(updated from the previous analysis to 4 June 2021). Hazard ratios for hospitalisation are combined with odds ratios against symptomatic disease from the test negative case control analysis described above to estimate vaccine effectiveness against hospitalisation. Methods and detailed results are available in Stowe et al., 2021. Similar vaccine effectiveness against hospitalisation was seen with the Alpha and Delta variants (Table 9). Table 9. Vaccine effectiveness against hospitalisation for Alpha and Delta variants Vaccination status Vaccine Effectiveness (%) Alpha Delta Dose 1 78 (64 to 87) 80 (69 to 88) Dose 2 93 (80 to 97) 96 (91 to 98) International surveillance GISAID includes data on sequences available internationally. As of 22 June 2021, sequences from 71 countries (excluding UK) have been identified in GISAID of Delta: In total 14,606 sequences from: Angola (4dlands 3,554 2,772 6,326 6.9% Yorkshire and Humber 2,649 6,865 9,514 10.3% Unknown region 223 188 411 0.4% Total 50,283 41,773 92,056 - 1 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 SARS-CoV-2 variants of concern and variants under investigation 41 Figure 14. Confirmed (sequencing) and probable (genotyping) Delta cases by specimen date and detection method as of 21 June 2021 (Find accessible data used in this graph in underlying data.). SARS-CoV-2 variants of concern and variants under investigation 42 Figure 15. Confirmed (sequencing) and probable (genotyping) Delta cases by specimen date and region of residence as of 21 June 2021 (Find accessible data used in this graph in underlying data.). SARS-CoV-2 variants of concern and variants under investigation 43 Figure 16. Age-sex pyramid of confirmed (sequencing) and probable (genotyping) Delta cases as of 21 June 2021 (Find accessible data used in this graph in underlying data.). SARS-CoV-2 variants of concern and variants under investigation 44 Table 11. Additional spike mutations of interest detected in Delta genomes in the UK, as of 23 June 2021 Amino acid change Nucleotide change Total number of sequences (UK) Number of unlinked sequences Number of sequences 23 March to 22 April 2021 Number of sequences 23 April to 22 May 2021 Number variants under investigation 47 This data uses the numbers of genomes in the national genomic dataset rather than case numbers. Unlinked sequences refers to genomes which have not been linked to a primary PCR result in the English database and include individuals from outside of England. Further investigations of K417N genomes are being undertaken. * Note that G142D is in a part of the genome with consistently reduced coverage in the Delta variant (due to the lineage-defining deletion from position 22029-22035, which affects one of the PCR primer sites in the ARTIC v3 protocol). While it is only reported as detected in ~60% of sequences, the remaining 40% of sequences are almost all “N” at that position (the code for ‘insufficient data’), rather than being confirmed ”G” (the reference allele). As the mutation occurred early in the history of the lineage the majority of sequences (>99%) in this lineage can be assumed to harbour the mutation. Surveillance through S gene detection The S gene target in a 3-target assay (S, N and ORF1ab) used in some Lighthouse Laboratories is not detected in Alpha. However, this S gene is also detected in Beta, Kappa, Delta, VUI-21APR-03 (B.1.617.3) and other variants. Specimens with a detectable S gene (also referred to as S gene positive) are defined as those with cycle threshold (CT) values of ≤30 in all 3 gene targets: S, N, and ORF1ab. A detectable S gene in a positive SARS-CoV-2 sample has been established as a useful proxy for the Delta variant in England since mid-May 2021. The proportion of confirmed Delta specimens among S gene positives has been above 95% in the most recent 6 weeks of data (since 11 May 2021). The number and proportion of S gene positive samples in England) has also steadily increased since mid-April, with 33,101 cases reported in the week starting 14 June; 98.2% of all cases tested on the TaqPath assay and reported to PHE that week. Local authorities in the North West continue to stand out in terms of numbers of S gene positives (Figure 19). S gene analyses presented here have been reduced since the introduction of genotyping. SARS-CoV-2 variants of concern and variants under investigation 48 Figure 17. Weekly distribution of variants among sequenced S gene positive SARS-CoV-2 specimens Specimen dates between 5 January 2021 and 14 June 2021, data as of 21 June 2021. Gray shading applied to 14 most recent days of data as these are affected by reporting delay. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 49 Figure 18. Weekly number and proportion of England Pillar 2 COVID-19 cases with SGTF and detectable S gene target among those tested with the TaqPath assay Specimen dates between 1 September 2020 to 21 June 2021, data as of 21 June 2021. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 50 Figure 19. 7-day COVID-19 case rates per 100,000 population vs proportion S gene positive cases