2 lineages and the recent emergence of the new Variant of Concern P.1. Home/p1-variant-dominant-strainin-brazil-reported-in-new-yorkts: what does it mean? SRHD. https://srhd.org/news/2021/coronavirus-mutationsand-variants-what-does-it-mean.Published April 1, 2021. Accessed April 24, 2021. 35. Callaway E. Multitude of coronavirus variants found in the US - but the threat is unclear. Nature News. https:// www.nature.com/articles/d41586-021-00564-4. Published March 5, 2021. A There are 4 current variants of concern and 9 variants under investigation (Table 1). This report has been published to continue to share detailed surveillance of Delta (VOC21APR-02, B.1.617.2) and Lambda (C.37, VUI-21JUN-01). A separate report is published covering our routine data on all other variants of concern and variants under investigation. These additional specialist technical briefings represent early data and analysis on an emerging variant and findings have a high level of uncertainty. Principal changes and findings this week are: • the Delta variant accounted for approximately 95% of sequenced and 92% genotyped cases from 7 to 21 June 2021 • an operational issue at a sequencing facility resulted in a reduction in genome coverage for specimen dates 10 to 15 June 2021 (sequenced between 14 to 18 June) and may impact variant sequencing counts in figures and tables for this limited period; genotyping was not affected (see Note 1) • C.37 (Lambda), previously a signal in monitoring, was designated a new Variant Under Investigation on 23 June 2021 based on global spread and a novel combination of mutations; further data is provided • very preliminary results for live virus neutralisation of AY.1 (a lineage of Delta with K417N), with a small number of sera from vaccine recipients are reassuring, however further testing is required (data provided by Genotype to Phenotype consortium) • PCR cycle threshold (Ct) values appear to be persistently lower in Delta than Alpha cases based on routine national testing data The risk assessment for Delta is published separately and was last updated on 25 June 2021. As Delta is now the dominant variant in the UK, epidemiological data in the weekly surveillance report is highly relevant and available. Note 1: From 14 to 18 June 2021 an operational issue at a sequencing site resulted in a reduction in the number of samples with sequencing data of sufficient quality for variant assignment. There were 19,502 samples reported to PHE as impacted by the incident. PHE has received approximately 10,000 sample identifiers from the list of those affected of which sequencing data has been obtained for approximately 4,300 and genotyping data for 3,300 have a reflex assay result. Approximately 9,000 samples are pending analysis and for approximately 2,400 samples variant assignment is not possible. This issue resulted in a reduction in genome coverage for specimen dates 10 to 15 June 2021 and SARS-CoV-2 variants of concern and variants under investigation 4 may impact variant counts in figures and tables for this limited period. The unusable samples were from locations distributed around the UK and the proportions of different variants by region should be correct. In addition, the genotyping results means that this has limited impact in the interpretation of the overall data. Published information on variants The collection page gives content on variants, including prior technical briefings. Definitions for variants of concern, variants under investigation and signals in monitoring are detailed in technical briefing 8. Data on variants not detailed here is published in the variant data update. Variant risk assessments are available in prior technical briefings. A repository containing the up-to-date genomic definitions for all variants of concern (VOC) and variants under investigation (VUI) as curated by Public Health England was created on 5 March 2021. The repository can be accessed on GitHub. WHO nomenclature from 31 May 2021 is incorporated. A table incorporating WHO and UK designations and Pango lineages is provided (Table 1); thereafter variants are referred to using their WHO designation where this exists, and the UK designation where it does not. 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. SARS-CoV-2 variants of concern and variants under investigation 5 Part 1: Surveillance overview Variants under surveillance Table 1 shows the current variants of concern (VOC) and variants under investigation (VUI). Figure 1 shows the proportion of cases sequenced over time. Summary epidemiology on each variant is shown in Table 2, case numbers are also updated online. Tables 2, 3 and 4 show hospitalisation and death data. Figure 2 shows cumulative cases of variants over time. Table 1. Variant lineage and designation as of 21 June 2021 (provisionally extinct variants removed) World Health Organization nomenclature as of