2024
A new lineage nomenclature to aid genomic surveillance of dengue virus
Hill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.Peer-Reviewed Original ResearchConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settings
2022
Genomics-informed outbreak investigations of SARS-CoV-2 using civet
O’Toole Á, Hill V, Jackson B, Dewar R, Sahadeo N, Colquhoun R, Rooke S, McCrone J, Duggan K, McHugh M, Nicholls S, Poplawski R, Consortium T, Project C, Aanensen D, Holden M, Connor T, Loman N, Goodfellow I, Carrington C, Templeton K, Rambaut A. Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health 2022, 2: e0000704. PMID: 36962792, PMCID: PMC10021969, DOI: 10.1371/journal.pgph.0000704.Peer-Reviewed Original ResearchWealth of sequence dataGenomic surveillance effortsInvestigation of SARS-CoV-2Outbreak investigationPhylogenetic resultsGenomic informationSequence dataVirus diversityPublic health bodiesCivetSARS-CoV-2Distribution reportsSequenceHealth bodiesCluster discoveryDiversityPublic healthSimilarity analysisSARS-CoV-2 pandemicSurveillance effortsGlobal datasetVirusLocal surveillanceLocal outbreaksNational level
2021
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
Jackson B, Boni M, Bull M, Colleran A, Colquhoun R, Darby A, Haldenby S, Hill V, Lucaci A, McCrone J, Nicholls S, O’Toole Á, Pacchiarini N, Poplawski R, Scher E, Todd F, Webster H, Whitehead M, Wierzbicki C, Consortium T, Loman N, Connor T, Robertson D, Pybus O, Rambaut A. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell 2021, 184: 5179-5188.e8. PMID: 34499854, PMCID: PMC8367733, DOI: 10.1016/j.cell.2021.08.014.Peer-Reviewed Original ResearchConceptsLocations of recombination breakpointsLineage-defining mutationsMultiple independent originsSets of mutationsSingle-nucleotide polymorphismsGenomic locationsInterlineage recombinationRecombination breakpointsParental virusRecombinant virusesB.1.1.7 variant of concernTransmission advantageGenomeVariant of concernSpike regionB.1.1.7 variantMutationsSequenced casesB.1.1.7VirusRecombinationSARS-CoV-2 virusTransmission clustersSARS-CoV-2Non-B.Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O’Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone J, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood S, Aanensen D, Holmes E, Pybus O, Rambaut A. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution 2021, 7: veab064. PMID: 34527285, PMCID: PMC8344591, DOI: 10.1093/ve/veab064.Peer-Reviewed Original ResearchSARS-CoV-2 genomic dataSARS-CoV-2 genome sequencesPhylogenetic assignmentGenome sequenceGenomics communityGenomic dataPangolin toolOutbreak lineageGenomic epidemiologyVirus genomeLineagesTransmission lineagesGenomePangolinsSARS-CoV-2Nomenclature schemeComputational toolsVirusPangoSequenceSevere acute respiratory syndromeAcute respiratory syndromeEstablishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
du Plessis L, McCrone J, Zarebski A, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor T, Faria N, Jackson B, Loman N, O’Toole Á, Nicholls S, Parag K, Scher E, Vasylyeva T, Volz E, Watts A, Bogoch I, Khan K, Consortium† C, Aanensen D, Kraemer M, Rambaut A, Pybus O. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021, 371: 708-712. PMID: 33419936, PMCID: PMC7877493, DOI: 10.1126/science.abf2946.Peer-Reviewed Original Research
2020
The emergence of SARS-CoV-2 in Europe and North America
Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science 2020, 370: 564-570. PMID: 32912998, PMCID: PMC7810038, DOI: 10.1126/science.abc8169.Peer-Reviewed Original ResearchA dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut A, Holmes E, O’Toole Á, Hill V, McCrone J, Ruis C, du Plessis L, Pybus O. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 2020, 5: 1403-1407. PMID: 32669681, PMCID: PMC7610519, DOI: 10.1038/s41564-020-0770-5.Peer-Reviewed Original ResearchConceptsDiversity of SARS-CoV-2Virus lineagesVirus genome sequencesSARS-CoV-2 lineagesPhylogenetic frameworkGenome sequencePhylogenetic diversityGlobal spread of SARS-CoV-2Nomenclatural proposalsGenomic epidemiologyVirus nomenclatureSARS-CoV-2LineagesLineage labelingHuman coronavirusesGlobal spreadNomenclatureSequenceSpread of SARS-CoV-2Virus