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Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.

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cam.issuedOnline2021-07-30
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.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.date.accessioned2021-10-18T08:52:08Z
dc.date.available2021-10-18T08:52:08Z
dc.date.issued2021
dc.date.updated2021-10-18T08:52:08Z
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.identifier.doi10.17863/CAM.77013
dc.identifier.eissn2057-1577
dc.identifier.issn2057-1577
dc.identifier.otherPMC8344591
dc.identifier.other34527285
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/329565
dc.languageeng
dc.language.isoeng
dc.publisherOxford University Press (OUP)
dc.publisher.urlhttp://dx.doi.org/10.1093/ve/veab064
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceessn: 2057-1577
dc.sourcenlmid: 101664675
dc.subjectSARS-CoV-2
dc.subjectgenomic surveillance
dc.subjectlineage
dc.subjectphylogenetics
dc.subjectsoftware
dc.titleAssignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
dc.typeArticle
dcterms.dateAccepted2021-07-05
prism.issueIdentifier2
prism.publicationNameVirus Evol
prism.volume7
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)
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1093/ve/veab064

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