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

Nadim Rahman; Colman O'cathail; Ahmad Zyoud; Alexey Sokolov; Bas Oude Munnink; Björn Grüning; Carla Cummins; Clara Amid; David F. Nieuwenhuijse; Dávid Visontai; David Yu Yuan; Dipayan Gupta; Divyae K. Prasad; Gábor Máté Gulyás; Gabriele Rinck; Jasmine McKinnon; Jeena Rajan; Jeff Knaggs; Jeffrey Edward Skiby; József Stéger; Judit Szarvas; Khadim Gueye; Krisztián Papp; Maarten Hoek; Manish Kumar; Marianna A. Ventouratou; Marie Catherine Bouquieaux; Martin Koliba; Milena Mansurova; Muhammad Haseeb; Nathalie Worp; Peter W. Harrison; Rasko Leinonen; Ross Thorne; Sandeep Selvakumar; Sarah Hunt; Sundar Venkataraman; Suran Jayathilaka; Timothée Cezard; Wolfgang Maier; Zahra Waheed; Zamin Iqbal; Frank Møller Aarestrup; Istvan Csabai; Marion Koopmans; Tony Burdett; Guy Cochrane

doi:10.1099/mgen.0.001188

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

Nadim Rahman^*, Colman O'cathail^*, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Björn Grüning, Carla Cummins, Clara Amid, David F. Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae K. Prasad, Gábor Máté Gulyás, Gabriele Rinck, Jasmine McKinnon, Jeena Rajan, Jeff Knaggs, Jeffrey Edward Skiby, József StégerJudit Szarvas, Khadim Gueye, Krisztián Papp, Maarten Hoek, Manish Kumar, Marianna A. Ventouratou, Marie Catherine Bouquieaux, Martin Koliba, Milena Mansurova, Muhammad Haseeb, Nathalie Worp, Peter W. Harrison, Rasko Leinonen, Ross Thorne, Sandeep Selvakumar, Sarah Hunt, Sundar Venkataraman, Suran Jayathilaka, Timothée Cezard, Wolfgang Maier, Zahra Waheed, Zamin Iqbal, Frank Møller Aarestrup, Istvan Csabai, Marion Koopmans, Tony Burdett, Guy Cochrane^*

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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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 vari-ants, 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.

Original language	English
Article number	001188
Journal	Microbial Genomics
Volume	10
Issue number	2
Number of pages	21
ISSN	2057-5858
DOIs	https://doi.org/10.1099/mgen.0.001188
Publication status	Published - 2024

Keywords

SARS-CoV- 2
COVID-19
Open data
Data sharing
Genomics sequencing
Emerging variants

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1099/mgen.0.001188Licence: CC BY

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Rahman, N., O'cathail, C., Zyoud, A., Sokolov, A., Munnink, B. O., Grüning, B., Cummins, C., Amid, C., Nieuwenhuijse, D. F., Visontai, D., Yuan, D. Y., Gupta, D., Prasad, D. K., Gulyás, G. M., Rinck, G., McKinnon, J., Rajan, J., Knaggs, J., Skiby, J. E., ... Cochrane, G. (2024). Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microbial Genomics, 10(2), Article 001188. https://doi.org/10.1099/mgen.0.001188

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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 vari-ants, 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.",

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author = "Nadim Rahman and Colman O'cathail and Ahmad Zyoud and Alexey Sokolov and Munnink, {Bas Oude} and Bj{\"o}rn Gr{\"u}ning and Carla Cummins and Clara Amid and Nieuwenhuijse, {David F.} and D{\'a}vid Visontai and Yuan, {David Yu} and Dipayan Gupta and Prasad, {Divyae K.} and Guly{\'a}s, {G{\'a}bor M{\'a}t{\'e}} and Gabriele Rinck and Jasmine McKinnon and Jeena Rajan and Jeff Knaggs and Skiby, {Jeffrey Edward} and J{\'o}zsef St{\'e}ger and Judit Szarvas and Khadim Gueye and Kriszti{\'a}n Papp and Maarten Hoek and Manish Kumar and Ventouratou, {Marianna A.} and Bouquieaux, {Marie Catherine} and Martin Koliba and Milena Mansurova and Muhammad Haseeb and Nathalie Worp and Harrison, {Peter W.} and Rasko Leinonen and Ross Thorne and Sandeep Selvakumar and Sarah Hunt and Sundar Venkataraman and Suran Jayathilaka and Timoth{\'e}e Cezard and Wolfgang Maier and Zahra Waheed and Zamin Iqbal and Aarestrup, {Frank M{\o}ller} and Istvan Csabai and Marion Koopmans and Tony Burdett and Guy Cochrane",

note = "Publisher Copyright: 8 {\textcopyright} 2024 The Authors.",

year = "2024",

doi = "10.1099/mgen.0.001188",

language = "English",

volume = "10",

journal = "Microbial Genomics",

issn = "2057-5858",

publisher = "Microbiology Society",

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Rahman, N, O'cathail, C, Zyoud, A, Sokolov, A, Munnink, BO, Grüning, B, Cummins, C, Amid, C, Nieuwenhuijse, DF, Visontai, D, Yuan, DY, Gupta, D, Prasad, DK, Gulyás, GM, Rinck, G, McKinnon, J, Rajan, J, Knaggs, J, Skiby, JE, Stéger, J, Szarvas, J, Gueye, K, Papp, K, Hoek, M, Kumar, M, Ventouratou, MA, Bouquieaux, MC, Koliba, M, Mansurova, M, Haseeb, M, Worp, N, Harrison, PW, Leinonen, R, Thorne, R, Selvakumar, S, Hunt, S, Venkataraman, S, Jayathilaka, S, Cezard, T, Maier, W, Waheed, Z, Iqbal, Z, Aarestrup, FM, Csabai, I, Koopmans, M, Burdett, T & Cochrane, G 2024, 'Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses', Microbial Genomics, vol. 10, no. 2, 001188. https://doi.org/10.1099/mgen.0.001188

TY - JOUR

T1 - Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

AU - Rahman, Nadim

AU - O'cathail, Colman

AU - Zyoud, Ahmad

AU - Sokolov, Alexey

AU - Munnink, Bas Oude

AU - Grüning, Björn

AU - Cummins, Carla

AU - Amid, Clara

AU - Nieuwenhuijse, David F.

AU - Visontai, Dávid

AU - Yuan, David Yu

AU - Gupta, Dipayan

AU - Prasad, Divyae K.

AU - Gulyás, Gábor Máté

AU - Rinck, Gabriele

AU - McKinnon, Jasmine

AU - Rajan, Jeena

AU - Knaggs, Jeff

AU - Skiby, Jeffrey Edward

AU - Stéger, József

AU - Szarvas, Judit

AU - Gueye, Khadim

AU - Papp, Krisztián

AU - Hoek, Maarten

AU - Kumar, Manish

AU - Ventouratou, Marianna A.

AU - Bouquieaux, Marie Catherine

AU - Koliba, Martin

AU - Mansurova, Milena

AU - Haseeb, Muhammad

AU - Worp, Nathalie

AU - Harrison, Peter W.

AU - Leinonen, Rasko

AU - Thorne, Ross

AU - Selvakumar, Sandeep

AU - Hunt, Sarah

AU - Venkataraman, Sundar

AU - Jayathilaka, Suran

AU - Cezard, Timothée

AU - Maier, Wolfgang

AU - Waheed, Zahra

AU - Iqbal, Zamin

AU - Aarestrup, Frank Møller

AU - Csabai, Istvan

AU - Koopmans, Marion

AU - Burdett, Tony

AU - Cochrane, Guy

PY - 2024

Y1 - 2024

N2 - 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 vari-ants, 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.

AB - 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 vari-ants, 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.

KW - SARS-CoV- 2

KW - COVID-19

KW - Open data

KW - Data sharing

KW - Genomics sequencing

KW - Emerging variants

U2 - 10.1099/mgen.0.001188

DO - 10.1099/mgen.0.001188

M3 - Journal article

C2 - 38358325

AN - SCOPUS:85185348063

SN - 2057-5858

VL - 10

JO - Microbial Genomics

JF - Microbial Genomics

IS - 2

M1 - 001188

ER -

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

Abstract

Keywords

UN SDGs

Access to Document

OpenUrl availability

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