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

  1. Samuel M. Nicholls
  2. Radoslaw Poplawski
  3. Matthew J. Bull
  4. Anthony Underwood
  5. Michael Chapman
  6. Khalil Abu-Dahab
  7. Ben Taylor
  8. Ben Jackson
  9. Sara Rey
  10. Roberto Amato
  11. Rich Livett
  12. Sónia Gonçalves
  13. Ewan M. Harrison
  14. Sharon J. Peacock
  15. David M Aanensen
  16. Andrew Rambaut
  17. Thomas R. Connor
  18. Nicholas J. Loman
  19. The COVID-19 Genomics UK (COG-UK) Consortium

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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.

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    SciScore for 10.1101/2020.10.06.328328: (What is this?)

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    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

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  2. Version published to 10.1101/2020.10.06.328328 on bioRxiv