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 settingsEarly Release - Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022–April 2023 - Volume 30, Number 2—February 2024 - Emerging Infectious Diseases journal - CDC
Jones F, Morrison A, Santiago G, Rysava K, Zimler R, Heberlein L, Kopp E, , Saunders K, Baudin S, Rico E, Mejía-Echeverri Á, Taylor-Salmon E, Hill V, Breban M, Vogels C, Grubaugh N, Paul L, Michael S, Johansson M, Adams L, Munoz-Jordan J, Paz-Bailey G, Stanek D. Early Release - Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022–April 2023 - Volume 30, Number 2—February 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 376-379. PMID: 38232709, PMCID: PMC10826764, DOI: 10.3201/eid3002.231615.Peer-Reviewed Original Research
2022
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Aggarwal D, Warne B, Jahun A, Hamilton W, Fieldman T, du Plessis L, Hill V, Blane B, Watkins E, Wright E, Hall G, Ludden C, Myers R, Hosmillo M, Chaudhry Y, Pinckert M, Georgana I, Izuagbe R, Leek D, Nsonwu O, Hughes G, Packer S, Page A, Metaxaki M, Fuller S, Weale G, Holgate J, Brown C, Howes R, McFarlane D, Dougan G, Pybus O, Angelis D, Maxwell P, Peacock S, Weekes M, Illingworth C, Harrison E, Matheson N, Goodfellow I. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications 2022, 13: 751. PMID: 35136068, PMCID: PMC8826310, DOI: 10.1038/s41467-021-27942-w.Peer-Reviewed Original ResearchConceptsDeterminants of SARS-CoV-2 transmissionPublic health policiesHigher education settingsLocal infection control measuresAt-risk populationsSARS-CoV-2 transmissionHealth policyEffective interventionsEducational settingsGenomic epidemiology of SARS-CoV-2SARS-CoV-2 isolatesAt-riskGenetic clustersPhylogenetic comparisonsEpidemiology of SARS-CoV-2Infection control measuresGenomic epidemiologyNational lockdownSARS-CoV-2Social gatheringsUK universitiesStudent casesStudent accommodationSurrounding communityUniversity
2021
Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity
Butera Y, Mukantwari E, Artesi M, Umuringa J, O’Toole Á, Hill V, Rooke S, Hong S, Dellicour S, Majyambere O, Bontems S, Boujemla B, Quick J, Resende P, Loman N, Umumararungu E, Kabanda A, Murindahabi M, Tuyisenge P, Gashegu M, Rwabihama J, Sindayiheba R, Gikic D, Souopgui J, Ndifon W, Rutayisire R, Gatare S, Mpunga T, Ngamije D, Bours V, Rambaut A, Nsanzimana S, Baele G, Durkin K, Mutesa L, Rujeni N. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications 2021, 12: 5705. PMID: 34588460, PMCID: PMC8481346, DOI: 10.1038/s41467-021-25985-7.Peer-Reviewed Original ResearchConceptsGenome sequenceGenome sequences of SARS-CoV-2SARS-CoV-2 whole genome sequencingSequences of SARS-CoV-2Whole-genome sequencingPhylogeographic inferenceLineage diversityStrains of SARS-CoV-2Genomic surveillanceLocally circulating strainsSub-lineagesSeed introductionSARS-CoV-2Variant distributionSequenceViral introductionLineagesDiversityGeneration 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.Establishment 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
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2
Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone J, Andersen K, Worobey M, Nelson M, Rambaut A, Suchard M. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications 2020, 11: 5110. PMID: 33037213, PMCID: PMC7547076, DOI: 10.1038/s41467-020-18877-9.Peer-Reviewed Original ResearchConceptsBayesian phylogeographic inferencePhylogeographic inferenceSARS-CoV-2 genomeIndividual travel history dataImpact of sampling biasTravel history dataGenomic samplesPhylogeographic analysisSARS-CoV-2Sampling effortPosterior predictive accuracyUndersampled locationsGenomeVirus migrationSpatiotemporal biasesSpread of SARS-CoV-2Sampling biasTransmission hypothesisSampling locationsIndividual's travel historyLineagesVirus spreadDiversityThe 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