2021-12-30 General

Mitigation Measures

This article says that people can now apply for the federal Canada Worker Lockdown Benefit of up to $300/week, retroactive to 19 Dec.

Variants

This report from Ontario Public Health says that, after adjusting for vaccination status, the risk of severe illness from Omicron is 54% that from Delta. This preprint (from August) says that Delta had about 3x the risk of hospitalization and 2x the risk of death as from COVID Classic, so that says that the risk of death from Omicron is about the same as from COVID Classic, and about 1.5 more likely to cause hospitalization.

Something which was kind of buried was that there had been no Omicron deaths yet. Maybe they just hadn’t had time to die yet?


This preprint looked at hospitalizations in in Gauteng South Africa, which was one of the first places to get hammered by Omicron:

wave 2wave 3wave 4
dominant variantBeta?DeltaOmicron
case hospitalization rate18.9%13.7%4.9%
admissions for severe disease60.1%66.9%28.8%
pediatric admissions of total admissions3.97%3.52%17.68%

My math says that fourth wave patients had 85% less chance of having severe disease compared to Delta wave patients in Gauteng.


This preprint, which looked at 49 hospitals across South Africa, had very similar findings:

wave 3wave 4
max patients23516342
percent admitted to hospital from ER~68%41.3%
median age5936
percent presenting with acute respiratory condition91.2%31.6%
percent requiring oxygen therapy74%17.6%
percent admitted to ICU29.9%18.5%
median length of stay7-8 days3 days
death rate29.1%2.7%

Ha! People commented on the sharpness of the Omicron point in Gauteng, and I said I thought I saw a tweet saying to be careful because lots of migrants left town in December? I found it again, here it is. The tweet’s author is one of the scientists who f found Omicron.

Treatments

This pre-preprint is slightly beyond me technically, but I believe I figured out enough of what it says. As you might have heard, SARS-CoV-2 gets into cells mostly by using using the spike protein to “unlock” the ACE2 receptor. Apparently, most bat coronaviruses don’t do this, they mostly use endosomal fusion, which I think is where the host cell wall folds around the thing outside, making a little bubble that then comes into the cell:

Well, this pre-preprint says that Omicron, unlike the other variants, mostly uses endosomal fusion to get into the cells! This has major implications for treatments.

  • Paxlovir is still fine because it doesn’t care how SARS-CoV-2 gets into the cell; Paxlovir acts on SARS-CoV-2 once it is inside the cell.
  • I believe that some (many?) of the monoclonol antibodies work by jamming up the spike/ACE2 receptor pairing; this preprint would explain why so many of the monoclonal antibodies no longer work.

The endosomal fusion is chivvied along by molecules called cathepsins, and this pre-preprint found that a inhibitor of cathepsins B and L called E64d (AKA Aloxistatin) kept Omicron from getting into the cells. I don’t know if E64d is usable as a medicine by itself, it might be too powerful / not targeted enough. It is certainly available: you can buy it bulk from a biological reagents distributor (for research purposes only).

Interestingly, hydroxychloroquine, the drug which Trump was pushing for a while, works by blocking endosomal fusion. So while hydroxychloroquine didn’t work against COVID Classic, maybe it would work against Omicron?

I discovered quite a few papers which talked about SARS-CoV-2 and cathepsins, so maybe drugs in this area will be coming soon?


I don’ t know if I am going to have time to dive into this topic, but this Twitter thread starts by discussing whether or not there is any scientific basis to the folk remedy of gargling salt water to help a sore throat. Okay, fine, but gets really interesting: apparently gargling is A Thing in Japan, that it’s common to gargle as soon as you get home. AND Japan has a stunningly low COVID-19 level right now. It’s especially surprising when you compare Japan’s case rate to South Korea’s case rate. South Korea and Japan have populations are genetically a lot closer than either country likes to admit, so it’s something cultural or administrative.

Also note that Japan had a big wave before, so gargling wasn’t effective enough against other strains, but also it’s clear that Omicron is infects the upper respiratory systems more than other strains and less of the lower respiratory infection than other strains.

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