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VEO report on mutations and variation in publicly shared SARS-CoV-2 raw sequencing data, Report No. 10, 15 December 2021

Wednesday 15 Dec 21
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Contact

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

In its tenth 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 Platform in the context of the VEO project, which aims to develop tools and data analytics for pandemic and outbreak preparedness.

Summary:

  • Update on mobilisation of raw reads, now totaling sequencing data sets from 2,656,983 viral raw read sets from 85 countries, a 42% 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 Oxford Nanopore data has been deployed on the Google Cloud Platform, allowing us to process the backlog of data. All 213,259 Oxford Nanopore samples have been processed.
  • While data mobilisation is progressing, the contribution of countries in Europe is very low. Pathogen sequencing in most countries has been taken up as part of a public health effort, in part supported by HERA/ECDC. Agreements are needed to ensure release of raw data towards global sharing effort.

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