The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has becom...

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Bibliographic Details
Published in:bioRxiv 2021-03
Main Authors: De Silva, Nishadi H, Bhai, Jyothish, Chakiachvili, Marc, Contreras-Moreira, Bruno, Cummins, Carla, Frankish, Adam, Gall, Astrid, Genez, Thiago, Howe, Kevin L, Hunt, Sarah E, Martin, Fergal J, Moore, Benjamin, Ogeh, Denye, Parker, Anne, Parton, Andrew, Ruffier, Magali, Manoj Pandian Sakthivel, Sheppard, Dan, Tate, John, Thormann, Anja, Thybert, David, Trevanion, Stephen J, Winterbottom, Andrea, Zerbino, Daniel R, Finn, Robert D, Flicek, Paul, Yates, Andrew D
Format: Article
Language:English
Subjects:
Bioinformatics
Coronaviruses
COVID-19
Epidemiology
Pandemics
Severe acute respiratory syndrome coronavirus 2
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Summary:The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser, incorporating a new Ensembl gene set, multiple variant sets (including novel variation calls), and annotation from several relevant resources integrated into the reference SARS-CoV-2 assembly. This work included key adaptations of existing Ensembl genome annotation methods to model ribosomal slippage, stringent filters to elucidate the highest confidence variants and utilisation of our comparative genomics pipelines on viruses for the first time. Since May 2020, the content has been regularly updated and tools such as the Ensembl Variant Effect Predictor have been integrated. The Ensembl COVID-19 browser is freely available at https://covid-19.ensembl.org. Competing Interest Statement Paul Flicek is a member of the scientific advisory boards of Fabric Genomics, Inc., and Eagle Genomics, Ltd. Footnotes * Refinements to the text have been made throughout the manuscript with details to updates to our gene annotation methods and other workflows. Furthermore, information on new variants have been added, all the figures have been re-drawn and sections on code availability and conflicts of interest updated. * https://covid-19.ensembl.org
ISSN:2692-8205
DOI:10.1101/2020.12.18.422865