Repurposing COVID-19 pipelines for the monkeypox virus

20 June 2022


One aim of the BY-COVID project is to build a framework enabling data from newly emerging infectious disease threats to be made rapidly and widely accessible. The current monkeypox outbreak is providing a use case to show how BY-COVID services can be adapted to new infectious agents.

As of 8 June 2022, 1285 laboratory confirmed cases of monkeypox have been reported to the WHO from 28 countries in four WHO Regions where monkeypox has not previously been reported. Genomic and related data is important for monitoring the spread of the monkeypox disease and understanding more about why the outbreak is occuring.

Since the outbreak was first reported, BY-COVID partners have worked to repurpose pipelines built for COVID-19 to the monkeypox virus, demonstrating a fast and efficient response in a new outbreak scenario.

For example, the European COVID-19 Data Platform has developed guidelines on monkeypox data submission, and the Galaxy Project has developed workflows for the analysis of monkeypox virus sequencing data to enable variant analysis and the generation of consensus sequences. Over time, further tools and services will be connected to help in the interpretation of these data.

The successful re-use of COVID-19 data services for a different infectious agent shows how the BY-COVID project is contributing to the creation of a sustainable European infrastructure for pandemic preparedness.

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