among those tested with TaqPath assay, by upper tier local authority (UTLA) of residence. Specimen dates between 5 June 2021 and 18 June 2021, data as of 21 June 2021 (3 most recent days excluded due to reporting delay). Restricted to UTLAs with >20 cases tested on TaqPath assay. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 51 Growth rate of S gene positive and negative cases1 Figures 20, 21, and 22 show growth rate and doubling times of S gene positive (all 3 PCR targets positive) and negative (S gene target failure), produced by fitting a generalized additive model with a quasi-Poisson. The left vertical axis in the figures describe the daily growth rates; and the right vertical axis the corresponding daily doubling times, that is number of days required for cases to double at that particular growth rate. The dashed lines represent uncertainty (95% CI), which grows when the number of data points used for the estimation is smaller. Note that, if an epidemic trend changes from growth to decline, the growth rates change from positive to negative, while the doubling times become longer and longer, cross infinity when the trend is temporarily flat, and turn into halving times (that is number of days it takes for cases to halve), represented as negative doubling times. 1 This information is provided by the Joint Biosecurity Centre SARS-CoV-2 variants of concern and variants under investigation 52 Figure 20. Growth rate and doubling time of S gene positive and negative cases by region as of 18 June 2021 Case rate doubling times for S gene positive cases in England have plateaued and show signs of a decline in recent weeks. This may be partially due to decreases in coverage of CT data in the East Midlands, East of England, South East, Yorkshire and the Humber. Trends in the North West are currently unclear, despite good coverage of CT data. Case data is presented until the 18 June 2021 The growth rate for the all 3 positive count has plateaued or decreased in late May and SARS-CoV-2 variants of concern and variants under investigation 53 early June for all age groups, with most rapid growth in the 25 to 34 year age group and the 75 to 84 year old age group. Doubling times are low in Pakistani and Indian Ethnicity, whilst growth rates are around 8 days in White ethnicity, 10 in Black ethnicity, 11 in other Asian ethnicity, 8 amongst those who prefer not to say. Find accessible data used in this graph in underlying data. SARS-CoV-2 variants of concern and variants under investigation 54 Figure 21. Growth rate and doubling time of S gene positive and negative cases by ethnicity as of 18 June 2021 SARS-CoV-2 variants of concern and variants under investigation 55 Doubling times are low in Pakistani and Indian Ethnicity, whilst growth rates are around 8 days in White ethnicity, 10 in Black ethnicity, 11 in other Asian ethnicity, 8 amongst those who prefer not to say. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 56 Figure 22. Growth rate and doubling time of S gene positive and negative cases by age as of 18 June 2021. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 57 The growth rate for the all 3 positive count has plateaued or decreased in late May and early June for all age groups, with most rapid growth in the 25 to 34 year age group and the 75 to 84 year old age group. PCR cycle threshold data PCR cycle threshold (Ct) values appear to be persistently lower in Delta than Alpha cases based on test and trace surveillance data (Figures 23 and 24, below). SARS-CoV-2 variants of concern and variants under investigation 58 Figure 23. Average Cycle threshold values for S gene positive samples (all 3 PCR targets positive) Average Ct values for S+ (all 3 PCR targets positive) are currently below 20, significantly lower than the average Ct values for SGTF, which have been increasing since late May 2021, and are now around 30. There has been a drop in recent average OR-dropout Ct values though this is in a very small number of cases, and has since stabilised. SARS-CoV-2 variants of concern and variants under investigation 59 Figure 24 shows the count of cases by gene target, and the mean cycle threshold (Ct) value by the number of days since symptom onset (Symptom onset date – appointment date). This figures shows the average Ct values between 2 periods, 1 September 2020 to 15 January 2021, when Alpha was on the increase with 1 April 2021 onwards when Delta was on the increase. The data is limited to these periods to account for the fact that Ct values may reflect the dynamics of the epidemic, rather than infectivity at a moment in time. For each period, the mean SGTF cases (proxy for the Alpha variant) and S+ cases (proxy for the wild type in 1 September 2020 to 15 January 2021 period, left pane Figure 24 and Delta variant in 1 April 2021 onwards period, right pane Figure 24) since date of onset of symptoms are compared. During 1 September 2020 to 15 January 2021 period, the mean Ct values for SGTF/Alpha cases is slightly lower than S+/wild type from day 1 onwards. At day 3 the mean lowest Ct for SGTF/Alpha is 19.7 which is 1.4 lower than S+/wild type cases. During 1 April 2021 onwards period, the mean Ct values for S+/Delta cases is slightly lower from day