Read on Twitter
Breaking—UK 
VARIANT MAPPED:
We have now a detailed map of the likely spread of the VUI-202012/01 #SARSCoV2 variant among *63,000 positive #COVID19 cases throughout England*!
All thanks to a brilliant stroke of luck—allowing a *shortcut PCR test* instead of full 
test.
VARIANT MAPPED:We have now a detailed map of the likely spread of the VUI-202012/01 #SARSCoV2 variant among *63,000 positive #COVID19 cases throughout England*!All thanks to a brilliant stroke of luck—allowing a *shortcut PCR test* instead of full test.
2) Long story short, there is a special PCR test used by Lighthouse labs that tests for 3 genes of #SARSCoV2. But new UK variant has a key Deletion at 69/70–this PCR only positive for 2 genes, but no longer records positive signal for mutated spike gene!
This gives a SHORTCUT
This gives a SHORTCUT
3) While some other variants also have the 69-70 deletion mutation, the VUI-202012/01 is the main variant that has it—97% of all viruses with the special spike deletion belong to the troublesome new strain. Hence we can use the “S Gene failure” as a proxy shortcut PCR test! HUGE!
4) And so we can now FULLY MAP the location of all the likely problem UK variant throughout England that used this special 3-gene LIghthouse Lab PCR shortcut instead of needing to slowly sequence the RNA on slower expensive tests.
Here: % variant (*S Gene Failure PCR)
tests. Here: % variant (*S Gene Failure PCR)
5) The map represents the overall average in England between Sept and December. But what about over time! Let’s break it further by time and region here in this figure. ORANGE is the special S Gene failure — proxy for the VUI-202012/01 variant. #COVID19
https://khub.net/documents/135939561/338928724/New+SARS-COV-2+variant+-+information+and+risk+assessment.pdf/b56d4591-0466-1a18-28dc-010e0fdeef53?t=1608569319930
https://khub.net/documents/135939561/338928724/New+SARS-COV-2+variant+-+information+and+risk+assessment.pdf/b56d4591-0466-1a18-28dc-010e0fdeef53?t=1608569319930
6) Some seem to call it the 3 gene PCR test by Lighthouse Labs, while others call the special test the TaqPath PCR test. I’m not in the U.K., so I don’t know how to order this test per se. but hope this is useful to people! https://twitter.com/drericding/status/1340911649532882944
7) and what is the implied R(t) increase? Well, there’s some different calculations- either +0.39 unweighted or +0.93 if weighted analysis, or 48% increase in transmission rate.
8) here is also further details on the new mutation and children. https://twitter.com/drericding/status/1341231738249486337
