Covid-19 – Page 3 – A rambling mind

NPIs, variants and vaccine models

Chart 17 model output for deaths, active cases and Seriously Sick to 800 days. 2nd virus variant from September 23rd, day 235. 3rd variant from January 1st 2021, Day 335. 250k vacs/day from January 1st (day 335) and 400k vacs/day from February 1st (day 366) and thereafter. 15% NPI reduction on March 7th, model Day 401.

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

Repeated elements of the 12-compartment model flowchart with repeated Incubation, Sick, Seriously Sick, and Better compartments, all infective, with transfer rates

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

New 12-compartment model flowchart with additional vaccination compartment V and repeated Incubation, Sick, Seriously Sick, and Better compartments, all infective, in addition to the Uninfected, Vaccinated, Recovered and Deceased compartments

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

Chart 14 model output to 800 days. Realistic case scenario. New virus variant. Vaccinations start Jan 1st 2021 (Day 335) at 100k/day, at 95% efficacy, rising to 300k/day at 95% efficacy, until April 12th 2022. 10% Dec 16th Intervention enhancement. 20% intervention enhancement after New Year.

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?

Chart 13 model outputs to 425 days, April 1st, 2021, no vaccinations compared with a 3-phase vaccination programme, as at December 8th

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*

Chart 13 model outputs to 450 days, April 27th, 2021, no vaccinations compared with a 3-phase vaccination programme, as at December 1st

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

Comparative vaccination charts for the UK to 800 days. Continuation of current NPIs on the left; and an graduated vaccine intervention on the right from January 1st 2021

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.

Vaccine, vaccine, vaccine, vaciiiine,…(don’t refuse it, just because you can)

New 8-compartment model flowchart with additional vaccination compartment V

In the news today, I read that Dolly Parton had given $1,000,000, through her Covid-19 Research Fund, to help fund the Moderna vaccine development. As The Times newspaper reported, this – erm – somewhat trumps the White House contribution to public safety. In her honour, Ryan Cordell composed and performed this ditty. The timing neatly coincides with the work I have been doing to incorporate vaccination into my Coronavirus model, and to that end I have been researching ways of modelling vaccination. I have made some appropriate changes, and run some model options for different vaccine efficacy; vaccinations per day; and date of starting the vaccination programme.

Make America well again

Model charts for the USA. Continuation of current policy until a postulated Biden intervention on February 20th 2021, on the left; and an early November 8th intervention on the right

I look at the impact of a postulated change in the timing of further measures to control the Covid-19 epidemic in the USA, against a current background of rapidly increasing daily case numbers and deaths. I also show an updated projection for the UK, both compared with Worldometers forecasts

Recent events and Coronavirus model update

Chart 11 showing the effect on cumulative and daily UK model and reported deaths and cases of a 2-week circuit-breaker measure on October 19th

Many countries, including the UK, are experiencing a resurgence of Covid-19 cases recently, although, thankfully, with a much lower death rate. I have run several iterations of my model in the meantime, introducing several lockdown adjustment points, since my last blog post, as the situation has developed. The key feature is the sharp rise cases, and to a lesser extent, deaths, around the time of the lockdown easing in the summer. I have applied a 10% increase in current intervention effectiveness on October 19th (although there are some differences in the half-term dates across the UK), followed by a partial relaxation after 2 weeks, -5%, reducing the circuit-breaker measure by half – so not back to the level we are at currently. The effect of that change is shown in the final chart in the blog post.