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Centre for Genomic Pathogen Surveillance

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Centre for Genomic Pathogen Surveillance
Centre for Genomic Pathogen Surveillance is located in Oxfordshire
Centre for Genomic Pathogen Surveillance
Location within Oxfordshire
General information
TypeGenomic Epidemiology Research Centre
AddressBig Data Institute, Old Road Campus, University of Oxford, Headington, OX3 7LF
Coordinates51°45′10″N 1°13′02″W / 51.7528154°N 1.2170949°W / 51.7528154; -1.2170949
Elevation15 m (49 ft)
Completed2015
OwnerOxford University

The Centre for Genomic Pathogen Surveillance is a computational genomics research institute in Oxfordshire.

History

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The Centre for Genomic Pathogen Surveillance opened in 2015 as a joint project between Imperial College London and Wellcome Sanger Institute. In 2017 it was announced that the centre would house a new Global Health Research Unit funded by the National Institute for Health Research (NIHR) to look at antibiotic resistance.[1][2] This has seen the centre becoming involved with surveillance of antibiotic resistance in a number of countries, for example, the Philippines.[3]

From 2018 to 2021 the Wellcome Sanger Institute and University of Oxford co-hosted the CGPS. From September 2021 the CGPS has been based at the University of Oxford.

During the COVID-19 pandemic, the centre received funding as part of the COG-UK consortium.[4]

On 22 September 2022 it was announced that the Centre for Genomic Pathogen Surveillance, part of the Big Data Institute at the University of Oxford, was awarded funding worth £7m for their work as an NIHR Global Health Research Unit (GHRU) for the next five years. The Centre’s research and capacity building work focuses on delivering genomics and enabling data for the surveillance of antimicrobial resistance (AMR).[5]

Structure

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The centre's director is David Aanensen.[6][7]

The centre is principally funded, and directed, by the Department of Health and Social Care.[8] In 2019, it was agreed that there would be collaboration between the Centre for Genomic Pathogen Surveillance, the European Centre for Disease Prevention and Control, and the Wellcome Sanger Institute, towards improving the monitoring and tracking of infectious diseases across Europe.[9]

Applications created at the centre

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Under the auspices of the centre, the Epicollect5 (used for data entry from distributed observers, e.g. by 'citizen science' programs), Microreact,[10][11] and Pathogenwatch applications have been generated and shared.[6] Microreact[12] has seen extensive use during the COVID-19 pandemic, and is a component of the Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin) software tool.[7][13][14]

Location

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The centre is located at the Big Data Institute, Nuffield Department of Medicine, University of Oxford.

See also

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References

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  1. ^ "Funding and Awards". fundingawards.nihr.ac.uk. Retrieved 2 March 2021.
  2. ^ "The Centre for Genomic Pathogen Surveillance to house the Global Health Research Unit to monitor antibiotic resistant bacteria around the globe". www.sanger.ac.uk. 21 July 2017. Retrieved 7 March 2021.
  3. ^ Argimón, Silvia; Masim, Melissa A. L.; Gayeta, June M.; Lagrada, Marietta L.; MacAranas, Polle K. V.; Cohen, Victoria; Limas, Marilyn T.; Espiritu, Holly O.; Palarca, Janziel C.; Chilam, Jeremiah; Jamoralin, Manuel C.; Villamin, Alfred S.; Borlasa, Janice B.; Olorosa, Agnettah M.; Hernandez, Lara F. T.; Boehme, Karis D.; Jeffrey, Benjamin; Abudahab, Khalil; Hufano, Charmian M.; Sia, Sonia B.; Stelling, John; Holden, Matthew T. G.; Aanensen, David M.; Carlos, Celia C. (1 June 2020). "Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines". Nature Communications. 11 (1): 2719. Bibcode:2020NatCo..11.2719A. doi:10.1038/s41467-020-16322-5. PMC 7264328. PMID 32483195. S2CID 219156667.
  4. ^ Paul Brackley (20 November 2020). "£12.2m funding will help Cambridge-led COG-UK expand Covid-19 genomic surveillance". www.cambridgeindependent.co.uk. Retrieved 8 March 2021.
  5. ^ "Major new NIHR Global Health Research Unit to focus on data science and genomic surveillance of antimicrobial resistance — Oxford Big Data Institute". www.bdi.ox.ac.uk. Retrieved 4 November 2022.
  6. ^ a b Professor David Aanensen, Director of the Centre for Genomic Pathogen Surveillance and Group Leader www.sanger.ac.uk, accessed 7 March 2021
  7. ^ a b David Aanensen Director of The Centre for Genomic Pathogen Surveillance 2021 www.ndm.ox.ac.uk, accessed 7 March 2021
  8. ^ NIHR Home page www.nihr.ac.uk, accessed 2 March 2021
  9. ^ Commitment to collaborate on using genomics for pathogen surveillance across Europe 14 March 2019 www.sanger.ac.uk, accessed 7 March 2021
  10. ^ Hospitals in Europe are contributing to the spread of extremely drug-resistant bacteria 30 July 2019, www.zmescience.com, accessed 8 March 2021
  11. ^ Superbug infections tracked across Europe 5 May 2016 www.sciencedaily.com, accessed 8 March 2021
  12. ^ "Microreact has been developed by the Centre for Genomic Pathogen Surveillance at Imperial College London and the Wellcome Genome Campus" microreact.org, accessed 8 March 2021
  13. ^ "Pangolin web application release". virological.org. May 2020. Retrieved 18 February 2021.
  14. ^ How the Covid-19 Genomics UK Consortium sequenced Sars-Cov-2 12 April 2021 www.computerweekly.com, accessed 26 May 2021
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