID positive. It’s most likely one of these highly contagious omicron variants that are less severe, similar to Dr. Fauci recently. Yes, Joe Biden is at elevated risk by age and he looks a little frail at times. But he’s also (presumably) vaccinated, and is highly likely to be getting one of the acute treatments already. If Trump can make it through a more dangerous variant earlier in the pandemic, before vaccines were available, I have confidence Joe will pull through.

–Quickly updating some previous coronavirus reporting, we mentioned (and caveated) a NBER report on the economics of some of these lockdown policies back in April. You can find it here. At the time, we said NBER appeared, as near as we could tell, to be unbiased with a reputation for factual based analysis. However, not this paper, but others released by NBER have been called into question this week. Investigative reporting found that a paper favorable to Uber was published by an NBER fellow, who received $100K from Uber to write this report. Although the publication disclosed that the NBER author had worked as a paid consultant for Uber, it did NOT mention that included this payment at the time the article was being written. Certainly, more transparency would have been beneficial, as it does call into question the conclusions of the paper, which has now been cited a little under 1,000 times by other scholarly works. You can read more about this disclosure issue here.

To me, it does add extra caveats to the NBER paper I mentioned in April though. If this is the state of NBERs conflict of interest disclosure requirements, it does make me nervous in a paper as tribally charged as the conclusions of the lockdown paper could be, and NBER clearly permitting some pay to play among its fellows, that there could be a sponsorship issue lurking in the dark in this and similar articles. Plenty of political advocacy groups have $100K sloshing around in their funds after all, and reasons to justify the beliefs of their particular tribe…

–The other big COVID news this week was mainstream outlets catching up to the questions around vaccination and short term disruptions to menstrual cycles in women. You’ll recall we mentioned some research about this back in January–you can read that here. That was a reasonably sized paper showing that, especially after the second dose, women’s length of period was increased by maybe a day versus the unvaccinated, with little lasting effect. There has been a subsequent pre-print of an Apple (the company) based survey However, that was just looking at the length of menstruation, and not the volume.

This week COVID effects on the menstrual cycle were back in headlines due to the publication of this paper. The long story short here is that in a web based survey of tens of thousands of women, 42% reported unusually heavy bleeding with vaccination. The most common associations on multivariate regression analysis were older age, history of being pregnant before (especially if having given birth), used hormonal contraception, had conditions like endometriosis or fibroids, were non-white (hispanic especially), or had fever or fatigue after vaccination. However, the common associations between both pre- and post-menopausal women were hormone contraceptive use, history of pregnancy, and fever/fatigue (“Pfizer flu” and “Moderna malaise” symptoms). Many who had symptoms of increased bleeding did not have them until more than a week after the vaccine doses, which is outside of the usual vaccine side effect reporting window. This was all apparently self-limited, with only 31 respondents bothering to report it to a physician.

It’s worth mentioning that other vaccines have been associated with reports of similar, self-limited increased menstrual bleeding. The authors of our current paper under discussion cited a 1913 typhoid vaccine study as having “heavy bleeding” in half of the females enrolled, but I can’t access the full paper to be sure, and will take their word for it. A study of over 70,000 Japanese women receiving an HPV vaccine showed an elevated risk of heavy menstrual bleeding and irregular periods as significant associations, but also similarly apparently self-limited.

Also worth mentioning that SARS-CoV-2 itself has been associated with reports of menstrual irregularity. In a small study in Arizona, ~20 out of a little over 120 women with active COVID reported changes to their period. Most commonly, this was irregular length of menses, and increased pre-menstrual symptoms, although some reported heavier and breakthrough bleeding. Some also reported skipped periods too. Changes to a woman’s period were, unsurprisingly, more likely in those who reported more severe COVID symptoms. Another small study (a little over 200 patients) looked at hormonal changes with active COVID infection, and found no significant changes in female sex hormones or ovarian reserve. Interestingly, 20% of their study population had prolongation of menses (similar to the paper mentioned back in January) or a decrease in menstrual flow. But in short, they found no long term suppression of the ovaries–the changes in menses they did observe were short lived and reversed quickly.

–So what have we learned? The more symptoms from your vaccine, or COVID, the more likely some transient changes to your menses might be. This may include breakthrough bleeding in post-hormonal women or women on hormonal contraception, or changes in volume of flow, or prolongation of menses by a day. Ish. Nothing to freak out about, and not specific to the COVID vaccines. In fact, the research showing other vaccines have impacted periods in similar ways, and COVID itself can do it (especially the more symptomatic your COVID is), suggests this probably has more to do with systemic immune reaction than anything specific to SARS-CoV-2 or its components.

–The transience of menstrual effects and their universality among other vaccine types and COVID itself is also another solid argument AGAINST some of the concerns that COVID vaccines may have reproductive effects, especially the last study we mentioned. If COVID itself is not affecting measurements of female sex hormones, or ovarian reserve in a prolonged way, well, active COVID comes with a quite healthy dose of spike protein too. Also, there are STILL no reports of sudden spikes in demand for infertility services, which one would certainly expect by now, and to be correlated to vaccination status if the vaccines were really a significant fertility risk.

Random science news that we will somehow connect to COVID in the end

–Interesting meta-analysis out this week suggesting that the serotonin theory of depression, which posits that depression is biochemically an alteration in brain chemistry resulting in reduced serotonin signalling in key parts of your noggin’, has been doggedly resistant to experimental confirmation.

In other words, there is growing suspicion that the serotonin theory is wrong. And that theory underlies MOST of the drugs commonly used to treat depression! These are also commonly prescribed drugs, but, it must be said, those drugs have shown efficacy in reducing depression symptoms over the years, especially in severe depression.

In fact, for all the new questions on the serotonin hypothesis, one psychiatrist we trust commented that these findings are consistent with the view that what we call “depression” is really a group of symptoms that are the end of several distinct roads, and looking for one specific biomarker of one possible path to those symptoms may not work. You may just lose that forest in the trees. This may explain why serotonin measures have struggled to “prove” the hypothesis–if serotonin deficiency is only one path to depressive symptoms, the serotonin signal may be getting lost in the noise from the other paths, which cannot currently be distinguished from each other by the symptoms that qualify one for these studies! Our trusted psychiatrist threw out specific examples of limited social interaction, poor exercise, overworking, sleep disturbance from near constant blue screen exposure, all of which change neural pathways and signaling and have associated increased risk of depressive symptoms. In approximation of their words, “ultimately,” we may find that “this [one] type of depression is due to serotonin, this [other] one is due to life stressors/ loss, this is due to childhood trauma [damaging] the amygdala, etc.”

Speaking to one of those risk factors of depressive symptoms, though, previous meta-analyses (or scientific summaries of multiple studies to see the aggregate effect) of aerobic exercise three times a week have shown a strong anti-depressant effect, causing some physicians who treat depression a lot to postulate most adults with depression can be managed with this kind of exercise. The efficacy of exercise in combating at least mild to moderate clinical depression is even more believable when one considers that the serotonin theory, underpinning most drug based therapy of depression, may be on its last scientific legs. And exercise comes with plenty of other benefits–including risk reduction of severe COVID, by reducing the chances of obesity, for instance.

Knew I could get that back to COVID somehow… : )

Of course, talk to your physician before you do anything with the medications you are taking, including anti-depressants, but it may be worth having some conversations on alternatives to anti-depressants.

Socioeconomic

–Yes, yes… Nordstrom gas pipeline brinksmanship, Europe burning oil and gas again from anywhere it can to get by, France turning off street lights to conserve energy, Europe sweltering under the heat wave without much in the way of air conditioning, continued farmer protests, trucker protests in Portland, protests in Ecuador still getting chippy, Sri Lanka still a disaster, and still many questions about food yields and prices this coming autumn. You’ve seen all that too. I won’t re-hash it all here.

–Rumors increase regarding mass Chinese refusal to pay mortgages on properties that are underwater on their loan-to-current-market-value and/or not being completed by the bankrupt Chinese property developers we have mentioned over the past year, like Evergrande. This may be spreading to suppliers of those developers refusing to make good on notes for supplies they provided to the developers on credit, and now have little hope of ever getting paid for. This will increasingly transfer risk of the defaults in the property developers to the Chinese banking system as all these loans now begin to underperform. Those would be the same banks that we have seen on leaked videos having the occasional crowd of protestors show up, suddenly unable to withdraw their money, for various excuses coming from the banks. As a refresher, Chinese real estate is thought to be the single largest asset class in the world, at somewhere between $52-70 trillion dollars, and is the preferred investment vehicle of the Chinese middle class, with many owning multiple, often vacant, properties in expectation that they can always be flipped at a higher price. Even if the sector survives this current problem, what happens when the accelerating demographic collapse in China hits over the next couple decades, and there is no one to buy these multiple investment apartments/houses is anyone’s guess.

So ponder that while also reading this think piece: https://drpippa.substack.com/p/taiwan?s=r&utm_campaign=post&utm_medium=email

–Another good think piece here–CTRL-F “Entropy, Energy and How Societies Fail” and read that entire exchange of comments. Like Ben at the end, I have nothing to add to it.

–Related, the chicken has a modest proposal here worth reading.

–Full disclosure, as some of the conclusions in these two last think pieces are “talking my book”, I am long uranium and companies involved in the building, maintenance and supply of nuclear reactors, with no intention of selling those positions any time soon. I am also not a financial advisor, so that is absolutely not financial advice–I just feel like ethically speaking, you should know that and do your own research before you get any market ideas of your own from those!

–Your chances of catching coronavirus are about the inverse of my actual chances of winning that Mega Millions drawing this weekend.

<Paladin>