2024
Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC
Grubaugh N, Torres-Hernández D, Murillo-Ortiz M, Dávalos D, Lopez P, Hurtado I, Breban M, Bourgikos E, Hill V, López-Medina E. Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 2391-2395. PMID: 39378873, PMCID: PMC11521178, DOI: 10.3201/eid3011.241031.Peer-Reviewed Original ResearchA 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
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK
Hill V, Du Plessis L, Peacock T, Aggarwal D, Colquhoun R, Carabelli A, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone J, O'Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay W, Barrett J, Chand M, Connor T, Goodfellow I, Gupta R, Harrison E, Loman N, Myers R, Robertson D, Pybus O, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution 2022, 8: veac080. PMID: 36533153, PMCID: PMC9752794, DOI: 10.1093/ve/veac080.Peer-Reviewed Original ResearchEvolutionary ratesIncreased evolutionary rateVariant of concernNon-human animal populationsRate of evolutionLineage B.1.1.7SARS-CoV-2 lineagesSARS-CoV-2 lineage B.1.1.7Monophyletic cladeAncestral branchGenomic locationsPhylogenetic branchesMolecular evolutionMutational eventsGenomic surveillanceInfect immunocompetent hostsAlpha genomeSARS-CoV-2 variantsSARS-CoV-2Animal populationsSARS-CoV-2 variant of concernMutationsMutation profilesLineagesVariants
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 introductionLineagesDiversityAssignment 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 syndromeAddendum: A 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. Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 2021, 6: 415-415. PMID: 33514928, PMCID: PMC7845574, DOI: 10.1038/s41564-021-00872-5.Peer-Reviewed Original ResearchEstablishment 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 spreadDiversityA 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