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MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

View ORCID ProfileSamuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, View ORCID ProfileMichael Chapman, Khalil Abu-Dahab, Ben Taylor, Ben Jackson, Sara Rey, Roberto Amato, Rich Livett, Sónia Gonçalves, View ORCID ProfileEwan M. Harrison, Sharon J. Peacock, David M Aanensen, Andrew Rambaut, View ORCID ProfileThomas R. Connor, View ORCID ProfileNicholas J. Loman, The COVID-19 Genomics UK (COG-UK) Consortium
doi: https://doi.org/10.1101/2020.10.06.328328
Samuel M. Nicholls
1Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Radoslaw Poplawski
1Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Matthew J. Bull
2Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
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Anthony Underwood
3Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
4Oxford Big Data Institute
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Michael Chapman
5Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton, UK
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Khalil Abu-Dahab
3Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
4Oxford Big Data Institute
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Ben Taylor
3Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
4Oxford Big Data Institute
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Ben Jackson
6University of Edinburgh
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Sara Rey
2Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
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Roberto Amato
7Wellcome Sanger Institute, Hinxton, UK
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Rich Livett
7Wellcome Sanger Institute, Hinxton, UK
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Sónia Gonçalves
7Wellcome Sanger Institute, Hinxton, UK
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Ewan M. Harrison
7Wellcome Sanger Institute, Hinxton, UK
8University of Cambridge, Department of Medicine, Cambridge, UK
9University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK
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Sharon J. Peacock
8University of Cambridge, Department of Medicine, Cambridge, UK
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David M Aanensen
3Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
4Oxford Big Data Institute
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Andrew Rambaut
6University of Edinburgh
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Thomas R. Connor
2Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
10School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
11Quadram Institute Bioscience, Norwich, UK
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Nicholas J. Loman
1Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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  • ORCID record for Nicholas J. Loman
  • For correspondence: n.j.loman@bham.ac.uk
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Abstract

Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data.

In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies.

We describe the development and deployment of Majora, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵12 https://www.cogconsortium.uk

  • ↵** Full list of consortium names and affiliations are in the Supplementary Materials

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 07, 2020.
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MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, Michael Chapman, Khalil Abu-Dahab, Ben Taylor, Ben Jackson, Sara Rey, Roberto Amato, Rich Livett, Sónia Gonçalves, Ewan M. Harrison, Sharon J. Peacock, David M Aanensen, Andrew Rambaut, Thomas R. Connor, Nicholas J. Loman, The COVID-19 Genomics UK (COG-UK) Consortium
bioRxiv 2020.10.06.328328; doi: https://doi.org/10.1101/2020.10.06.328328
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MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, Michael Chapman, Khalil Abu-Dahab, Ben Taylor, Ben Jackson, Sara Rey, Roberto Amato, Rich Livett, Sónia Gonçalves, Ewan M. Harrison, Sharon J. Peacock, David M Aanensen, Andrew Rambaut, Thomas R. Connor, Nicholas J. Loman, The COVID-19 Genomics UK (COG-UK) Consortium
bioRxiv 2020.10.06.328328; doi: https://doi.org/10.1101/2020.10.06.328328

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