CV. SARS-CoV-2 variants of concern and variants under investigation in England

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Recopilado por Carlos Cabrera Lozada. Miembro Correspondiente Nacional, ANM puesto 16. ORCID: 0000-0002-3133-5183. 10/12/2021

Summary
This report has been published to share the detailed variant surveillance analyses which contribute to the variant risk assessments and designation of new variants of concern (VOCs) and variants under investigation (VUIs). This specialist technical briefing contains early data and analysis on emerging variants and findings have a high level of uncertainty.

A separate report is published covering surveillance data on all other VOCs and VUIs.

In summary:
• there are 5 current VOCs and 7 VUIs (Table 1)
• the technical briefing uses a data cut off of 6 December to allow time for analyses. Current national variant case numbers are published weekly. At the data cut off, there were 260 confirmed cases of Omicron VOC-21NOV-01 (B.1.1.529) (hereafter referred to as Omicron), identified through sequencing or genotyping in England. There are additional possible cases identified through S gene target failure (SGTF) and given the coverage of the different types of tests, the true number of cases is likely to be much higher. None of the cases of are known to have been hospitalised or died through routine data linkages.
• the Omicron global phylogeny shows the presence of 2 clades, a large group (BA.1) with the typical Omicron mutations and a small outlying group (BA.2) with some shared mutations with Omicron and some differences, including an absence of the deletion at S:69/70 which gives the SGTF result. BA.2 has not yet been observed in the United Kingdom (UK) data set and currently comprises only a small number of sequences
• Omicron continues to grow rapidly in all regions of England as measured by confirmed cases and SGTF cases. S gene target failure data were published on 8 December 2021. Case ascertainment of Omicron has been enhanced through increased sequencing of SGTF cases. Use of the assay which produces S gene target failure has not changed. Genotyping has changed in interpretation but not in coverage. These changes may affect the analyses presented, which are preliminary estimates and will be iterated • Omicron has also been detected in the wastewater in 5 samples collected between 26 and 28 November from 4 of the 477 sewage treatment works and sewerage network sites.

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