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dc.contributor.authorO'Toole, Áine
dc.contributor.authorScher, Emily
dc.contributor.authorUnderwood, Anthony
dc.contributor.authorJackson, Ben
dc.contributor.authorHill, Verity
dc.contributor.authorMcCrone, John T
dc.contributor.authorColquhoun, Rachel
dc.contributor.authorRuis, Chris
dc.contributor.authorAbu-Dahab, Khalil
dc.contributor.authorTaylor, Ben
dc.contributor.authorYeats, Corin
dc.contributor.authordu Plessis, Louis
dc.contributor.authorMaloney, Daniel
dc.contributor.authorMedd, Nathan
dc.contributor.authorAttwood, Stephen W
dc.contributor.authorAanensen, David M
dc.contributor.authorHolmes, Edward C
dc.contributor.authorPybus, Oliver G
dc.contributor.authorRambaut, Andrew
dc.date.accessioned2021-10-18T08:52:08Z
dc.date.available2021-10-18T08:52:08Z
dc.date.issued2021
dc.identifier.issn2057-1577
dc.identifier.otherPMC8344591
dc.identifier.other34527285
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/329565
dc.descriptionFunder: Oxford Martin School, University of Oxford
dc.description.abstractThe response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic's transmission lineages.
dc.languageeng
dc.publisherOxford University Press (OUP)
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceessn: 2057-1577
dc.sourcenlmid: 101664675
dc.subjectSoftware
dc.subjectLineage
dc.subjectphylogenetics
dc.subjectGenomic Surveillance
dc.subjectSars-cov-2
dc.titleAssignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
dc.typeArticle
dc.date.updated2021-10-18T08:52:08Z
prism.issueIdentifier2
prism.publicationNameVirus Evol
prism.volume7
dc.identifier.doi10.17863/CAM.77013
dcterms.dateAccepted2021-07-05
rioxxterms.versionofrecord10.1093/ve/veab064
rioxxterms.versionVoR
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidO'Toole, Áine [0000-0001-8083-474X]
dc.contributor.orcidScher, Emily [0000-0002-5401-5879]
dc.contributor.orcidJackson, Ben [0000-0002-9981-0649]
dc.contributor.orcidHill, Verity [0000-0002-3509-8146]
dc.contributor.orcidColquhoun, Rachel [0000-0002-5577-9897]
dc.contributor.orcidYeats, Corin [0000-0003-0080-6242]
dc.contributor.orcidMedd, Nathan [0000-0001-7833-5909]
dc.contributor.orcidAttwood, Stephen W [0000-0003-1717-1677]
dc.contributor.orcidHolmes, Edward C [0000-0001-9596-3552]
dc.contributor.orcidPybus, Oliver G [0000-0002-8797-2667]
dc.contributor.orcidRambaut, Andrew [0000-0003-4337-3707]
dc.identifier.eissn2057-1577
pubs.funder-project-idWellcome Trust (grant.203783/Z/16/Z, 206298/Z/17/Z)
pubs.funder-project-idFast Grants (2236)
pubs.funder-project-idEuropean Research Council (203783, 725422, 725422 - ReservoirDOCS)
cam.issuedOnline2021-07-05


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International