0 onwards, with convergence around day 9 which may be due to low numbers. At day 3 the mean lowest Ct for S+/Delta is 18.5 which is 1.3 lower than SGTF/Alpha at 19.7, almost identical to the difference at day 3 in 1 September 2020 to 15 January 2021 period, indicating the difference may be a true difference and not related to the dynamics of the epidemic at the time. SARS-CoV-2 variants of concern and variants under investigation 60 Figure 24. Cycle threshold values following date of symptom onset Average CT values Case counts Difference in days between Onset date and Appointment date all3PosCount S-DropOutCount all3PosMean S-DropOutMean SARS-CoV-2 variants of concern and variants under investigation 61 Delta with K417N Through routine scanning of variation in Delta a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2. Preliminary results for live virus neutralisation of AY.1 with a small number of sera from vaccine recipients are reassuring, however further testing is required (data provided by Genotype to Phenotype consortium). International Epidemiology As of 22 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83). Epidemiology There are currently 41 cases of Delta-AY.1 in England (39 confirmed sequencing and 2 probable genotyping). Cases have been detected in 7 different regions in England (Table 12, Figure 25). Delta-AY.2 has not been detected in England. Delta with K417N can be detected by genotyping assay, which means that rapid case identification and response activities can be undertaken. Until laboratory characterisation has been undertaken, Health Protection Teams will respond with high priority to case finding and control measures for cases of Delta with K417N. Neutralisation assays are now underway for Delta-AY.1 SARS-CoV-2 variants of concern and variants under investigation 62 Table 12. Number of confirmed (sequencing) and probable (genotyping) Delta-AY.1 cases, by region of residence as of 21 June 2021 Region Confirmed (sequencing) case number Probable (genotyping) case number1 Total case number Proportion of all cases East Midlands 1 0 1 2.4% East of England 0 0 0.0% London 7 1 8 19.5% North East 0 1 1 2.4% North West 3 0 3 7.3% South East 15 0 15 36.6% South West 2 0 2 4.9% West Midlands 10 0 10 24.4% Yorkshire and Humber 0 0 0.0% Unknown region 1 0 1 2.4% Total 39 2 41 - 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 63 Figure 25. Delta-AY.1 cases (confirmed sequencing and probable genotyping) by region of residence and specimen date as of 21 June 2021. Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data). SARS-CoV-2 variants of concern and variants under investigation 64 Figure 26. Confirmed (sequencing) and probable (genotyping) Delta-AY.1 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 65 Figure 27. Age-sex pyramid of confirmed (sequencing) and probable (genotyping) Delta-AY.1 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 66 Lambda (C.37, VUI-21JUN-01) Lambda was identified through international variant horizon scanning and was made a signal in monitoring by PHE on 14 April 2021 (lineage B.1.1.1 at the time). On 14 June 2021, WHO designated lineage C.37 as a new variant of interest, Lambda based on evidence of continued emergence and suspected phenotypic implications. Lambda was designated a variant under investigation (VUI-21JUN-01) by PHE on the 23 June 2021. Lambda carries a number of mutations with suspected phenotypic implications, such as a potential increased transmissibility or possible increased resistance to neutralizing antibodies2 . It is characterised by mutations in the spike protein, including G75V, T76I, del247/253, L452Q, F490S, D614G and T859N; however, there is currently limited evidence on the full extent of the impact associated with these genomic changes, and further robust studies into the phenotypic impacts are needed to better understand the impact on countermeasures and to control the spread. Further studies are also required to validate the continued effectiveness of vaccines.3 International Epidemiology As of 24 June 2021, 1,845 sequences on GISAID have been assigned to the C.37 lineage. C.37 sequences have been uploaded from Chile (707), USA (525), Peru (222), Germany (87), Argentina (86), Mexico (57), Spain (43), Ecuador (30), Israel (19), Colombia (15), France (13), Egypt (8), Switzerland (7), United Kingdom (6), Italy (5), Brazil (3), Canada (3), Netherlands (1), Aruba (1), Portugal