Evidence map›Paper›PMID 38358325›Full record

ArticleMicrobial genomics2024

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 and 37 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
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  5. Article
  6. The European Nucleotide Archive in 2023.Nucleic acids research · 2024
    Article
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  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

47 authors.

Nadim RahmanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Colman O'CathailEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Ahmad ZyoudEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Alexey SokolovEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Bas Oude MunninkErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Björn GrüningUniversity of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany.
Carla CumminsEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Clara AmidErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
David F NieuwenhuijseErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Dávid VisontaiEötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary.
David Yu YuanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Dipayan GuptaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Divyae K PrasadErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Gábor Máté GulyásTechnical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark.
Gabriele RinckEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Jasmine McKinnonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Jeena RajanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Jeff KnaggsEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Jeffrey Edward SkibyTechnical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark.
József StégerEötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary.
Judit SzarvasTechnical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark.
Khadim GueyeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Krisztián PappEötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary.
Maarten HoekErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Manish KumarEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Marianna A VentouratouEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Marie-Catherine BouquieauxErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Martin KolibaTechnical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark.
Milena MansurovaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Muhammad HaseebEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Nathalie WorpErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Peter W HarrisonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Rasko LeinonenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Ross ThorneEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Sandeep SelvakumarEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Sarah HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Sundar VenkataramanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Suran JayathilakaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Timothée CezardEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Wolfgang MaierUniversity of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany.
Zahra WaheedEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Zamin IqbalEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Frank Møller AarestrupTechnical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark.
Istvan CsabaiEötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary.
Marion KoopmansErasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
Tony BurdettEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Guy CochraneEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

COVID-19SARS-CoV-2GenomicsHumansInformation DisseminationPandemicsCOVID-19Data sharingEmerging variantsGenomics sequencingOpen dataSARS-CoV-2

Identifiers

PMID38358325
PMCPMC10926692

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.