PHE – A rambling mind

What are UK Government advisers seeing?

Recent variants with their identifiers, lineage, source country if known, total cases, and new cases since May 12th: source gov.uk

I have developed some model scenarios that show examples of what might be behind expert advice on the caution required with new SARS-Cov-2 variants. The scenarios indicate the importance of the UK vaccine programme, as we face variants with potentially different characteristics of transmission, severity of infection and responsiveness to vaccines. Understanding those variant characteristics is vital for projections.

Why the UK Government is worried about new variants

Chart 18 for scenarios UK433 & UK439: v3 transmission k11 = 1, comparing var_eff and fss fmort effects. Modelled 800 day outcomes to April 12th 2022 compared with reported deaths to May 23rd. Serious cases for all variants, with 2021 NPI relaxations up to June 21st 2021.

Tuning the age and vulnerability model

Chart 19 for the grouped model UK957: modelled 800 day outcome compared with reported data to April 21st for active cases and deaths, with 2021 NPI relaxations up to June 21st 2021

In my latest post on March 26th I described a new Coronavirus group model, based on work I had done as a UK case study in support of Prof. Alex de Visscher’s paper, in conjunction with Dr. Tom Sutton, on “Second-wave Dynamics of COVID-19: Impact of Behavioral Changes, Immunity Loss, New Strains, and Vaccination” which has now been published for peer review as a pre-print on Springer’s site at https://www.researchsquare.com/article/rs-195879/v1. I have now added the latest UK vaccination progress figures, and the UK Government’s announced intentions for the near future regarding Non Pharmaceutical Interventions (NPIs). I have also updated mortality and infection characteristics for the four different population groups in the model.

Age and vulnerability related Coronavirus modelling

Chart 209 showing modelled and reported cumulative cases and deaths to 800 days in the groups model

In my most recent post on February 12th, I described modelling work I had done in support of Prof. Alex de Visscher’s paper, in conjunction with Dr. Tom Sutton, on “Second-wave Dynamics of COVID-19: Impact of Behavioral Changes, Immunity Loss, New Strains, and Vaccination” which has now been published for peer review as a pre-print on Springer’s site at https://www.researchsquare.com/article/rs-195879/v1. I have now added vaccination and multiple variants I had already added to our previous model into the new grouped population model, and this blog post reports on progress with that new model.

Model update following UK revision of Covid-19 deaths reporting

Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, on March 23rd, modified in 5 steps by -.3%, -0% -0% and -0% successively

On August 12th, the UK Government revised their counting methodology and reporting of deaths from Covid-19, bringing Public Health England’s reporting into line with that from the other home countries, Wales, Northern Ireland and Scotland. I have re-calibrated and re-forecast my model to adapt to this new basis.

The effect of lockdown easing in the UK

My forecast for the UK deaths as at July 30th, including trend line for reported deaths, for 83.5% lockdown effectiveness

As reported in my previous post, there has been a gradual reduction in the rate of decline of cases and deaths in the UK relative to my model forecasts. This decline had already been noted, as I reported before, by The Office for National Statistics and their research partners, the University of Oxford, and reported on the ONS website.
I had adjusted the original lockdown effectiveness in my model (from 23rd March) to reflect this emerging change, but as the model had been predicting correct behaviour up until mid to late May, I will present here the original model forecasts compared to the current reported deaths trend.