New strain and the R number

There has been news over the last few days about the new strain detected in the South England, with 17 new cases reported in Scotland by today (19th December). Some estimates suggest an increase in the reproductive number of about 0.4.

I run my simple SIR model to fit the UK-wide data and in my model the increase seems to be more than 0.4 – but then R is so much model dependent that it is difficult to compare. Still, it shows how rapid the current increase is, despite all the lockdown measures:

In turn, this is what the results of some simple SIR models look like for Scotland with data up to 30th November (I do not have more recent data at hand) and with the 0.4 increase in the rate starting this week:

This shows how potentially damaging the new outbreak is for the attempt to bring down the disease numbers before the increased mobility (see the green line in the plot above) prior to and during Christmas will result in another outbreak. The graph above is assuming that – apart from the 0.4 increase due to the new strain – there is no effect of this mobility, so the situation is even more risky.

But assuming the increase of the same magnitude as seen in the whole UK data, makes it even more serious:

Well, the message is – this is indeed quite serious and this time I do not think the UK and Scottish government are too soft and too late.

Vaccination webinar

A wee reminder that today I will be taking part in a webinar organised by The Conversation on the topic of “Living with coronavirus vaccine”. You can watch it live via these links on either Facebook, YouTube or Twitter from 4pm GMT on December 1.

Wee means “small” or “little” in Scotland, so this is a “little” reminder.


An interesting discussion about the AstraZeneca – Oxford vaccine. Moderna and Pfizer/BioNTech were very clear with the protocol and with the reporting. I described the details of the statistical basis of the trials in The Conversation article. Moderna group even released a very detailed report on side effects.

In contrast, the Oxford trial seems to have been conducted in a less rigorous way and we are missing the data to analyse it in the same detail. The 62% to 90% efficacy switch with 1/2 dose at the first treatment will need more study; it has been reported that the “optimal” dose has only been given to 2,3oo people and there were issues with who received the “optimal dose”.

This just stresses how important it is to understand the statistical details behind the vaccine trials. None of the trials addressed long-term efficacy and safety, and the efficacy (and safety) in different age/vulnerability groups are still open.