Multiple variants – Page 2

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.

Exploring new variants, vaccines and NPIs

Chart 303 for the grouped model UK929: modelled 800 day outcome for all variants for serious cases and deaths, with 2021 NPI relaxations up to June 21st 2021

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

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.

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.