Exploring new variants, vaccines and NPIs

There has been increasing concern recently about SARS-Cov-2 variants that might escape vaccines to some extent, as well as having different transmission rates (as the Kent variant does), and causing different severity of illness with higher mortality. I have added a vaccination efficacy modifier, var_eff, by variant, as a multiplier to the standard vaccination efficacy, vac_eff, to help model such potential variants that have a partial or total capability to escape vaccines, and this post shows examples of how that works, using a third variant introduced to the model on January 1st 2021. In addition, I have completed adding fSS (the fraction of people becoming seriously sick from each variant) and fmort (fatality of the variant) by Covid variant.

Tuning the age and vulnerability model

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

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.

NPIs, variants and vaccine models

This paper reports some parametric Coronavirus model runs I have made that compare, in particular, how the UK vaccine programme allows some NPI relaxation compared with a case with no vaccination. The outcome is that the vaccine programme in the UK has the potential to reduce the imposition of NPIs on March 7th by about 15%, without costing lives, this being the next time we in the UK are due for a major NPI review, potentially involving the return of schools at around March 7th.

The timing of multiple Coronavirus variants

Since my most recent posts on December 23rd and January 5th I have adjusted my model algorithms to model more than two variants, so that once better data is available on new variant characteristics, I can respond more quickly. The scenarios I have modelled show that presented with the threat of new variants, early proactive, preventative and decisive action in necessary as soon as a variant is identified. If a new variant is allowed to multiply and grow before appropriate Non Pharmaceutical Interventions are introduced (just as in the first days of the UK pandemic in March 2020, and with our UK March 23rd response) control of the virus is quickly lost.

Concurrent Coronavirus two variant modelling

I present an analysis of the pandemic situation in the UK, with two Coronavirus variants present since December 16th, and sensitivities to different New Year 2021 Non Pharmaceutical Interventions (NPIs), but always with the background of vaccine dispensing, which started in the UK on December 8th.

Exploring the possible impact of the new variant coronavirus

I cautiously welcomed “the end of the beginning”, and events since then have borne out the need for caution, with the discovery of a mutant variant of the SARS-Cov-2 virus (denoted VUI-202012/01) which seems to have a much greater transmission rate, as much as 70% more than the strain of SARS-Cov-2 we have seen previously in the UK. I have developed a further version of my Coronavirus model which now includes not only intervention capability but also a vaccination module, as reported before, and now the ability to add further virus strains with different transmission characteristics.

USA Thanksgiving lessons for UK Christmas and New Year?

We are aware that the rates of cases and deaths in the USA have increased steeply recently, and it seems that the natural public relaxation in precautions against Covid-19 for the Thanksgiving holiday period have exacerbated this. I have run my model with reductions to the USA intervention effectiveness during the Thanksgiving period (reflecting the increase in travel and social interactions in the USA) followed by reintroduction of the intervention effectiveness afterwards, to see the effect on the immediate projections. I have then applied similar changes to my UK models, to anticipate what the possible effect of such relaxations over the UK festive period might be. This is very much a sensitivity test of some scenarios, not a forecast.

The end of the beginning*

Now that it seems clear that a vaccination programme in the UK might start as early as next week, I have re-run my Covid-19 vaccination model for the UK, updating the November 25th scenarios (which begin on January 1st 2021) to reflect some potential UK outcomes.

Modelling of vaccine strategies

In my most recent post on November 18th, about updating my Coronavirus model to handle the impact of vaccines, I gave some examples of how case numbers, and more specifically death rates might be improved for the UK through a vaccination programme. Now that there seem to be several vaccines imminent, with efficacies ranging from 70% (Astra-Zeneca/Oxford) through 90% (A-Z/O via a different inoculation regime, and Pfizer), to 95% (Moderna) and several others in the mix, I explore some sensitivities in more detail, and also apply the model to the USA.