Pandemic Update for 2022-01-22: Ultrapotent
Items of recent pandemic news: A resource for finding authorized therapeutics in the US; how long booster shots protect; an early study isolating ultrapotent antibodies from elite neutralizers; and a new variant on the Omicron variant. Plus a frippery.
Quotes of the week
- Tom Peacock — I would be very surprised if BA.2 caused a second wave at this point.
- Dr. Gregory Poland — Always, human decision-making fails in the face of exponentiality.
Omicron spinoff BA.2 gaining ground
Omicron is not one thing. The WHO and researchers around the world are tracking three versions of the variant: BA.1, BA.2, and BA.3. The first one is dominant worldwide, at an estimated 99% prevalence, and is the one people usually mean when they say Omicron. BA.1 has the mutation that causes the serendipitous signal in some PCR tests, the so-called “S gene target failure,” allowing for quick identification of a likely Omicron infection. BA.2 is missing this mutation and so early on was nicknamed “stealth Omicron.”
Now BA.2 is taking market share from BA.1 in a number of countries. Here are early reports from Denmark, where BA.2 has grown to around 50% of sequenced cases, and from Norway, where its share is also growing. Similar signals are coming out of India, the UK, and Germany.
As for what is known about BA.2, the answer is: not much beyond the above indications that it may have a fitness advantage over BA.1. Very early computational studies suggest that BA.2 may not differ much from BA.1 in its reaction to vaccines and antibodies. Here is a Twitter thread (unrolled version here) from Tom Peacock, the virologist who first raised the alarm on Omicron. It links to a further few threads from researchers on the front lines. In short, we know little yet about BA.2’s immune evasiveness or virulence. Peacock says:
Ultrapotent antibodies from elite neutralizers
Here is promising early research from scientists in Cologne, Germany, with collaborators across the US. They have isolated antibodies that demonstrate action against SARS-1, MERS, common cold coronaviruses, and SARS-CoV-2 — including against 6 existing variants, 19 spike escape mutations, and 4 theoretical variants that have not been seen in the wild (yet). One of the antibodies demonstrates “a flexible binding mode, targeting both ‘up’ and ‘down’ conformations of the RBD [receptor binding domain].”
The researchers found these ultrapotent antibodies in the serum of people who had recovered from Covid-19; in fact from the small fraction of those people whose bodies produced the most potent and effective B cells in response to the virus. The “elite neutralizers” comprised 10 out of the 963 people studied.
Results were published in Cell Host & Microbe. The paper is paywalled there, but is reproduced in many places across the web.
Many research groups are pursuing “next-generation mAbs that retain potency and effectiveness against circulating or emerging SARS-CoV-2 variants,” as the Cologne paper puts it. Eric Topol leads another such group and tweeted a link to the German research last month. It has not otherwise been picked up in the popular science press.
How long does a booster shot protect against Omicron?
As always when we talk about protection, we have to ask, Protection from what? The vaccines were designed to protect against severe disease and death. It happens, fortuitously and somewhat rarely in the field of vaccinology, that they also provide some temporary protection against infection.
A third, booster dose bumps up both kinds of protection temporarily.
Research has now roughly quantified how a booster dose of the Pfizer vaccine affects the protection against Omicron over time. MPR News has a summary of two papers (one, two) out of the UK. I created the figure to put the results in a nutshell.
Finding authorized therapeutics
We noted the tight supplies of Molnupiravir and Paxlovid earlier this month. The two government web pages linked in that report, which on January 5 showed how much of each therapeutic had been shipped to each state, no longer show that. Wanting to update the situation on therapeutic availability, I found a government page that lists supply of therapeutics at a much more granular level, down to the pharmacy or clinic, nationwide.
I was interested in particular to see how the supply of Paxlovid in Minnesota is holding up. Getting that information out of the HealthData.gov site is tortuous in the extreme; the site is not constructed and interfaced with consumer ease-of-use in mind. I ended up exporting the total data set and bringing it into Excel on my laptop. Click on the thumbnail for an answer to the question posed above (opens in a new window). For those who might want to explore the full data set, you can download my Excel worksheet. Or you can try your luck with the HealthData.gov page.
I don’t know how often the government data is updated. It probably depends on each state uploading its own data, and I would expect that this happens once a week at best. Notice in the Minnesota Paxlovid data that only a bit over half of the locations have reported how much of their allocation remains.
The earlier report found Minnesota in receipt of 880 courses of Paxlovid after the first week. The quantity reported here is exactly twice that, so it probably represents two weeks of supply to this state.
A very rough estimate of the demand for Paxlovid in Minnesota, near the peak of this Omicron wave, would be around 46,000 courses of the drug per week (assumptions: 11,000 new cases per day, 60% of whom meet the FDA’s criteria for Paxlovid).
Frippery: Baseball for sleeping
Your frippery today is a soporific: almost two hours of audio for a totally fictitious game of baseball between the Big Rapids Timbers and the Cadillac Cars. You could fall asleep to it. In fact that is rather the point. Listening to this broadcast, you have no skin in the game. It doesn’t matter at all.
The perpetrator of Sleep Radio is a Chicago-based media producer who calls himself Mr. King. In this interview he explains the genesis of the idea: “What if there [were] a baseball game that you could listen to, and there were no shouting, commercials at the same audio level, and you could actually fall asleep?”
The towns of Big Rapids and Cadillac both exist in Michigan, I found. They are north of Grand Rapids. But the ball teams are made up, as are Foghorn Field, the radio station WSLP AM, and the Northwoods Baseball Radio Network. (There is a Northwoods Radio, but it’s in Cloquet MN.)
“Fake Baseball for Sleeping,” Episode 001, is pitch-perfect — if you will pardon the expression. I grew up listening to the like on the radio every summer. Perhaps you did too. The advertisements for local businesses (Timbuk Three AV; Ted’s Fishing World) are beyond precious.
If you make the mistake of becoming attached to the outcome of the imaginary ball game, you are in for a letdown. The producer contrives to fade the meaningful audio — announcer, station promos, local ads — with respect to the background crowd noise on an imperceptible ramp over the last quarter hour of the podcast. If you need to know the final score of the Big Rapids Timbers and the Cadillac Cars — too bad, because all you will get is the gradually fading noise of an imaginary crowd as they wander off to their nonexistent homes after a fictitious summer game, ending in white noise that slips into slience. You might just as well have drifted off to sleep.
One commenter on the website described this ASMR podcast thusly: “Kind of like a glass of milk in some ways, and also like taking acid in other ways.”
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