1 Introduction

This paper contains estimates for the effective reproduction number \(R_{t,m}\) over time \(t\) in various nations and other regions \(m\) of United Kingdom. This is done using the methodology as described in [1]. These have been implemented in R using EpiEstim package [2] which is what is used here. The methodology and assumptions are described in more detail here.

This paper and itโ€™s results should be updated roughly daily and is available online.

2 Updates

As this paper is updated over time this section will summarise significant changes. The code producing this paper is tracked using Git. The Git commit hash for this project at the time of generating this paper was 9ae270591e15aff0e178e24a87211b1f423080ae.

The following updates have been made:

  • On 27 May 2021 methodology was updated to use up to date cases but an allowance for late reporting was added.
  • Further on 28 May 2021 plots and maps were updated to consistently not plot reproduction number estimates where the 95% confidence interval associated with that estimate is wider than 1.
  • A further update on 29 May 2021 was made. All plots and maps were updated to consistently not plot reproduction number estimates where the 95% confidence interval associated with that estimate is wider than 1.
  • On 9 January 2022 improvements to allowance for late reproted data was made.

3 Data

3.1 Source

Data is obtained [3]. This contains the daily cases, hospital admissions and deaths for United Kingdom by various geographies. Here the data is accessed by specimen date, admission date and date of death.

All data prior to 1 March 2020 are removed.

3.2 Allowance for late reporting

Based on a history of the data collected patterns of late reporting are developed. A maximum delay in reporting of 21 days is assumed and the last 28 days of reporting data is used to estimate the late reported cases, admissions and deaths.

4 Methodology

The methodology is described in detail here.

5 Results by Nation

5.1 Cases

Below a 7-day moving average of daily case count on a log scale by nation is plotted:

Daily Cases by Nation (7-day moving average)

Daily Cases by Nation (7-day moving average)

Daily Cases by Nation for Last 30-days (7-day moving average)

Daily Cases by Nation for Last 30-days (7-day moving average)

5.2 Admissions

Below we plot cumulative hospital admissions on a log scale.

Daily Admissions by Nation (7-day moving average)

Daily Admissions by Nation (7-day moving average)

Daily Admissions by Nation for Last 30-days (7-day moving average)

Daily Admissions by Nation for Last 30-days (7-day moving average)

5.3 Deaths

Below a 14-day moving average of daily deaths by nation on a log scale is plotted:

Daily Deaths by Nation (14-day moving average)

Daily Deaths by Nation (14-day moving average)

Daily Deaths by Nation for Last 60-days (14-day moving average)

Daily Deaths by Nation for Last 60-days (14-day moving average)

5.4 Current Reproduction Number Estimates by Nation

Below current (last weekly) reproduction number estimates are tabulated by nation.

Estimated Effective Reproduction Number by Nation
Nation Estimate Type Daily Count (Last Week) Week Ending Reproduction Number [95% Confidence Interval]
England cases 16,446 2022-06-26 1.20 [1.15 - 1.24]
England admissions 1,096 2022-06-25 1.26 [1.19 - 1.33]
England deaths 57 2022-06-25 1.09 [0.97 - 1.21]
Northern Ireland cases 260 2022-05-19 0.93 [0.88 - 0.97]
Northern Ireland admissions 33 2022-06-23 1.35 [1.17 - 1.54]
Northern Ireland deaths 1 2022-05-19 1.00 [0.46 - 1.74]
Scotland cases 2,282 2022-06-19 1.23 [1.18 - 1.27]
Scotland admissions 129 2022-06-17 1.28 [1.18 - 1.37]
Scotland deaths 2 2022-06-01 0.45 [0.25 - 0.69]
Wales cases 123 2022-06-22 1.42 [1.29 - 1.56]
Wales admissions 22 2022-06-24 1.56 [1.31 - 1.83]
Wales deaths 3 2022-06-22 1.82 [1.11 - 2.72]
Estimated Effective Reproduction Number by Nation

Estimated Effective Reproduction Number by Nation

5.5 Maps of Effective Reproduction Number

Below we plot the current effective reproduction number on maps with boundaries provided by [4]. Data where the confidence interval for the reproduction number is wider than 1 are excluded (shown as missing on the map).

5.5.1 Cases

5.5.2 Admissions

5.5.3 Deaths

5.6 Graphs over Time

Below we plot results for each nation.

5.6.1 England

5.6.2 Northern Ireland

5.6.3 Scotland

5.6.4 Wales

6 Results by Region

6.1 Cases

Below we daily case count is plotted on a log scale by region:

Daily Cases by Region (7-day moving average)

Daily Cases by Region (7-day moving average)

Daily Cases by Region for Last 30-days (7-day moving average)

Daily Cases by Region for Last 30-days (7-day moving average)

6.2 Deaths

Below a 14-day moving average of daily deaths by region is plotted on a log scale:

Daily Deaths by Region (14-day moving average)

Daily Deaths by Region (14-day moving average)

Daily Deaths by Region for Last 60-days (14-day moving average)

Daily Deaths by Region for Last 60-days (14-day moving average)

6.3 Current Reproduction Number Estimates by Region

Below current (last weekly) reproduction number estimates are tabulated by region.

Estimated Effective Reproduction Number by Region
Region Estimate Type Daily Count (Last Week) Week Ending Reproduction Number [95% Confidence Interval]
Northern Ireland cases 260 2022-05-19 0.93 [0.88 - 0.97]
Northern Ireland deaths 1 2022-05-19 1.00 [0.46 - 1.74]
Scotland cases 2,282 2022-06-19 1.23 [1.18 - 1.27]
Scotland deaths 2 2022-06-01 0.45 [0.25 - 0.69]
Wales cases 123 2022-06-22 1.42 [1.29 - 1.56]
Wales deaths 3 2022-06-22 1.82 [1.11 - 2.72]
North East cases 842 2022-06-26 1.20 [1.15 - 1.25]
North East deaths 4 2022-06-25 1.12 [0.75 - 1.57]
North West cases 2,041 2022-06-26 1.22 [1.16 - 1.28]
North West deaths 9 2022-06-25 1.39 [1.06 - 1.78]
Yorkshire and The Humber cases 1,349 2022-06-26 1.20 [1.15 - 1.25]
Yorkshire and The Humber deaths 5 2022-06-25 1.23 [0.87 - 1.67]
East Midlands cases 1,282 2022-06-26 1.20 [1.14 - 1.25]
East Midlands deaths 5 2022-06-25 1.17 [0.82 - 1.58]
West Midlands cases 1,477 2022-06-26 1.17 [1.11 - 1.23]
West Midlands deaths 8 2022-06-25 1.51 [1.11 - 1.96]
East of England cases 1,977 2022-06-26 1.24 [1.17 - 1.31]
East of England deaths 7 2022-06-25 0.96 [0.71 - 1.26]
London cases 2,353 2022-06-26 1.13 [1.09 - 1.17]
London deaths 7 2022-06-25 1.26 [0.93 - 1.65]
South East cases 3,122 2022-06-26 1.21 [1.16 - 1.26]
South East deaths 9 2022-06-25 1.08 [0.82 - 1.37]
South West cases 1,867 2022-06-26 1.26 [1.19 - 1.32]
South West deaths 6 2022-06-25 1.34 [0.96 - 1.78]
Estimated Effective Reproduction Number by Region

Estimated Effective Reproduction Number by Region

6.4 Maps of Effective Reproduction Number

Below we plot the current effective reproduction number on maps with boundaries provided by [5]. Data where the confidence interval for the reproduction number is wider than 1 are excluded (shown as missing on the map).

6.4.1 Cases