Tiny Timbs posted:

Why am I seeing "The population in South Africa skews younger so..." come up so often in comments about Omicron severity? Surely their stats include the age of the patients?

Petey posted:

* an R0 of 6, which is my read of where Trevor Bedford estimates it to be for Omicron (could be a bit lower, could be 2x higher, in his projections)

Tiny Timbs posted:

Why am I seeing "The population in South Africa skews younger so..." come up so often in comments about Omicron severity? Surely their stats include the age of the patients?

Fritz the Horse posted:

Bedford seems to estimate an initial Rt of around three in the interview linked above

Stickman posted:

Rt is different that R0. Rt reflects the average reproduction in the current population (with precautions + vax + prior exposure etc), while R0 attempts to remove at least NPIs and vaccinations and current level of prior exposure to reflect baseline reproduction that can then be modified by interventions/infections that confer some protections. R0 is still tricky to pin down too, because it's still population-dependent and what exactly gets included can depend on modeling goals. This is a pretty good brief discussion of how tricky things can get.

E: Should have looked at Petey's post - if we're plugging it into an epi calculator we'd need to use Rt instead!

Petey posted:

I'll go read that nymag link once I can find my way around the paywall.

Stickman posted:

Here's a pdf print-out.

fosborb posted:

Would you call this file a...... pre-print?

Owlofcreamcheese posted:

I'm not sure we ever DID know that delta was more deadly.

During the new york wave the actual ratio from cases in the US to deaths in the US was one death per 13 cases, now in the delta era we are around 1 death for 260 confirmed cases.

CLEARLY that isn't real. It's dead simple to know that isn't a real effect and I'm not claiming that is. It's obvious that it was just a result of testing barely existing during the new york original virus era.

But it also means all the real world death rate estimates for original vs delta are all pretty iffy. Delta killed way more people but because it spread much much more widely. The theory was it might also be more biologically dangerous. but that was with big error bars. If it was like 11% less fatal but just killed more because of bigger waves it's not like we measured with precision enough to actually have known. The estimates of delta ended up with it being very close to the original, with big estimate on top of estimate estimations on either's fatality. If it was some less deadly that would have fit within the estimate error bars.

Petey posted:

* an R0 of 6, which is my read of where Trevor Bedford estimates it to be for Omicron (could be a bit lower, could be 2x higher, in his projections)

Stickman posted:

Here's a pdf print-out.

quote:

Some governments expect vaccines to enable future infections or reinfections to act as immune boosters [31], but there is evidence that even after multiple infections and full vaccination, reinfection can result in more severe disease [32]. A study of US healthcare workers found that hospitalization was more likely following reinfection [33]. The UK SIREN study suggested that although prior infection provided ~80% protection against reinfection at 5 months, compared with controls, symptomatic re-infections were still seen with high virus loads and potential for transmission.

CAT INTERCEPTOR posted:

It was more deadly to the *UN*vaccinated. New York by the time Delta got there was by the main a vaccinated population so yes the death rate was a hell of a lot lower as a result of that

Platystemon posted:

I don’t like that this is his working hypothesis.

I mean, it’s a fine hypothesis, it’s just disastrous if true.

Owlofcreamcheese posted:

What even is "disastrous" about that tweet? South Africa isn't the only place on earth with large populations of vaccinated or recovered people. I doubt even 10% of the US is immunologically naive at this point.

Petey posted:

Is it about us dramatically undercounting the denominator of positive cases so the CFR looks higher?

Owlofcreamcheese posted:

For the initial new york outbreak?

Petey posted:

Platyslemon wasn't saying what TB posted was disastrous, they were saying that *my* (incorrect) interpretation of R0 = 6 would be disastrous, if true.

A GIANT PARSNIP posted:

Early testing priority was given to those already hospitalized, and those already hospitalized are more likely to die than your average case.

Platystemon posted:

Nah.

Trevor Bedford’s working hypothesis is that Omicron is that it’s no less severe than Delta in any particular group—vaccinated, unvaccinated, recovered—it’s just infecting a larger fraction of vaccinated and recovered people, while potentially causing illness similar to Delta in the unvaccinated.

That’s a bad scenario for everyone.

Such behaviour would constitute a case of Simpson’s paradox, the textbook example which in medicine is the low birth-weight paradox. Underweight babies born to smokers have better health outcomes than underweight babies born to nonsmokers. So, should doctors recommend that parents-to-be who are at risk of having underweight babies take up cigarettes?

No. Smoking doesn’t make any babies healthier. What it does do is decrease birth weight across the board, moving otherwise healthy babies into the underweight category. These otherwise healthy babies are at higher risk for bad outcomes than if they were of normal weight and born to nonsmokers, but they are at lower risk than the “traditionally” underweight babies, e.g. from malnutrition. Smoking makes every baby sicker, but creates the illusion of making underweight babies healthier by diluting the small number of seriously sick underweight babies with only mildly sick babies.

Petey posted:

Got it, thanks for clarifying.

(my tired eyes somehow misread your "I don’t like that this is his working hypothesis" as "I don’t think that this is his working hypothesis")

CAT INTERCEPTOR posted:

It was more deadly to the *UN*vaccinated. New York by the time Delta got there was by the main a vaccinated population so yes the death rate was a hell of a lot lower as a result of that

Stickman posted:

Interesting thread on modeling transmissibility vs immune evasion using initial SA data from SA's modeling team. Their best-fit estimates are transmissibility ~2-4x greater than Delta with 25-50% immune evasion, but there are some scenarios that estimate higher immune escape and lower relative transmissibility (if SA's initial outbreak occured in a population with very high prior infection or Delta is reinfecting a much higher % than their best estimate).

https://twitter.com/saCOVID19mc/status/1472680175301283847

Petey posted:

Something else that's been on my mind —

I worry a little bit about blue states / covid-cautious institutions, with strong testing and exclusion regimes, destabilizing themselves over the next few weeks. Let's say Omicron *is* much more mild but also *is* much more transmissable in a highly vaccinated population. I can easily imagine my university, with weekly PCR testing and a booster mandate, have lots of critical personnel — folks at the medical center, utilities, etc — getting exposed over holidays, popping PCR positive, and having to stay home from campus for 7-10 days under our current rules. At some point, do we run out of people to operate the utilities and the health clinic? Do we then have to revise our policies and procedures mid-outbreak? What kind of institutional trust will decay there?

Now take this and scale it up to hospitals and electrical grids in Massachusetts. I don't expect this specific thing to be an issue in Florida etc because I just expect people to come to work when they are sick but not sick enough to not work.

Note you already see this being trialed in the NFL, in terms of "don't need to test if you're vaccinated and asymptomatic," in order to keep the season going. The sports leagues have often led other major American institutions in their response all pandemic.

Stickman posted:

And yes OoCC, we measure with enough accuracy by comparing like-to-like, ie rates of death for delta and alpha over transition periods, adjusted for relevant demographics. That’s why the error bars aren’t too large to distinguish hypotheses, a thing that you just pulled out of your rear end.

quote:

A booster shot of the Moderna coronavirus vaccine significantly raises the level of antibodies that can thwart the Omicron variant, the company announced on Monday.

The news arrives as Omicron rapidly advances across the world, and most coronavirus vaccines seem unable to stave off infection from the highly contagious variant.

Moderna’s results show that the currently authorized booster dose of 50 micrograms — half the dose given for primary immunization — increased the level of antibodies by roughly 37-fold, the company said. A full dose of 100 micrograms was even more powerful, raising antibody levels about 83-fold compared with pre-boost levels, Moderna said.

Both doses produced side effects comparable to those seen after the two-dose primary series. But the dose of 100 micrograms showed slightly more frequent adverse reactions relative to the authorized 50-microgram dose.

The results are based on laboratory tests that do not capture the full range of the body’s immune response against the virus. Although vaccines may not prevent infection from the variant, they are expected to prevent severe illness in the vast majority of people.

The data have also not been published or reviewed by independent experts. Moderna said it was preparing a manuscript with the data that would be posted online.

The pharmaceutical companies Pfizer and BioNTech announced earlier this month that a booster shot of their vaccine also increased the level of antibodies against Omicron.

Moderna tested a third shot of several versions of its vaccine, each in 20 people. Before boosting, all the individuals had low levels of antibodies that can prevent Omicron infection. At Day 29, after receiving a third shot, the 50-microgram and 100-microgram doses of the current vaccine both sharply increased antibody levels.

The company also tested “multivalent” booster shots that incorporate mutations seen in the Beta and Delta variants, many of which are also present in Omicron. Those continuing trials each have 300 to 600 people enrolled in them. The 50-microgram and 100-microgram doses of the multivalent boosters increased antibody levels to similarly high levels, Moderna said.

Given how quickly Omicron is marching through the world, Moderna said, the company will focus its near-term efforts on extra shots of the original vaccine. It also plans to test a booster shot that is specific to the Omicron variant early next year and to include Omicron in a multivalent booster.

“To respond to this highly transmissible variant, Moderna will continue to rapidly advance an Omicron-specific booster candidate into clinical testing in case it becomes necessary in the future,” said Stéphane Bancel, Moderna’s chief executive officer.

enki42 posted:

Owlofcreamcheese posted:

Ontario is about 90% vaccinated.

At zero percent on that chart:

Is this chart showing that of every 1000 cases about 100 are unvaccinated and 900 are vaccinated?

OR

Is this chart showing there is 100 vaccinated cases for every 100 unvaccinated cases?


Because those seem very different!

enki42 posted:

So the relative protection that vaccines provide in Ontario is completely nose-diving now that Omicron is solidly dominant (80+% of cases). I don't think this can be translated to actual vaccine effectiveness, there's zero controls for age or other factors that would affect infection rates and vaccination rates, but your odds of contracting COVID are basically now identical in Ontario regardless of whether you've been vaccinated or not. (also things are moving too fast for the 7 day average to keep up, so note the actual data points)

"Vaccinated" in this case means 2+ shots, so some small proportion of this group is boosted.

enki42 posted:

I think the label of "vaccine effectiveness" for that line is super misleading, it's controlling for basically nothing. but yeah by the same token vaccines are definitely not doing an awful lot at the moment in Ontario.

Platystemon posted:

https://twitter.com/trvrb/status/1471654963419893762

I don’t like that this is his working hypothesis.

I mean, it’s a fine hypothesis, it’s just disastrous if true.

Alctel posted:

They still make it way more likely you'll stay out of hospital though, right?

Alctel posted:

They still make it way more likely you'll stay out of hospital though, right?

Main Paineframe posted:

I don't see what's disastrous about "breakthrough infections are mild"? Sounds like extremely good news, given how many people have already either gotten vaccinated or caught a previous strain.

A real disaster would be if breakthrough infections were exactly as bad as regular infections.

Main Paineframe posted:

A real disaster would be if breakthrough infections were exactly as bad as regular infections.

Petey posted:

Well, they were in prior waves — the breakthrough IFR in Delta was same as IFR in the unvaccinated.

The difference was the vaccines helped prevent infection, and thus lowered the total.

I think it's too early to say, yet, what the case will be with Omicron. Hopefully the vaccines will hold up against severe disease and death. But we have evidence from prior variants that once you're infected, the rates don't change.