2021-12-07 General

A lot of highly technical material dropped today, on a day when I was kind of busy, so I have not had enough time to really understand everything. AND information about Omicron is still in flux. So if you don’ t understand something here, it’s not just you.

Also, there will probably not be postings on Wednesday or Thursday. See you on Friday.


Well, as advertised, it took about two weeks to get data on neutralization of Omicron. The bad news is that there is huge immune evasion. (The report isn’t even a preprint, but here’s a mass media article on this study, from the South Africa.) They found the level of neutralizing antibodies against COVID Classic is 41x higher than against Omicron. While it is true that the numbers in neutralizing antibodies are non-linear and difficult to relate to how good the protection is, they reported the similar ratio for the Beta variant is 3x.

And here is ANOTHER pre-preprint (from Sweden) on the topic. This one says that the neutralizing ability is wildly variable, between 1x and 23x difference compared to the “founding strain” (which I interpret to mean the Wuhan strain). However, when they used the “WHO neutralization standard” (which is a collection of standardized samples) they found a 40x difference.

The good news from both studies, if you can call it that, is that people who had two shots plus an infection still had high enough antibody levels to clear Omicron. People with just two shots did not have high enough antibody levels to clear.

Translation: it’s bad.

To be fair, antibodies aren’t the only thing. You also get some protection from T cells and B cells. (Read this article if you want to feel better about the other parts of the immune system still having your back.) But those responses are slower; while they might keep you out of the hospital, they won’t keep you from getting infected.

Two shots plus a booster is probably intermediate between two shots (probably not good enough) and two shots plus an infection (probably good enough).

Because the immune evasion is high, that means that the R0 is lower. I have not seen an estimate yet, but a few days ago, a Smart Guy had this prediction:

As you can see, 41x is off the scale, so maybe R0 will be really low? Like 2.5? That would make it just like COVID classic all over again: a virus with an R somewhere around 3 and a population that had no immunity to it. (That would also suggest that the reason that case counts are so high in South Africa is because they have lousy masking/distancing/restrictions. I find that a little hard to believe, but maybe?)

We still don’t know what the severity of Omicron infections is. I have heard people opine that it might be good if Omicron is just like a common cold, then we could let it rip and get immunity that way. Unfortunately, given that Delta immunity doesn’t translate into Omicron immunity, why should we believe that Omicron immunity would give you Delta immunity? I think maybe we are going to have to think of these as two different diseases. 🙁


Good news! This article reports that GSK, the makers of the monoclonal antibody sotrovimab, say that sotrovimab is still effective against Omicron. This is good news for two reasons:

  1. There is still an effective treatment.
  2. Drug companies figure out what antibodies to test by looking at what humans made. This means that at least some humans naturally made an antibody (sotrovimab) that fights Omicron, yay!


Good news! This article reports that Medicago has finished their Phase 3 trials with good results: 75% against Delta infection. Go Canada! 🇨🇦

The first results from COM-COV2 are out! This is the big mix&match study out of England. Now, I thought that they were looking at vaccine effectiveness in humans, but this is data from test tubes. I hope there will be another study with data from humans.

Regardless, the study says to me that the more mRNA, the better.

First doseSecond doseIgG concentration (ELU/mL)

Mitigation Measures

This article reports that the Government of Canada is going to institute a vax mandate for all federally-regulated business sectors like banking, telecoms, and shipping.


This article points out one of the problems with rapid tests (in the USA): they frequently don’t get reported to the health agencies, and never get whole genome sequencing. This makes it hard for health agencies to know what is going on.

More bad news: this article reports that there is a variant of Omicron which does not have the S-dropout, which means that the standard PCR can’t recognize easily which are Omicron and which are not.

Opinion: I think that testing is going to be a huge problem once Omicron hits with full force. Omicron is going to spread widely, so there will be lots of testing needed. Even if Omicron turns out to be more like a cold, Delta is not, so then you’d need to distinguish between Omicron and Delta, and I don’t think any country’s testing is set up to handle that. Furthermore, it’s even harder to distinguish stealth Omicron from Delta. 🙁