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

Transmissibility: All the +

Immune Evasiveness: All the +

Vaccine Effectiveness: Check (for hospitalization)

Also as a reminder:

Yes, we’ll get to that major headline event that began last night in the socioeconomic section. Briefly.

Coronavirus

–Most of your current activity is omicron driven and in South East Asia at the moment. Continental Europe is either at the crest of their omicron waves or starting to come down. Activity in the US is way down, coast to coast. The UK remains quite low. Bellweather South Africa has minimal activity right now too.

–Leading off the science-y portion, as I know many of the readers have kids (or grandkids) in the 5-11 age group, is a recent paper on the rate of hospitalization and severity of COVID, MIS-C (the Kawasaki disease like syndrome that complicates some pediatric COVID cases), influenza and RSV. The paper is reasonably well done, although they had to compare to an “average” influenza and RSV year (2017), as the flu season during the 2021 COVID waves was mild.

The money data are in the Table, and I have screenshot the top portion (since the rest has only one significant finding):

The second line, the total hospitalization incidence per 100,000 kids, is worth mentioning. What that shows is that children age 5-11 were 3 times more likely to be hospitalized with flu than with COVID. They were also more likely to be hospitalized by RSV than COVID.

I know a lot of you worry, because they are kids, and not only that, they are your kids. But keep that in mind.

Yes, I know, you would -think- this context would be provided more often in media coverage of COVID risks to kids this age.

And before you ask, Hypothetical Reader, I am going to continue to stay away from the implications this has for mask policy in schools, because, as I went into before, your impression of that is where you fall on acceptable risk:benefit. On the other hand, worth asking yourself if your risk:benefit calculation changes knowing these facts about the flu.

That said, the rest of the data bears mention too. What that also shows is that hospitalization for MIS-C was actually a little more common than hospitalization for just COVID in kids age 5-11. The rates of sepsis, shock and myocarditis were also much higher for MIS-C than the other three presentations. Considering those are part and parcel of the Ah-nold like response driving MIS-C, that’s no big surprise. In fact, rates of myocarditis, sepsis, shock etc. are pretty minimal outside of MIS-C, according to this paper.

DO NOT READ THE INCIDENCE PER 100,000 OF MIS-C TO BE THAT 50% OF 5-11 YEAR OLD KIDS WHO GET COVID GET MIS-C.

THAT IS –NOT– WHAT THIS DATA SAYS.

YES I AM SHOUTING BECAUSE I WANT THAT TO BE CLEAR.

Remember, this counts ONLY COVID and MIS-C cases that resulted in hospitalization in this age group, and more than 99% of infections at this age will NOT wind up in the hospital. Both MIS-C and COVID bad enough for a hospital bed are VERY rare in this age. If a COVID infection in a 5-11 year old does wind up admitted though, yes, 50:50 shot it’s for MIS-C.

–More data is becoming available on BA.2, which is a cousin of omicron. CNN, in particular, took a pre-peer review publication of test tube and hamster studies from Japan and ran with it for some scare headlines after we went to “press” last week. We won’t do a full sciencepalooza on the Japanese studies, which you can find here. What they show is that BA.2 may be more severe in hamsters, and more resistant to antibodies, both therapeutic and vaccine or natural immunity acquired, than omicron. They also show that BA.2 is 1.4 times more infectious than omicron. It’s worth noting that “more resistant” to antibodies is only a few fold difference, which is less of a leap than for previous variants that have definitively been more breakthrough prone. Further, antibodies from patients recently recovered from omicron itself retained good neutralization of BA.2. So if you caught omicron recently, you are likely pretty well protected from BA.2

The Japanese authors argue that based on these findings, BA.2 should be considered different enough from omicron and with sufficiently worrisome lab features to get its own letter of the Greek alphabet. They highlight data showing that BA.2 is especially prevalent right now in Denmark, Sweden and India. A little more than 10% of new cases in South Africa are also attributable to BA.2

Alright, so here’s the thing. If the lab data is correct, we should have early signs from these countries of a highly contagious severe COVID. As I type this, Denmark has dropped all COVID restrictions and has leveled off its omicron peak, with new cases beginning to declining. Out of several hundred thousand cases in the last week, from what data I can find, a grand total of 44 are classed as severe. Granted, Denmark has a >80% vaccination rate. Denmark is also debating ending its vaccination campaign this spring, and will not be encouraging booster vaccination of children as Danish health authorities are convinced by the low rate of hospitalization despite the very high positive rate of omicron during this wave that they have sufficient population immunity already.

For harder data, we again have the South Africans who continue to be world class in timeliness of clinical data collection and reporting. You can find their pre-print clinical experience with BA.2 here. My only quibble with this data is that they are using PCR for spike protein as a proxy to identify BA.2, and not sequencing, but that’s irrelevant as there is no significant clinical difference between omicron and spike protein positive COVID (which includes BA.2) in South Africa since BA.2 was identified there.

Meanwhile, in India, as of late last week they were entering “green” COVID levels and lauding their covaxin vaccine (developed in India, and uses inactivated SARS-CoV-2, much like a traditional vaccine). The covaxin vaccine muted omicron enough that the company developing it in India is submitting it to the FDA for consideration.

A COVID Technical Lead at WHO has also gone on record for the WHO stating that while BA.2 appears to be more contagious, thus far, there is no evidence it is more severe than omicron. Again, omicron did not even make it to a bad flu in terms of severity.

So even if it has scary lab features in Japan, BA.2 so far, in the real world, has -NOT- been as severe as the laboratory data suggests, and I suspect will continue to be omicron-level or less.

–Hopefully the rate of mass media seizing on the scariest data they can find, and then reporting without asking, or reporting, the key clinical relevance, will decline with omicron as well.

–Quite the interesting article in the NYT this week, wrapping up a bunch of recent research on vaccines, which patients need a booster, and quotes from a variety of experts as the recent data changes the NYT’s thinking about the pandemic at the moment. I’ve linked the Yahoo version here, so you can read the full article without worrying about the NYT pay wall. And you should read it–you will find yourself saying “Hey, the update mentioned this, multiple times, over the last few months…”

Over and over again.

I’m going to pick out some of my favorite quotes below, with links to our previous discussions, where you can drift down memory lane and recall us saying the exact same thing, months ago.

“As people across the world grapple with the prospect of living with the coronavirus for the foreseeable future, one question looms large: How soon before they need yet another shot?

Not for many months, and perhaps not for years, according to a flurry of new studies.

Three doses of a COVID vaccine — or even just two [emphasis mine]— are enough to protect most people from serious illness and death for a long time, the studies suggest.”

We covered the data showing that those under 65 were not especially prone to breakthrough, and thus unlikely to require a booster here (in the original Sciencepalooza) and our simple, straight summary of the booster data and vaccine effectiveness was here. In early September 2021.

We have been consistent in saying that the data suggest that those 65 and up, or with pre-existing known severe COVID risk factors, may benefit from a booster.

Oh look… here’s a quote a little further down in the NYT article!

“…said John Wherry, director of the Institute for immunology at the University of Pennsylvania. Although people who are over 65 or at high risk of illness may benefit from a fourth vaccine dose, it may be unnecessary for most people, he added.”

As we discussed around the omicron outbreak, the booster for those under 60 with NO high risk factors for COVID is really just peace of mind that you have minimized your risks of hospitalization as best as you can. We said repeatedly that the Pfizer antibody data that somehow prompted CDC’s “booster the world!” plan, despite being flawed and all of 20 some patients, was underwhelming. You can find that post here.

For what’s it worth, my antibody level was well above what would be expected of the boosted range a year after my initial two doses. I, personally, have not gotten a booster and have no plans to do so near term. I am under 60, with no major risk factors for severe COVID. We even ran a risk calculator hypothetical to show how unlikely a healthy 32 year old, with the two dose vaccine, would be to die from COVID, and re-iterated our booster recommendation for the 60+ and high risk, and optional for everyone else call here.

“Specialized immune cells called T cells produced after immunization by four brands of COVID vaccine — Pfizer-BioNTech, Moderna, Johnson & Johnson and Novavax — are about 80% as powerful against omicron as other variants, the research found. Given how different omicron’s mutations are from previous variants, it is very likely that T cells would mount a similarly robust attack on any future variant as well, researchers said.

This matches what scientists have found for the SARS coronavirus, which killed nearly 800 people in a 2003 epidemic in Asia. In people exposed to that virus, T cells have lasted more than 17 years. Evidence so far indicates that the immune cells for the new coronavirus — sometimes called memory cells — may also decline very slowly, experts said.”

We first discussed the important role that T-cells would play in mediating immunity to SARS-CoV-2 in August of 2020. We explained how T-cells work to control viruses (Varsity Level “Among Us” players) in November of 2020, when discussing how the COVID vaccines work and provoke B- and T-cell responses. Back in May of 2021, we covered studies available then that showed natural immunity, and vaccine immunity, showed memory B- and T-cell responses, which also covered emerging variants well, and that natural immunity memory cells were durable for at least a year (the longest they had measured to that point). In October of 2021, we Sciencepalooza’d the paper underlying a very misleading Yahoo article, which showed that memory T-cells in particular did better recognizing SARS-CoV-2 variants if you ran into them again. We bring up the detection of memory B- and T-cell responses to SARS-CoV-1 17 years later mentioned in the NYT quote above in that same October, 2021 update–but we first mentioned those papers in October of 2020.

“Throughout the pandemic, a disproportionate amount of research attention has gone to antibodies, the body’s first line of defense against a virus. That is partly because these molecules are relatively easy to study. They can be measured from a drop of blood…

“Most people don’t even know what they are — a lot of doctors and scientists are not completely clear what a T cell is,” said Dr. Dan Barouch, a virus expert at Beth Israel Deaconess Medical Center in Boston who led one of the T-cell studies.”

“Fundamentally, I would argue that T cells are probably more important than what many people have given them credit for,” Barouch said.”

At any rate. Better late than never to our archive, NYT.

–Speaking of NYT articles, another one made a major splash on social media, highlighting the CDC has -not- been reporting all of the COVID data it has been collecting, particularly hospitalization rates based on age and vaccination status. You can read that article here (again, Yahoo so no pay wall for the whole thing).

The most important quotes:

“When the CDC published the first significant data two weeks ago on the effectiveness of boosters in adults younger than 65, it left out the numbers for a huge portion of that population: 18- to 49-year-olds, the group the data showed was least likely to benefit from extra shots, because the first two doses already left them well-protected [emphasis mine].”

Hold on… hold on… give me a second…. Just gonna’ scroll up a bit and CTRL-C… and CTRL-V…

We covered the data showing that those under 65 were not especially prone to breakthrough, and thus unlikely to require a booster here (in the original Sciencepalooza) and our simple, straight summary of the booster data and vaccine effectiveness was here. In early September 2021.

There we go. Perfect.

Anyways, turns out as we were Sciencepaloozaing the published vaccine data, the CDC has been camping on the definitive data set! We were just extrapolating the limited, and international, data that was available at the time. From the NYT article linked above again:

“Much of the withheld information could help state and local health officials better target their efforts to bring the virus under control. Detailed, timely data on hospitalizations by age and race would help health officials identify and help the populations at highest risk. Information on hospitalizations and death by age and vaccination status would have helped inform whether healthy adults needed booster shots. And wastewater surveillance across the nation would spot outbreaks and emerging variants early.

Without the booster data for 18- to 49-year-olds, the outside experts whom federal health agencies look to for advice had to rely on numbers from Israel to make their recommendations on the shots.”

I hear ya’, outside experts whom federal health agencies look to for advice. We have also called for the studies and data needed to better identify whether and which adults need booster shots from these pages a lot, especially recently.

Why has the CDC been slow to release this data? Again, from the linked NYT article quoting the CDC spokesperson (with the quote that launched a thousand tweets about this article):

“Another reason is fear that the information might be misinterpreted, Nordlund said.”

Failure to release the data because of fears it might be misinterpreted is also why Scotland recently announced THEY had stopped releasing data on COVID severity, hospitalization and vaccination status.

“The cover up is worse than the crime.” –Famous saying.

Failure to disclose is the worse of the two evils here. Misinterpretation can be combated–we do that a lot in these updates. To the point of readers sending us useful highlights of confirmation bias and they role they play in conspiracy theories (that thread may be turning up shortly–stay tuned!). Not releasing the data only feeds the conspiracy theories, as now they are free to make any conjecture they want, and will immediately deny the accuracy of any data you now release hereafter, claiming you have massaged it after hiding it for so long.

You want to join the Bonfire of the Credibilities, CDC? This is how you join the Bonfire of Credibilities. You can read the article at the link for the quotes the NYT got from other experts castigating the CDC in basically the same way, for the same reason.

But we’re not done with quotes from the linked NYT article! Part of the problem releasing data from CDC is the political oversight and review of anything they try to publish. Yes, if you thought CDC was totally apolitical, like the science that Dr. Fauci claims to be the avatar for, these quotes are for you:

“The CDC also has multiple bureaucratic divisions that must sign off on important publications, and its officials must alert the Department of Health and Human Services — which oversees the agency — and the White House of their plans. The agency often shares data with states and partners before making data public. Those steps can add delays.

“The CDC is a political organization as much as it is a public health organization,” said Samuel Scarpino, managing director of pathogen surveillance at the Rockefeller Foundation’s Pandemic Prevention Institute. “The steps that it takes to get something like this released are often well outside of the control of many of the scientists that work at the CDC.”

If you missed our link out last week to a truculent heme-onc covering shortcomings in the methods and conclusions for publications that the CDC has put out (across two administrations now), and the same heme-onc conjecturing on political reasons for the selective data disclosure and interpretation in CDC publications, no time like the present to click the link…

–Our next is presented without comment (but when you see it… LOL):

–There is no report on what medications, if any, the Queen of England is receiving for her (reportedly) mild case of breakthrough COVID.

Socioeconomic:

–I have a giant section on financial repression and how the current move towards a cashless, Venmo-style society has risks on this spectrum, with some great discussion prompted by the Canadian Emergency Powers Act enacted, then redacted (after international expressions of concern), this week.

Those are part and parcel of the predictable consequences of the pandemic, as far as socioeconomics go, and yes, have echoes back to the Black Death.

But they seem out of tune today, given the geopolitical events of last night.

So we will present those thoughts on digital currencies and the important role they will play this decade on the tilt of scales between greater freedom and greater authoritarianism–hopefully next week.

–Quickly before the major event to cover, I have missed the whole Wordle craze, although I have pieced together that it’s a word game app that is very popular. Thus, the apparent controversy that Wordle got harder after the NYT recently acquired it was new to me. But thanks to a reader who sent along this thread, highlighting that the controversy is really a good illustration of confirmation bias in action, how that can perpetuate conspiracy theories, and how neither side of the artificial schismogenesis between the US body politic is immune: https://twitter.com/mjshally/status/1495458810177245184?s=21

I still wonder if part of the perception that Wordle got harder under the NYT umbrella is the well known fact that the NYT crossword puzzles do tend to get harder as the week rolls on? Priming the pump for this particular confirmation bias?

–But obviously, the Russian invasion of Ukraine deserves more of your focus this week. Credit where credit is due, the US intelligence community was 100% on this one. They might not get everything right, but their alarm turned out to be prescient here. (As did Epsilon Theory, based on analysis of Putin’s narrative over the last several months).

This is the return to history we said would accompany the end of the Pax Americana.

Yes, it will likely get a lot worse before it gets better.

For the history here, the undergrad courses I took in Russian history emphasized that Russia’s geopolitical goals are driven by its geography. Russia wants as much space as possible, because most of Russia is flat with few natural barriers to invasion–and Russia has been brutally invaded multiple times in ways Russia remembers. Russia also seeks a warm water port, which it got a few years back with Crimea. Very short summaries of this, “why Ukraine, why now?”, and further implications are here (which happens to highlight another important point here–this is the first time in a long time that Russia cannot win a war of attrition) and in a short Twitter thread by the same author here, although the maps have a goofy tilt.

What “worse” might look like is laid out here, which builds to the last two paragraphs.

The worst possible scenario is described here. Keep in mind that it is deliberately the worst possible scenario, and not a particularly likely one, despite the ongoing crisis.

–And yes, between sanctions, disruptions to oil and gas supply (mostly a scramble to source from anyone but Russia), other commodities where Russia is a key global producer, and the fact that the #4 and #1 global producers of wheat are now shooting at each other because one invaded the other there will definitely be more inflationary pain around the world.

On top of what was already pandemic related.

–The world is still truly and fully cranked to Maximum Stupid.

–As we have said before, this will be a decade where a century happens. The fault lines will lie on the geopolitics of the end of the Pax Americana, and the end of the pandemic, with its Bonfire of Credibilities and what will need to be changed institutions, its economic fallout, and the tottering balance between individual liberty and turnkey authoritarianism.

Yes, the bad moon is rising.

All possibilities are open. Outcomes better, and worse, are before us.

You must resist the strong temptation for schismogenesis and the forces seeking to promote it.

What is coming now along those fault lines above will only arrive with greater swiftness and intensity from here on in. Your courage, your compassion, your wisdom will all be tested. Physical, emotional and spiritual challenges are well on the way. No matter how tiny of your corner of the world may be, your choices will matter.

“A day may come when the courage of men fails, when we forsake our friends and break all bonds of fellowship, but it is not this day”

Aragon, LOTR

To modify another quote this week, you may not be interested in history, but very soon, history will be interested in you.

To our wisdom.

–Give ’em hell Ukraine.

–Your chances of catching coronavirus this week, despite the downturn in activity, are equivalent to the chances that you didn’t start the fire, but will help add some verses nonetheless.

<Paladin>