Today a story has been going around about a cluster of B.1.617 cases in Israel. This is the India-associated strain.

Unfortunately, this is in some places being spun as a possible example of vaccine escape. But the numbers suggest exactly the opposite!

timesofisrael.com/children-from-…
Here are the numbers.

24 with recent travel history.
17 with no travel history
5 children
4 vaccinated

Approximately 85% of the adult population in Israel has been fully vaccinated. So what does this tell us about vaccine effectiveness against B.1.617 in adults?
I'll just do point estimates.

Assume the 5 children were <16 and thus unvaccinated.

That gives us 32 cases among unvaccinated adults, and 4 cases among vaccinated adults.

The basic calculation for effectiveness then gives us a remarkable 98% against B.1.617.
But those with travel histories may have had much worse exposures, you might object.

Fair enough.

Let's look just at the people with no travel history.

We don't know this, but let's assume the worst-case for the vaccine: all 5 children+4 vaxxed had no travel history.
Now—even with these worst-case assumptions—we estimate 92% effectiveness for the vaccine using the same calculation.

( 9/0.15-4/0.85) / (9/0.15) = 0.92.

Worst case point estimates is that the Pfizer vaccine is as effective against B.1.617 as it is against wild type.
(Tweet above was replaced because of a transcription error — The original calculation was correct but when writing it out on paper I transposed two values.)

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More from @CT_Bergstrom

27 Apr
1. Today’s antivax propaganda comes from a….vaccine manufacturer?

Unfortunately, yes. The manufacturer of the Sputnik V vaccine is tweeting absolutely nonsense statistics in an effort to question the safety record of its competitors. Image
2. Their unfounded claim is that we are observing higher death rates among Pfizer recipients.

This is rubbish. In our book, we address the way in which people will try to bamboozle you with the unwarranted authority of numbers by throwing lots of stats at you.
3. But statistics (1) are only as good as the methods used to derive them, and (2) are only useful when they allow you to make fair and meaningful comparisons.

The Sputnik V numbers fail spectacularly on both accounts.
Read 14 tweets
27 Apr
Osprey and dinner
Crows arrive on the scene.

"Wait, how much will you give me if I ride him?
The approach.
Read 7 tweets
24 Apr
Genomics and the poetry of racist injustice:

Let's start with the poetry, because if you read that, it doesn't matter one iota whether you make the connection to genomics.

Please, please take a moment and read this. Slowly, aloud, and more than once.

newyorker.com/magazine/2020/…
What does this have to do with genomics?

To pack a huge amount of information into very small genomes, viruses make use of overlapping reading frames. From Bergstrom and Dugatkin (2016), the HBV genome:
We present an extremely stupid example of what this would look like using three-letter English words instead of codon triplets.
Read 5 tweets
23 Apr
In the '20s, without consent of the parents, an Ivy League school actually used the remains of African American children murdered by the state as a teaching tool.

No, NOT the 1920s. This very year.

theguardian.com/us-news/2021/a…
TW: Disturbing disregard for the deceased.
“`Nobody said you can do that, holding up their bones for the camera. That’s not how we process our dead. This is beyond words. The anthropology professor is holding the bones of a 14-year-old girl whose mother is still alive and grieving,' Michael Africa Jr said."
Read 6 tweets
19 Apr
This is a very nice thread about a different way to teach and use Bayes’s rule. I’ve always found this odds ratio framing much more intuitive.
Since people are still on about that headline: my problem with it is that it suggests the lazy "arcana" narrative about a piece of obscure math that turned out to be useful, whereas the article does a nice job of explaining Bayes's rule as a foundational piece of probability.
The real key to me is to whom the word "obscure" is intended to refer. No one would refer to the mRNA in an mRNA vaccine as "an obscure alternative form of genetic material", even though most readers (pre-2021) would not know the term.
Read 4 tweets
18 Apr
Yes, because it's common knowledge that a multiple murderer fleeing the cops and likely facing the death penalty in Texas will take every possible precaution to avoid injuring members of the general public.
Citizens in Wisconsin this afternoon should feel similarly secure in the knowledge that their mass shooter on the loose is not a threat either.
Thirteen year old boy: threat.

Handcuffed detainee: threat.

Unarmed 90 pound grandmother: threat.

Former police marksman accused of child sex abuse, on the lam after murdering three: no risk to the general community.
Read 4 tweets

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