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VEO report on mutations and variation in publicly shared SARS-CoV-2 raw sequencing data, Report No. 13, 28 September 2022

Thursday 29 Sep 22
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Marion Koopmans
Coordinator of VEO, Co-coordinator of COMPARE
Erasmus Universitair Medisch Centrum Rotterdam
VEO submits the 13th report on mutations and variation in publicly shared SARS-CoV-2 raw sequencing data.

In its 13th report to the European Commission, VEO Consortium members summarize mobilisation and analysis of SARS-CoV-2 sequence data submitted to the European COVID-19 Data Portal in the context of the VEO project, which aims to develop tools and data analytics for pandemic and outbreak preparedness.

Summary:

  • This update describes a major step forward in the development of the COVID-19 Data Portal: the portal now provides SARS-CoV-2 sequence data and analysis tools via a new feature, the CoVEO app (https://www.covid19dataportal.org/coveo). The CoVEO app was developed to allow analysis of the incoming raw sequence data for specific mutations or combinations of mutations.
  • Update on mobilisation of raw reads, now totaling sequencing datasets from 5,684,416 viral raw read sets from 96 countries, a 21% increase since the previous report.
  • The variant nomenclature has been updated, and tables on countries depositing data on VOC and VOI have been included. Information on Omicron is included.
  • The variant calling workflow for the Illumina data has been deployed on the Google Cloud Platform, allowing us to process some of the backlog of data. 500,165 Illumina and 12,560 Oxford Nanopore samples have been processed in the period since the last report.

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27 NOVEMBER 2022