1/ The MHRA has approved a longer gap between doses for both the AstraZeneca vaccine and the Pfizer vaccine. The latter has concerned some people. Specifically many are citing a figure of 52% for protection after the first dose.

Here is why this 52% figure isn't useful [1/n] Image
2/ The 52% value is a real figure, which comes from the Pfizer trial, for the period between the first and second doses. Here is what that period of time looked like (fda.gov/media/144325/d…):

In red are people who received placebo and in blue are those who received the vaccine Image
3/ We can see that until day 3 we have near identical results in both groups. This is *expected* - no vaccine has an effect until days later when the immune system has had time to develop a response against it.
4/ As an immune response builds the lines slowly diverge from each other. By day 10 they have completely different trajectories. We do have to be careful here, analysing the data post-hoc. But it is clear that (as one expects a priori) full protection isn't realised immediately.
5/ *The 52% figure is the average protection over these 21 days*, so it includes that initial time before the immune system has had time to create a response.
6/ If one instead looks at the day 10 to day 22 period one instead gets an efficacy value of 86% (there will be confidence intervals around that).

Analysis here: theosanderson.github.io/adhoc_covid/pf…
7/ Whereas if one looks at the day 0 to day 10 period there is an efficacy of 10%.
8/ The 52% figure is a mush of those two completely different scenarios. It's not useful. People shouldn't be citing it in this context.
9/ The Moderna vaccine documents (similar vaccine class) actually break down the results after the first dose into 14 day periods and show a very similar effect fda.gov/media/144434/d… Image
10/ There's lots to reasonably discuss about single-dosing. The big question is what the efficacy against severe COVID is in days 21-90. But please stop using this 52% figure.
11/ Document from the JCVI featuring essentially the same analysis: app.box.com/s/uwwn2dv4o2d0…

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More from @theosanderson

9 Jan
1/ Some people are looking at this map and saying: "it must have come from Europe". Here are a few reasons why that is unlikely.
2/ Though B.1.1.7 was especially prominent in Kent, the 2nd sequence ever sequenced was found in London, a day after the 1st. Due to superspreading it isn't possible to pinpoint for sure whether it originated in Kent or London. (If London, there's no argument for the continent).
3/ And suppose we did believe the new variant was introduced from abroad. Would we expect it to be introduced by sea or air? Far more arrivals to the UK in August/September occurred by air compared to sea.
Read 9 tweets
8 Jan
PHE has released the underlying data behind the B.1.1.7 technical report, allowing us to see the spread of the new variant in more detail
Data and reports: gov.uk/government/pub…
B.1.1.7 in London
Read 7 tweets
7 Jan
Completely understand why people are peeved, esp. given GISAID policy. But eventually we should build a system with best of both worlds
- labs rewarded for making data publicly available quickly
- this data freely analysed by anyone, and those analyses communicated (=published)
The failure to do the first of these is a major limiting factor at the moment, funders..
Read 4 tweets
7 Jan
Monoclonal antibodies targeting the IL6 receptor reduce mortality by 25% for ICU patients, on top of dexamethasone benefits.

I think for 800 patients that's a 95% confidence interval of around 8%-40% reduction. As ever hope to see a preprint out ASAP.
Also reported to reduce ICU stay by 7-10 days which would be a massive boon in current situation. gov.uk/government/new…
Read 4 tweets
29 Dec 20
Had fun™ trying to extract S-dropout rates from the graph in the PHE report using an automated eyedropper. Take the values with a big pinch of salt!

CSV output with the source: github.com/theosanderson/…
And we can then compare this to the rate of growth in case figures week-on-week. (N.B. the already published analysis from PHE and others does this in much better more sophisticated ways, it's just interesting to explore)
Read 4 tweets
28 Dec 20
1/ New PHE technical report on B.1.1.7 variant assets.publishing.service.gov.uk/government/upl…
2/ S dropout now appears a very good indication of B.1.1.7 in all regions.
3/ Roughly a third of swab tests are carried out with the TaqPath assay that serendipitously allows this S dropout detection of B.1.1.7.
Read 10 tweets

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