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Comment by npostavs on Omicron Post #13: Outlook · 2022-01-08T14:42:01.714Z · LW · GW

[Canada's] last day of data is likely a reporting delay there.

I think it's likely more about testing capacity. E.g., Ontario restricted tests to high risk population since Dec 31.

Comment by npostavs on Omicron Post #6 · 2021-12-14T13:34:50.945Z · LW · GW

If by "region around Washington" you meant the graph labeled "Capital Region", I think that refers to the capital of Denmark.

Comment by npostavs on Looking for reasoned discussion on Geert Vanden Bossche's ideas? +6 Months on... · 2021-12-03T19:22:18.678Z · LW · GW

It seems difficult to pin down Bossche's predictions as right or wrong.

Has his previous theory's been proven right?

His previous claim, as I understand it, is that mass vaccination will produce immune evading and more dangerous variants. I think the fact that the variants we've seen so far either emerged before widespread vaccination (alpha), or in places with low vaccination rates (the rest) is at least weak evidence against his claim.

Perhaps he would argue the low vaccination rates did produce those variants, even though the rates were low. But how could we tell?

Will his current theory's been proven right?

He says:

Omicron is likely to start out as a mild disease because short-lived, poorly functional anti-S antibodies (Abs) that resulted from previous asymptomatic infection (e.g., with another previously dominant variant) will no longer recognize Omicron. [...] However, the overall pattern of ‘mild’ disease would only prevail until Omicron becomes dominant and causes high infection rates. When this happens, short-lived, low affinity anti-S Abs will start to compete with innate Abs in an increasing part of the population as a direct result of the enhanced likelihood of re- exposure shortly after previous infection.

How would we distinguish this from the case where Omicron seems mild at the beginning because 90%+ of covid cases are mild, and then once the numbers are high enough we start seeing the smaller fraction of severe cases?

There is one prediction that looks almost tractable enough to (eventually) decide:

It is undeniable that mass vaccination will only drive the virus [...] to use alternate receptor domains on permissive cells. The fitness cost that may come with such a dramatic mutation is likely to be rewarded with enhanced pathogenicity. I am truly afraid that these dynamics will eventually allow for the natural selection of individuals with uncompromised innate immunity while eliminating those without it. While such natural selection would lead to an eradication of SARS-CoV-2 as innate immunity sterilizes the virus and blocks transmission [...] the price paid for ending the pandemic by virus eradication is not comparable to the one paid for by generating herd immunity and allowing the virus to enter an endemic state.

So I guess if we reach endemic state following mass vaccination (the general concensus is that eradication is basically impossible by now so I judge this extremely likely), then his theory will be proven wrong. And if many hundreds of millions die followed by eradication of the virus then he was right. Check back in a year or two?

The problem is that he can still claim half-credit if the virus uses an alternate receptor domain, but that doesn't lead to a high kill rate. And regardless we still won't know whether his counterfactual herd-immunity via natural immunity route would have avoided this.

Comment by npostavs on Omicron Variant Post #2 · 2021-12-01T21:50:28.186Z · LW · GW

Wikipedia says:

It is a viral vector vaccine based on a human adenovirus that has been modified to contain the gene for making the spike protein of the SARS-CoV-2 virus that causes COVID-19

So it's not better than the mRNA vaccines in this sense, as far as I understand (I don't know if that makes it a bad idea, as such).

The inactivated virus type vaccines are

Chinese CoronaVac and the Sinopharm BIBP and WIBP vaccines; the Indian Covaxin; later this year the Russian CoviVac; the Kazakhstani vaccine QazVac; and the Iranian COVIran Barekat.

But those are probably much harder to get for readers in Western countries. And they've generally been found to be less effective, I think; possibly because the inactivation process damages the proteins.

Comment by npostavs on Which booster shot to get and when? · 2021-11-22T23:04:20.474Z · LW · GW

Does it really show that? Looks hoplessly confounded to me:

Among fully vaccinated persons, 93 of 122 (76%) Pfizer-BioNTech recipients and 0 of 50 (0%) Moderna recipients had been vaccinated ≥4 months before the outbreak (p<0.001). A larger proportion of Pfizer-BioNTech recipients had diabetes (p = 0.02) or hypertension (p<0.001) than Moderna or Janssen COVID-19 vaccine recipients, and a higher proportion of Pfizer-BioNTech and Janssen recipients had a history of smoking (p<0.001) than Moderna recipients 

Comment by npostavs on Randomized, Controlled's Shortform · 2021-10-22T00:10:25.682Z · LW · GW

This is the system that is planning to finally [replace their fax machines by the end of 2021](https://www.cbc.ca/news/science/ontario-fax-machines-1.5955753) (which means they'll probably get that done around 2025), so I'd say expecting up-to-date VOC tests is being too optimistic.

Comment by npostavs on Randomized, Controlled's Shortform · 2021-10-19T00:54:00.095Z · LW · GW

I see a some cases of Delta on the 2nd graph of the Public Health Ontario page, but much less than 99% (e.g., 7 Delta to 205 No Mutation for week of October 6). Likewise, the Toronto dashboard has mostly delta in the VOC graph since July (it's a bit hard to see without excluding the Alpha counts from earlier which are much higher and make the y-axis too big).

https://www.publichealthontario.ca/-/media/data-files/covid-19-data-tool-technical-notes.pdf?la=en says:

Lineage B.1.617.2 (Delta) includes cases identified by genomic analysis. Mutations common to 
B.1.617.2 are not included in the current VOC mutation test.

Which I interpret to mean they're just not testing most cases for "Delta-ness". Since non-Delta variants are just about zero, 99% Delta seems like a good guess.