Centre for Genomic Pathogen Surveillance

{{Short description|UK computational genomics research institute}}

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| address = Big Data Institute, Old Road Campus, University of Oxford, Headington, OX3 7LF

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

History

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.{{Cite web |url=https://fundingawards.nihr.ac.uk/award/16/136/111 |title=Funding and Awards |work=fundingawards.nihr.ac.uk |access-date=2 March 2021}}{{Cite web |url=https://www.sanger.ac.uk/news_item/new-global-health-initiative-genomic-surveillance-antimicrobial-resistance-funded-nihr/ |title=The Centre for Genomic Pathogen Surveillance to house the Global Health Research Unit to monitor antibiotic resistant bacteria around the globe |date=21 July 2017 |work=www.sanger.ac.uk |access-date=7 March 2021}} This has seen the centre becoming involved with surveillance of antibiotic resistance in a number of countries, for example, the Philippines.{{Cite journal |url= |title=Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines |date=1 June 2020 |journal=Nature Communications |doi=10.1038/s41467-020-16322-5 |last1=Argimón |first1=Silvia |last2=Masim |first2=Melissa A. L. |last3=Gayeta |first3=June M. |last4=Lagrada |first4=Marietta L. |last5=MacAranas |first5=Polle K. V. |last6=Cohen |first6=Victoria |last7=Limas |first7=Marilyn T. |last8=Espiritu |first8=Holly O. |last9=Palarca |first9=Janziel C. |last10=Chilam |first10=Jeremiah |last11=Jamoralin |first11=Manuel C. |last12=Villamin |first12=Alfred S. |last13=Borlasa |first13=Janice B. |last14=Olorosa |first14=Agnettah M. |last15=Hernandez |first15=Lara F. T. |last16=Boehme |first16=Karis D. |last17=Jeffrey |first17=Benjamin |last18=Abudahab |first18=Khalil |last19=Hufano |first19=Charmian M. |last20=Sia |first20=Sonia B. |last21=Stelling |first21=John |last22=Holden |first22=Matthew T. G. |last23=Aanensen |first23=David M. |last24=Carlos |first24=Celia C. |volume=11 |issue=1 |page=2719 |pmid=32483195 |bibcode=2020NatCo..11.2719A |s2cid=219156667 |pmc=7264328 }}

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.{{Cite web |url=https://www.cambridgeindependent.co.uk/news/12-2m-funding-will-help-cambridge-led-cog-uk-expand-covid-19-genomic-surveillance-9130122/ |author=Paul Brackley |title=£12.2m funding will help Cambridge-led COG-UK expand Covid-19 genomic surveillance |date=20 November 2020 |work=www.cambridgeindependent.co.uk |access-date=8 March 2021}}

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).{{Cite web |title=Major new NIHR Global Health Research Unit to focus on data science and genomic surveillance of antimicrobial resistance — Oxford Big Data Institute |url=https://www.bdi.ox.ac.uk/news/major-new-nihr-global-health-research-unit-to-focus-on-data-science-and-genomic-surveillance-of-antimicrobial-resistance |access-date=2022-11-04 |website=www.bdi.ox.ac.uk}}

Structure

The centre's director is David Aanensen.[https://www.sanger.ac.uk/person/aanensen-david/ Professor David Aanensen, Director of the Centre for Genomic Pathogen Surveillance and Group Leader] www.sanger.ac.uk, accessed 7 March 2021[https://www.ndm.ox.ac.uk/team/david-aanensen David Aanensen Director of The Centre for Genomic Pathogen Surveillance] 2021 www.ndm.ox.ac.uk, accessed 7 March 2021

The centre is principally funded, and directed, by the Department of Health and Social Care.[https://www.nihr.ac.uk/ NIHR Home page] www.nihr.ac.uk, accessed 2 March 2021 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.[https://www.sanger.ac.uk/news_item/commitment-collaborate-using-genomics-pathogen-surveillance-across-europe/ Commitment to collaborate on using genomics for pathogen surveillance across Europe] 14 March 2019 www.sanger.ac.uk, accessed 7 March 2021

Applications created at the centre

Under the auspices of the centre, the Epicollect5 (used for data entry from distributed observers, e.g. by 'citizen science' programs), Microreact,[https://www.zmescience.com/medicine/hospital-extremely-resistant-bacteria-155168/ Hospitals in Europe are contributing to the spread of extremely drug-resistant bacteria] 30 July 2019, www.zmescience.com, accessed 8 March 2021[https://www.sciencedaily.com/releases/2016/05/160505135015.htm Superbug infections tracked across Europe] 5 May 2016 www.sciencedaily.com, accessed 8 March 2021 and Pathogenwatch applications have been generated and shared. Microreact[https://microreact.org/about "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 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.{{cite web|date=May 2020|title=Pangolin web application release|url=https://virological.org/t/pangolin-web-application-release/482|access-date=18 February 2021|website=virological.org}}[https://www.computerweekly.com/feature/How-the-Covid-19-Genomics-UK-Consortium-sequenced-Sars-Cov-2 How the Covid-19 Genomics UK Consortium sequenced Sars-Cov-2] 12 April 2021 www.computerweekly.com, accessed 26 May 2021