2024
A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK
Colquhoun R, O’Toole Á, Hill V, McCrone J, Yu X, Nicholls S, Poplawski R, Whalley T, Groves N, Ellaby N, Loman N, Connor T, Rambaut A. A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK. Virus Evolution 2024, 10: veae083. PMID: 39493537, PMCID: PMC11529618, DOI: 10.1093/ve/veae083.Peer-Reviewed Original ResearchSARS-CoV-2 genome sequencesSARS-CoV-2 genomeGlobal phylogenetic contextCOVID-19 Genomics UKCOG-UKVariant callingGenome sequencePhylogenetic contextGenomic epidemiologyGenomic surveillanceSARS-CoV-2Public health decision makingHealth decision makingGenomeSequenceSARS-CoV-2 pandemicPhylogeneticallyUnited KingdomQuality controlDecision makingCOVID-19Increasing amountA 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
Progress and challenges in virus genomic epidemiology
Hill V, Ruis C, Bajaj S, Pybus O, Kraemer M. Progress and challenges in virus genomic epidemiology. Trends In Parasitology 2021, 37: 1038-1049. PMID: 34620561, DOI: 10.1016/j.pt.2021.08.007.Peer-Reviewed Original ResearchConceptsGenomic dataSource of genomic dataDecreasing costs of genome sequencingCost of genome sequencingViral genome datasetGenome sequencePathogen genomesGenomic datasetsGenomic epidemiologySpatial scale of transmissionTransmission patternsSpatial scalesScale of transmissionGenomeAssociated metadataPathogensSequenceDisease transmissionGenomic 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 syndromeCLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Nicholls S, Poplawski R, Bull M, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun R, Rowe W, Jackson B, Hill V, O’Toole Á, Rey S, Southgate J, Amato R, Livett R, Gonçalves S, Harrison E, Peacock S, Aanensen D, Rambaut A, Connor T, Loman N. CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology 2021, 22: 196. PMID: 34210356, PMCID: PMC8247108, DOI: 10.1186/s13059-021-02395-y.Peer-Reviewed Original Research
2020
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz E, Hill V, McCrone J, Price A, Jorgensen D, O’Toole Á, Southgate J, Johnson R, Jackson B, Nascimento F, Rey S, Nicholls S, Colquhoun R, da Silva Filipe A, Shepherd J, Pascall D, Shah R, Jesudason N, Li K, Jarrett R, Pacchiarini N, Bull M, Geidelberg L, Siveroni I, Consortium C, Koshy C, Wise E, Cortes N, Lynch J, Kidd S, Mori M, Fairley D, Curran T, McKenna J, Adams H, Fraser C, Golubchik T, Bonsall D, Moore C, Caddy S, Khokhar F, Wantoch M, Reynolds N, Warne B, Maksimovic J, Spellman K, McCluggage K, John M, Beer R, Afifi S, Morgan S, Marchbank A, Price A, Kitchen C, Gulliver H, Merrick I, Southgate J, Guest M, Munn R, Workman T, Connor T, Fuller W, Bresner C, Snell L, Charalampous T, Nebbia G, Batra R, Edgeworth J, Robson S, Beckett A, Loveson K, Aanensen D, Underwood A, Yeats C, Abudahab K, Taylor B, Menegazzo M, Clark G, Smith W, Khakh M, Fleming V, Lister M, Howson-Wells H, Berry L, Boswell T, Joseph A, Willingham I, Bird P, Helmer T, Fallon K, Holmes C, Tang J, Raviprakash V, Campbell S, Sheriff N, Loose M, Holmes N, Moore C, Carlile M, Wright V, Sang F, Debebe J, Coll F, Signell A, Betancor G, Wilson H, Feltwell T, Houldcroft C, Eldirdiri S, Kenyon A, Davis T, Pybus O, du Plessis L, Zarebski A, Raghwani J, Kraemer M, Francois S, Attwood S, Vasylyeva T, Torok M, Hamilton W, Goodfellow I, Hall G, Jahun A, Chaudhry Y, Hosmillo M, Pinckert M, Georgana I, Yakovleva A, Meredith L, Moses S, Lowe H, Ryan F, Fisher C, Awan A, Boyes J, Breuer J, Harris K, Brown J, Shah D, Atkinson L, Lee J, Alcolea-Medina A, Moore N, Cortes N, Williams R, Chapman M, Levett L, Heaney J, Smith D, Bashton M, Young G, Allan J, Loh J, Randell P, Cox A, Madona P, Holmes A, Bolt F, Price J, Mookerjee S, Rowan A, Taylor G, Ragonnet-Cronin M, Nascimento F, Jorgensen D, Siveroni I, Johnson R, Boyd O, Geidelberg L, Volz E, Brunker K, Smollett K, Loman N, Quick J, McMurray C, Stockton J, Nicholls S, Rowe W, Poplawski R, Martinez-Nunez R, Mason J, Robinson T, O'Toole E, Watts J, Breen C, Cowell A, Ludden C, Sluga G, Machin N, Ahmad S, George R, Halstead F, Sivaprakasam V, Thomson E, Shepherd J, Asamaphan P, Niebel M, Li K, Shah R, Jesudason N, Parr Y, Tong L, Broos A, Mair D, Nichols J, Carmichael S, Nomikou K, Aranday-Cortes E, Johnson N, Starinskij I, da Silva Filipe A, Robertson D, Orton R, Hughes J, Vattipally S, Singer J, Hale A, Macfarlane-Smith L, Harper K, Taha Y, Payne B, Burton-Fanning S, Waugh S, Collins J, Eltringham G, Templeton K, McHugh M, Dewar R, Wastenge E, Dervisevic S, Stanley R, Prakash R, Stuart C, Elumogo N, Sethi D, Meader E, Coupland L, Potter W, Graham C, Barton E, Padgett D, Scott G, Swindells E, Greenaway J, Nelson A, Yew W, Silva P, Andersson M, Shaw R, Peto T, Justice A, Eyre D, Crooke D, Hoosdally S, Sloan T, Duckworth N, Walsh S, Chauhan A, Glaysher S, Bicknell K, Wyllie S, Butcher E, Elliott S, Lloyd A, Impey R, Levene N, Monaghan L, Bradley D, Allara E, Pearson C, Muir P, Vipond I, Hopes R, Pymont H, Hutchings S, Curran M, Parmar S, Lackenby A, Mbisa T, Platt S, Miah S, Bibby D, Manso C, Hubb J, Chand M, Dabrera G, Ramsay M, Bradshaw D, Thornton A, Myers R, Schaefer U, Groves N, Gallagher E, Lee D, Williams D, Ellaby N, Harrison I, Hartman H, Manesis N, Patel V, Bishop C, Chalker V, Osman H, Bosworth A, Robinson E, Holden M, Shaaban S, Birchley A, Adams A, Davies A, Gaskin A, Plimmer A, Gatica-Wilcox B, McKerr C, Moore C, Williams C, Heyburn D, De Lacy E, Hilvers E, Downing F, Shankar G, Jones H, Asad H, Coombes J, Watkins J, Evans J, Fina L, Gifford L, Gilbert L, Graham L, Perry M, Morgan M, Bull M, Cronin M, Pacchiarini N, Craine N, Jones R, Howe R, Corden S, Rey S, Kumziene-Summerhayes S, Taylor S, Cottrell S, Jones S, Edwards S, O’Grady J, Page A, Wain J, Webber M, Mather A, Baker D, Rudder S, Yasir M, Thomson N, Aydin A, Tedim A, Kay G, Trotter A, Gilroy R, Alikhan N, de Oliveira Martins L, Le-Viet T, Meadows L, Kolyva A, Diaz M, Bell A, Gutierrez A, Charles I, Adriaenssens E, Kingsley R, Casey A, Simpson D, Molnar Z, Thompson T, Acheson E, Masoli J, Knight B, Hattersley A, Ellard S, Auckland C, Mahungu T, Irish-Tavares D, Haque T, Bourgeois Y, Scarlett G, Partridge D, Raza M, Evans C, Johnson K, Liggett S, Baker P, Essex S, Lyons R, Caller L, Castellano S, Williams R, Kristiansen M, Roy S, Williams C, Dyal P, Tutill H, Panchbhaya Y, Forrest L, Niola P, Findlay J, Brooks T, Gavriil A, Mestek-Boukhibar L, Weeks S, Pandey S, Berry L, Jones K, Richter A, Beggs A, Smith C, Bucca G, Hesketh A, Harrison E, Peacock S, Palmer S, Churcher C, Bellis K, Girgis S, Naydenova P, Blane B, Sridhar S, Ruis C, Forrest S, Cormie C, Gill H, Dias J, Higginson E, Maes M, Young J, Kermack L, Hadjirin N, Aggarwal D, Griffith L, Swingler T, Davidson R, Rambaut A, Williams T, Balcazar C, Gallagher M, O'Toole Á, Rooke S, Jackson B, Colquhoun R, Ashworth J, Hill V, McCrone J, Scher E, Yu X, Williamson K, Stanton T, Michell S, Bewshea C, Temperton B, Michelsen M, Warwick-Dugdale J, Manley R, Farbos A, Harrison J, Sambles C, Studholme D, Jeffries A, Darby A, Hiscox J, Paterson S, Iturriza-Gomara M, Jackson K, Lucaci A, Vamos E, Hughes M, Rainbow L, Eccles R, Nelson C, Whitehead M, Turtle L, Haldenby S, Gregory R, Gemmell M, Kwiatkowski D, de Silva T, Smith N, Angyal A, Lindsey B, Groves D, Green L, Wang D, Freeman T, Parker M, Keeley A, Parsons P, Tucker R, Brown R, Wyles M, Constantinidou C, Unnikrishnan M, Ott S, Cheng J, Bridgewater H, Frost L, Taylor-Joyce G, Stark R, Baxter L, Alam M, Brown P, McClure P, Chappell J, Tsoleridis T, Ball J, Gramatopoulos D, Buck D, Todd J, Green A, Trebes A, MacIntyre-Cockett G, de Cesare M, Langford C, Alderton A, Amato R, Goncalves S, Jackson D, Johnston I, Sillitoe J, Palmer S, Lawniczak M, Berriman M, Danesh J, Livett R, Shirley L, Farr B, Quail M, Thurston S, Park N, Betteridge E, Weldon D, Goodwin S, Nelson R, Beaver C, Letchford L, Jackson D, Foulser L, McMinn L, Prestwood L, Kay S, Kane L, Dorman M, Martincorena I, Puethe C, Keatley J, Tonkin-Hill G, Smith C, Jamrozy D, Beale M, Patel M, Ariani C, Spencer-Chapman M, Drury E, Lo S, Rajatileka S, Scott C, James K, Buddenborg S, Berger D, Patel G, Garcia-Casado M, Dibling T, McGuigan S, Rogers H, Hunter A, Souster E, Neaverson A, Goodfellow I, Loman N, Pybus O, Robertson D, Thomson E, Rambaut A, Connor T. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell 2020, 184: 64-75.e11. PMID: 33275900, PMCID: PMC7674007, DOI: 10.1016/j.cell.2020.11.020.Peer-Reviewed Original ResearchConceptsD614GPositive selectionSignals of positive selectionRandom founder effectsPopulation genetic analysesSARS-CoV-2 sequencesSpike D614GMutation D614GFounder effectVariant D614GGenetic analysisSARS-CoV-2Spike mutation D614GGlobal dispersalVariantsAssociated with higher viral loadYoung age of patientsAge of patientsHigh viral loadPathogensSequenceViral loadClinical severityA 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-2VirusGenomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
Lu J, du Plessis L, Liu Z, Hill V, Kang M, Lin H, Sun J, François S, Kraemer M, Faria N, McCrone J, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, Bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus O, Ke C. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell 2020, 181: 997-1003.e9. PMID: 32359424, PMCID: PMC7192124, DOI: 10.1016/j.cell.2020.04.023.Peer-Reviewed Original ResearchConceptsGenetic diversity of SARS-CoV-2Combination of metagenomic sequencingDiversity of SARS-CoV-2Genomic epidemiology of SARS-CoV-2Genetic diversityAmplicon approachPhylogenetic analysisMetagenomic sequencingPhylogenetic clusteringChina’s most populous province,Genetic variationEpidemiology of SARS-CoV-2Genomic epidemiologyIndependent introductionsSARS-CoV-2Molecular epidemiologyMolecular surveillanceGenomeLocal transmission chainsTransmission chainCentral ChinaSequenceSARS-CoV-2 infectionGuangdong Province
2019
Bayesian Estimation of Past Population Dynamics in BEAST 1.10 Using the Skygrid Coalescent Model
Hill V, Baele G. Bayesian Estimation of Past Population Dynamics in BEAST 1.10 Using the Skygrid Coalescent Model. Molecular Biology And Evolution 2019, 36: 2620-2628. PMID: 31364710, PMCID: PMC6805224, DOI: 10.1093/molbev/msz172.Peer-Reviewed Original ResearchCoalescence modelAnalysis of molecular sequencesEffective population sizeMolecular sequence dataPopulation dynamicsMolecular clock modelBayesian analysis of molecular sequencesPhylogenetic treeSequence dataMolecular sequencesPopulation sizeCross-platform programBayesian analysisClock modelMarkov chain Monte CarloBayesian inferenceBEASTBayesian estimationSkygridSequenceDrawing inferenceTrees