A survey into the contribution of regional/national pathogen data platforms and on the resources needed to develop and maintain them

Abstract

Background Regional/national SARS-CoV-2 genomic data platforms (DP) have played a key role during the Covid-19 pandemic to centralize data, curate, process and re-share them in a consistent form and pseudonymized/anonymized to international repositories. In Europe, several countries were able to establish such infrastructures rapidly and put them in production over the course of 2021, some earlier. Methods This survey aimed to estimate the effort that was needed to establish and run these DPs during the sequencing peak of the pandemic in 2021, including activities from data curation to data brokering, and what it would take to expand these DPs to other pathogens and antimicrobial resistance from 2023 onwards. Results Overall, a median of 10 person-months (PM) were used by each DP over 2021 and a median of 18 PM (per year) would be needed to expand activities from 2023 onwards. This survey shows that short-term funding remains commonplace and a struggle for the majority of DPs. Key supporters and arguments (e.g. centered around efficiency and cost-savings) for public health authorities and research funding bodies have also been identified to help individual data platforms in strengthening their funding proposals. Conclusions Ultimately, we propose that DPs get connected into a supra-national entity to build a stronger case and get access to major infrastructure funding grants at the European and global levels.