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Theo Sanderson

29 Dec, 4 tweets, 2 min read

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!

theosanderson.github.io/adhoc_covid/ph…

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)

Actually looks like this went pretty well

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More from @theosanderson

Theo Sanderson

@theosanderson

30 Dec

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]

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

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.

Read 10 tweets

Theo Sanderson

@theosanderson

28 Dec

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

Theo Sanderson

@theosanderson

28 Dec

1/ We have two sources of information about the spread of the new variant. The most reliable is genomics data, but this has a lag period, and most samples can't be tested in this way.

The second is "S dropout", but it doesn't uniquely identify B.1.1.7

Graph below and short🧵

2/ B.1.1.7 has a deletion of 6 letters of RNA in the S gene, which happens to make one of the three PCR tests performed on each swab sample in the Lighthouse labs give a negative result. So these "S-negatives" can be a proxy for B.1.1.7.

3/ BUT there are other strains that also have this same "H69/70 deletion" variant. Indeed the first was seen in the UK in April, long before B1.1.7. The graph above shows these in blue. The graph represents the percentage of all genomes sequenced in these areas at various times.

Read 13 tweets