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 ResearchMeSH KeywordsDengueDengue VirusGenetic VariationGenome, ViralGenomicsGenotypeHumansPhylogenyTerminology as TopicConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settingsDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specific
2023
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.Peer-Reviewed Original ResearchConceptsChronic infectionEvolutionary ratesGenetic diversityIntrahost evolutionDistinct genotypesHigher viral genome copiesVirus evolutionary ratesSARS-CoV-2 evolutionUntreated chronic infectionAdvantageous mutationsNucleotide substitutionsViral genome copiesDivergent variantsInfection hypothesisVariant emergenceViral populationsInfectious virusInfectionHallmark changesGenome copiesDifferent genotypesDiversityGenotypesTemporal dynamicsEvolution
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
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 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.Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence
Kraemer M, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone J, Baele G, Parag K, Battle A, Gutierrez B, Jackson B, Colquhoun R, O’Toole Á, Klein B, Vespignani A, Consortium‡ C, Volz E, Faria N, Aanensen D, Loman N, du Plessis L, Cauchemez S, Rambaut A, Scarpino S, Pybus O. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science 2021, 373: 889-895. PMID: 34301854, PMCID: PMC9269003, DOI: 10.1126/science.abj0113.Peer-Reviewed Original ResearchCLIMB-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 ResearchAddendum: 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
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 severityAccommodating 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