I can present a brief update to our analyses of VOC 202012/01 from last week. VOC 202012/01 continues to spread in England, as shown in both sequencing data from COG-UK and Pillar 2 testing data provided by Public Health England. NOT PEER REVIEWED 1/7
While the sequencing data above are definitively VOC 202012/01, S-gene target failure (SGTF) is also associated with some other lineages. However, PHE estimates some 98% of SGTF are now VOC 202012/01 (assets.publishing.service.gov.uk/government/upl…). NOT PEER REVIEWED 2/7
Fitting a purely statistical model (logistic growth with a false positive rate representing non-VOC SGTF), we find that the spread of SGTF is consistent with a single increased growth rate for VOC 202012/01 across all NHS regions (grey ribbons). NOT PEER REVIEWED 3/7
We are not translating these into a % increase in transmission right now, because we are still fine-tuning the methodology. However, the growth shown above is consistent with last week's analysis, ie a transmission rate increase of >50%. More on this soon. NOT PEER REVIEWED 4/7
Looking at the spatial pattern of SGTF across upper-tier local authorities in England (here north at top and south at bottom), two distinct phases are seen, an initial growth in the south-east followed by spread to the rest of England. NOT PEER REVIEWED 5/7
A brief report on the methods is available here: cmmid.github.io/topics/covid19… Thanks to all coauthors, and to @CovidGenomicsUK and @PHE_uk for data. NOT PEER REVIEWED 6/7
A note on the "NOT PEER REVIEWED": this paper is now under peer review. 7/7

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More from @_nickdavies

1 Jan
@i_petersen Thanks Irene. See image, sorry for bad labelling! Essentially the major pattern is that it doesn't seem to have spread into 80+ quite as quickly. Over November, 0-19s were slightly overrepresented but that seems to have somewhat settled out now. (1/2) Image
@i_petersen UK scientists originally interpreted this as the variant spreading (slightly) more easily among children than preexisting variants. But with newer data now in, this may have just been a transient effect related to schools being open during the November lockdown. 2/2
@i_petersen I tried to fit way too much into one tweet here. Let me be a bit of a nerd and expand massively on this. First, by UK scientists I mean the scientists on SPI-M who I have been talking to about this, obviously I don't know what the general "UK scientist view" is. a/
Read 6 tweets
24 Dec 20
Just to comment on a few points that have come up in relation to the preprint we put out yesterday on VOC 202012/01, the new variant of SARS-CoV-2 in the UK. ()
Is the apparent spread of VOC due to increased testing? This comes up often when cases rise & indeed case data is subject to biases. But we don't fit to case data in the model. Hospitalisations, deaths, and relative frequency (not abs. number) of the new variant define the trend.
There are other ways of measuring community prevalence besides case data. For example, the ONS just released a new round of estimates based on swabbing random people in England. Also shows increases in prevalence in the 3 regions we highlight to Dec 18. ons.gov.uk/peoplepopulati… Image
Read 6 tweets
23 Dec 20
Late last week, it was announced that a new variant of SARS-CoV-2 (VOC 202012/01) was detected and appeared to be spreading rapidly in the south east of England. We analysed the transmissibility and severity of this new variant. [cmmid.github.io/topics/covid19…] NOT PEER REVIEWED 1/9
We fitted a mathematical model to the growth of VOC 202012/01 in these three regions of England. If current trends continue, the new variant could represent 90% of cases by mid-January. NOT PEER REVIEWED 2/9
We estimate the transmission rate of this variant is 50–74% higher than existing variants; no clear evidence it leads to higher rates of hospitalisation or death. Although rates of both appear slightly higher in the SE, this could easily be noise in the data. NOT PEER REVIEWED 3/
Read 9 tweets

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