Adam Kucharski – A rambling mind

Omicron BA.2, vaccination for 5-11 year-olds, and the honeymoon period

Chart 318 for scenario UK_701 with adult vaccinations and 5-11 vacs from April 1st 2022. 17th May 1.8% ,19th July 1%, 1st Sep 2%, mean NPI relaxations and 30th Nov +2% and 10th Dec +3% additional NPIs. Omicron v4 transmission k11 = 6, BA.2 v5 k11 = 8, var_eff = 25/50/70%, fSS 7% and fmort 1.05%. Model outcomes to December 3rd 2023. Reported active cases and deaths to February 19th 2022. Serious cases for 5 variants.

I haven’t needed to make significant updates to my Coronavirus model for a while, because it has been working well.
The original Omicron variant morphed into the new BA.2 variant, and although it seems no more dangerous than its predecessor, it is thought to be between 33%-50% more transmissible. I have assumed the lower value of 33% more transmissive for this post.
I have added Omicron BA.2 as fifth variant v5 to my model, with 8 times the transmissibility of Delta, compared with the original Omicron variant v4 in the model, at 6 times the Delta transmission rate.

Just as we thought it was safe to go back into the water

Chart 318 for scenario UK_17 with vaccinations. 17th May 1.8% ,19th July 1%, 1st Sep 2%, mean NPI relaxations and 30th Nov +2% and 10th Dec +3% additional NPIs. v4 transmission k11 = 3, var_eff = 25/50/70%, fSS 7% and fmort 1.05%. Model outcomes to October 29th 2022. Reported active cases and deaths to December 8th. Serious cases for 4 variants.

Omicron is feared to have higher infectiousness than the Delta variant, with even greater concerns should it turn out to cause more severe symptoms, higher mortality, and possibly worst of all, if it were able to evade current Covid-19 vaccines. I have made some parametric runs of my model to assess the possible effects.

The pandemic situation in Europe

Case rates are rising in many parts of Europe. https://www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences

The pandemic situation in continental Europe has been worsening rapidly, and I felt that it I should update some country comparisons in a dedicated post.It confirms that the sourcing of data for a Coronavirus model of any given country is a very specific task nowadays, given the considerable differences in the underlying demographics, cultures, Government actions (NPIs) and public responses in the various countries.
This blog post isn’t looking at the modelling per se, but concentrates on the very different outcomes we are seeing across Europe, and looking at some of the reasons why.

Delta variant impact on June 21st easing – delay or reduce?

Chart 318 for scenarios UK479 and UK465 with vaccinations and 2021 NPI relaxations up to June 21st with 4% and Aug 16th with 2% NPI effectiveness. v3 transmission k11 = 1, var_eff = 100%, fss and fmort as fort v1 and v2. Modelled 800 day outcomes to April 12th 2022 compared with reported active cases and deaths to June 4th. Serious cases for three variants.

Having explored what pandemic advisers might be seeing and highlighting to decision-makers in Government, I run scenarios with different settings for the planned June 21st relaxation of lockdown, the last in the series of relaxations over the first half of 2021, following the January 3rd lockdown. These model scenarios show examples of what the relative consequences of the June 21st relaxation as planned, versus four other options:- cancellation of the June 21st step altogether, two different delays, of 28 and 56 days, and lastly a 50% reduction in the scope of the June 21st relaxation.

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.

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.

Where’s the exit?

Imperial College and Harvard forecasts and illustrations of cyclical pandemic behaviour

My title for this post is drawn from a slide I have shown before, from the 17th April Cambridge Conversation webinar, which I reported in my April 17th blog post, and also in my April 22nd blog post on model refinement, illustrating the cyclical behavior of the Covid-19 epidemic in the absence of pharmaceutical interventions, with control of cases and deaths achieved, only to some extent, by Non-Pharmaceutical Interventions (NPIs).

Model updates for UK lockdown easing points

Charts 4 and 13 for the comparison of cumulative & daily reported & modelled deaths, plus trend line, on the basis of 83.5% effectiveness, modified in 4 steps by -1%, -5% -10% and +2% successively

As I reported in my previous post on 31st July, the model I use, originally authored by Prof. Alex de Visscher at Concordia University on Montreal, and described here, was to be updated to handle several phases of lockdown easing, and I’m glad to say that is now done. Alex has been kind enough already to adopt a method I had been considering, of introducing an array of dates and intervention effectiveness parameters, and I have been able to add the recent UK Government relaxation dates, and the estimated effectiveness of each into a new model code. I have run two sets of easing parameters as a sensitivity test.