Care visit. Some of the cases detected on the day of admission may have attended for a diagnosis unrelated to COVID19. ^ Total deaths in any setting (regardless of hospitalisation status) within 28 days of positive specimen date. SARS-CoV-2 variants of concern and variants under investigation 15 Figure 2. Cumulative cases in England of variants indexed by days since the fifth reported, data as of 21 June 2021 (Find accessible data used in this graph in underlying data). Figure 2 demonstrates the rapid growth of Delta cases since its first detection relative to other variants. SARS-CoV-2 variants of concern and variants under investigation 16 Variant prevalence The prevalence of different variants amongst all sequenced cases is presented in Figures 3 and 4, split by region in Figures 5 and 6 and by travel status in Figures 7 and 8. Technical briefings from 15 onwards include variant diagnoses made both by wholegenome sequencing and by a genotyping PCR test, including the categorisation of confirmed and probable variant results and a rules-based decision algorithm (RBDA) to identify variant and mutation (VAM) profiles from genotype assay mutation profiles. Genotyping is used to identify variants Alpha, Beta, Delta and Gamma; targets were updated in mid-May 2021 to prioritise accurate identification of Delta over Alpha. Genotyping allows shorter turnaround time (12-24h after initial confirmation of COVID-19) for a probable variant result. The initial panel of targets began trials in March 2021, using single nucleotide polymorphisms (SNPs): N501Y, E484K, K417N and K417T. Results have been reported and used for public health action since 29 March 2021. On 11 May 2021, after rapid validation of targets to allow identification of Delta variant, P681R was introduced in the panel to replace N501Y. Genotyping results have now been fully integrated into the Variant data reports and analyses. The changes in the use of genotyping over time should be considered when interpreting the prevalence incorporating genotypes. The ‘Other’ category in Figure 3 to 8 includes genomes where the quality is insufficient to determine variant status and genomes that do not meet the current definition for any designated variant under investigation or variant of concern. The total dataset used for this assessment includes enhanced testing and sequencing from individuals who have travelled, and surge testing and sequencing in outbreak areas. Sequencing numbers and coverage fall in the last week shown due partly to sequencing lag time, and new sequences are still being produced relating to sample dates in that week. The supplementary data for figures are available. Delta variant accounted for approximately 95% of sequenced and 92% genotyped cases from 7 to 21 June 2021. SARS-CoV-2 variants of concern and variants under investigation 17 Figure 3. Variant prevalence for all England available genotyped cases from 1 February 2021 as of 21 June 2021 (excluding 1 case where the specimen date was unknown). (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 18 Figure 4. Variant prevalence for all England available sequenced cases from 1 February 2021 as of 21 June 2021 (excluding 1 case where the specimen date was unknown). (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 19 Figure 5. Variant prevalence from 1 February 2021 as of 21 June 2021 by region for all genotyped cases in England (excluding 282 cases where the region or specimen date were unknown). (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 20 Figure 6. Variant prevalence from 1 February 2021 as of 21 June 2021 by region for all sequenced cases in England (excluding 282 cases where the region or specimen date were unknown). (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 21 Figure 7. Prevalence of variants over time: all genotyped cases in England, split by travel status as of 21 June 2021. Travel-linked variant data available until 13 June 2021 only. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 22 Figure 8. Prevalence of variants over time: all sequenced cases in England, split by travel status as of 21 June 2021. Travellinked variant data available until 13 June 2021 only. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 23 Travel status is assigned based an interval of ≤14 days between arrival date and positive specimen date. Travellers are derived through matching to Passenger Locator Forms, contact-tracing, international arrivals and local HPT survey data. Where no match to these datasets was found then the individuals are categorised as not-travel associated. Travel status was assigned on the basis of the individual's own history of travel (including transit), not contact with a traveller. The area in grey shows weeks where sequence data are still accumulating, therefore the proportions are less likely to accurately reflect prevalence. The total number of sequencing cases in each week is shown in the bars below, split by travel status.