—Overall, global daily cases are going down, but again with high local variance. Some parts of Europe are still experiencing higher case numbers. Spain and France, for example. South America is broadly trending down again—including Brazil (that will be important to note in a minute). Same for South Africa.

—Leading off, we have yet another publication that, despite the byline, I cannot comment on.
https://jamanetwork.com/journals/jama/fullarticle/2775647.

Questions should be addressed to the corresponding author, and thank you for your understanding.

—Going around the horn, we have a number of vaccine headlines from earlier in the week. Pfizer’s vaccine comes in vials where each vial contains 5 doses—but, they put in enough of a buffer that you can get a 6th dose out. Going after that 6th dose got approval, but a standard needle won’t reach the bottom to get that 6th dose. You need a special needle for that, which has of course gotten hard to find as everyone scrambles to find them. Manufacturing will fix that over the next few weeks to a month, and it extends the available supply of at least one of the major vaccines currently on the market.

—In other manufacturing news, AstraZeneca’s vaccine (heavily used in Europe) has been hit with manufacturing woes. One of their suppliers in Europe has a major shortfall, and so, for example, of 8 million doses supposed to arrive in Italy this quarter only 3.4 million are actually going to make it there.

The CEO of AstraZeneca has been taking several meetings across the continent “without coffee”, as our cousins across the pond phrase it.

They’re actually not alone. Pfizer has reduced shipments to Europe, mostly because a plant in Belgium that was supposed to supply them on the continent is in the middle of some upgrades.

The target across the various currently approved manufacturers is to have shipped 2 billion doses by 2021.

—Moderna is starting to test a slightly different booster including some of the spike protein variants in the newest “worry” strains of COVID. Not sure how necessary that is based on the clinical data so far (still no news of massive amounts of reinfections which would cause concern, or in vitro data suggesting a new variant was around the vaccine). But better to be proactive, I suppose.

—Lastly on vaccines, Merck, one of the leaders in vaccines in general, bagged its “also ran” COVID vaccines as data showed they are underperforming what is already available. I suspect you’ll be able to follow personnel announcements out of Merck over the coming year for “early retirements,” “taking a break to spend more time with family,” or “pursuit of exciting new opportunities at [NOT MERCK COMPANY HERE]” from their vaccine division, as I doubt the leadership of Merck is fond of the look right now.

—Wrapping up second vaccine doses on the floor here at work this week, so hopefully should have antibody comments (at least for my sample!) soon…

—On the variant front, still no evidence that any of the strains making the headlines are causing massive amounts of reinfections. Certainly by now, the South Africa and UK strains have had plenty of opportunity to do so. That they have not is good evidence that very probably will not.

Columbus strain of COVID (actually two strains, one which has the UK and South Africa N501Y spike protein variation and one with a different change to the spike protein) is likewise not showing an ability to re-infect.

All of these strains do indeed compromise some, but not all, of the PCR tests out there on the market. The CDC assay we use does NOT use the spike protein as a target, and so our assay performs just fine detecting these variants, as reported by the FDA. A few assays out there do use the spike protein though, and can come up false negative for a COVID infection (assay says no COVID, but COVID is really there). That has been used to screen for some of these variants, when another PCR target is available to test. You’ll see the spike protein target drop, but the other targets stay positive. That can then be sent for sequencing to confirm the variant identified.

My suspicion is that Columbus strain, particularly the Q677H spike variant, is across the US midwest. Ohio State reported it began to break out in late November-December in Ohio. I have heard rumblings from academic testing labs here in Indiana that their spike protein targeting PCRs saw some patterns suggesting a variant (my guess, the Q677H) was circulating here around the same time.

Since then, as we have mentioned, new cases and hospitalizations (admission and census) for COVID have cratered in both states and across much of the Midwest. I’m pretty confident that this is another “more contagious, but not more severe or more severe more often” variant at best.

—Unsurprisingly, South African variant has made its way to the US. All of these variants will get worldwide.

—The only one to watch closely at the moment is the Brazil variant. This is the P.1 variant, a descendent of B.1.1.28 and contains three spike mutations: N501Y, K417T and E484K. The E484K in particularly has been shown in petri dishes to interfere with binding of some monoclonal antibodies to SARS-CoV-2.

This variant was actually first described in Japan, found on routine screening in 4 travelers from Brazil.

Back in Brazil, this variant was found in 42% of cases in Manaus, the largest city in the Brazilian Amazon, in December. This region was thought to have been 75% infected by October of 2020, and the detection of this variant was part of a mini-surge in cases (all across Brazil really) in December through the early part of this year. Now, those stats are from the CDC website on variants of concern—but the paper they link to cite does not present ANY of that data. I have no idea where CDC got those percentages for this variant, but have no reason to suspect they are false, either.

What I can confirm is that there are now two case reports (the paper the CDC cited is the case report for one, and it mentions the other) of bona fide reinfection of SARS-CoV-2 patients by this variant.

Two case reports, while worse than no case reports, does not a trend make. Remember the CDC projections for “no vaccine” from last week. If this was a widespread ability of this variant, the pandemic should be reigniting across Brazil right now, and we should be hearing about more reinfected patients.

So far, that dog ain’t barking.

We will follow closely because of those case reports of reinfection by this variant, and in particular follow case trends and reports of lots of reinfected cases in Brazil suddenly.

As it stands today, more likely than not, this is also a strain that will not get around vaccine or immunity in the vast majority patients.

—Lastly, I thought the headline was from “The Onion,” but no, turns out this is true. You may have seen the headlines stating that wearing two masks, maybe even three, is better than one at reducing SARS-CoV-2 infection.

I mean, I don’t even know where to start on this. Yes, it’s true that each layer imposes an additional physical burden on the virus. It’s also true that if you wore so many layers of mask that you could no longer breathe, that would be 100% effective in stopping coronavirus from getting to your lungs.

You would suffocate, sure, but at least the ‘rona wouldn’t get you!

Let’s also recall the Black Death Choose Your Own Adventure.

If you decided to run for the hills and try to outrun the plague in its march across continents…

if you decided to stay put and go about your life while avoiding obviously sick people and situations of heightened risk (ye olden tyme social distancing)…

if you barricaded yourself in your house to try and wait it out (ye olden tyme shut down)…

or if you partied like there was no tomorrow figuring you were going to catch it anyways (ye olde tyme “yeet yeet”)…

you were right!

At least in terms of catching the Black Death and dying from it at the exact same rate as everyone who chose differently.

The moral of the Black Death story, among many we have forgotten, is by the time the pandemic agent is causing cases in your town, you are ALREADY exposed. You can take measures to reduce your chances in any individual encounter with the virus (social distancing, extra masks), but give the virus enough time and opportunity, and you will meet an infectious dose of it at some point. The only way to avoid this is herd immunity +/- vaccine finally strangling out infection chains when the virus runs out of encounters with susceptible hosts before it gets to you.

So you do you according to your own risk tolerance. If you want the psychological security of one (or more) extra layers of mask between you and any close encounter with the virus, despite knowing that most cases are transmitted by close contact at home (where you probably aren’t wearing even one layer of mask), go for it. It won’t hurt.

For my own part, one layer has got me through so far. I think I’ll keep rolling the dice and replacing masks at the current rate.

—On the off topic but social side, presented as a “food for thought” commentary on market events this past week. Those may be more significant than just the latest market speculation:

https://www.radigancarter.com/dispatches/the-wall-street-insurgency

Additional background:

More background:
https://twitter.com/kofinas/status/1353717266597236736

Worth mentioning, too: Nihilism was a major after effect of the Black Death too. And post World Wars Europe. Any time, really, the institutions of society had proven themselves not up to the challenge.

The current r/wallstreetbets “insurgent” strategy has a problem though. Some of the institutions and individuals they are targeting will ride up the long side with them, then short the whole way back down. Those institutions and individuals have the money to know the trade flows (and from whence it comes), be fast, and the money to change the rules in their favor.

So the real fun will start when the insurgency figures out how to target the –currency-…

—Your chances of catching coronavirus this week are equivalent to the chances someone has mentioned GameStop* to you in the last two weeks…

*–The author holds no positions long or short in $GME

<Paladin>