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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

ABSTRACT: The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

SUBMITTER: Rahman N

PROVIDER: S-EPMC10926692 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

Rahman Nadim N O'Cathail Colman C Zyoud Ahmad A Sokolov Alexey A Oude Munnink Bas B Grüning Björn B Cummins Carla C Amid Clara C Nieuwenhuijse David F DF Visontai Dávid D Yuan David Yu DY Gupta Dipayan D Prasad Divyae K DK Gulyás Gábor Máté GM Rinck Gabriele G McKinnon Jasmine J Rajan Jeena J Knaggs Jeff J Skiby Jeffrey Edward JE Stéger József J Szarvas Judit J Gueye Khadim K Papp Krisztián K Hoek Maarten M Kumar Manish M Ventouratou Marianna A MA Bouquieaux Marie-Catherine MC Koliba Martin M Mansurova Milena M Haseeb Muhammad M Worp Nathalie N Harrison Peter W PW Leinonen Rasko R Thorne Ross R Selvakumar Sandeep S Hunt Sarah S Venkataraman Sundar S Jayathilaka Suran S Cezard Timothée T Maier Wolfgang W Waheed Zahra Z Iqbal Zamin Z Aarestrup Frank Møller FM Csabai Istvan I Koopmans Marion M Burdett Tony T Cochrane Guy G

Microbial genomics 20240201 2

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, an ...[more]

PMID: 38358325

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Project description:E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or gene ontology level and also provides data for individual genes. E.PathDash reduces the time required to gain access to data from multiple hours per data set to seconds. Users can download high-quality images such as volcano plots and boxplots, differential gene expression results, and raw count data, making it fully interoperable with other tools. Importantly, users can rapidly toggle between experimental comparisons and different studies of the same phenomenon, enabling them to judge the extent to which observed responses are reproducible. As a proof of principle, we invited two cystic fibrosis scientists to use the application to explore scientific questions relevant to their specific research areas. Reassuringly, pathway activation analysis recapitulated results reported in original publications, but it also yielded new insights into pathogen responses to changes in their environments, validating the utility of the application. All software and data are freely accessible, and the application is available at scangeo.dartmouth.edu/EPathDash.ImportanceChronic respiratory illnesses impose a high disease burden on our communities and people with respiratory diseases are susceptible to robust bacterial infections from pathogens, including Pseudomonas aeruginosa and Staphylococcus aureus, that contribute to morbidity and mortality. Public gene expression datasets generated from these and other pathogens are abundantly available and an important resource for synthesizing existing pathogenic research, leading to interventions that improve patient outcomes. However, it can take many hours or weeks to render publicly available datasets usable; significant time and skills are needed to clean, standardize, and apply reproducible and robust bioinformatic pipelines to the data. Through collaboration with two microbiologists, we have shown that E.PathDash addresses this problem, enabling them to elucidate pathogen responses to a variety of over 400 experimental conditions and generate mechanistic hypotheses for cell-level behavior in response to disease-relevant exposures, all in a fraction of the time.

Dataset Information

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

Publications

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

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