2023
Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England
Brunner F, Payne A, Cairns E, Airey G, Gregory R, Pickwell N, Wilson M, Carlile M, Holmes N, Hill V, Child H, Tomlinson J, Ahmed S, Denise H, Rowe W, Frazer J, van Aerle R, Evens N, Porter J, Consortium T, Templeton K, Jeffries A, Loose M, Paterson S. Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. Water Research 2023, 247: 120804. PMID: 37925861, DOI: 10.1016/j.watres.2023.120804.Peer-Reviewed Original ResearchMeSH KeywordsCOVID-19EnglandGenomicsHumansSARS-CoV-2WastewaterWastewater-Based Epidemiological MonitoringConceptsVariant frequenciesAmplicon-based sequencingCommunity settingsVirus variantsEpidemiological estimatesEnglish populationGenomic surveillanceSARS-CoV-2Variant dynamicsSARS-CoV-2 pandemicOmicron variantClinical surveillanceVariantsNational levelEnglandSARS-CoV-2 Omicron variantDecision-makingPopulationIndividual testsPhylogenyReduce testingSurveillanceWastewater sitesVariant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
Dellicour S, Hong S, Hill V, Dimartino D, Marier C, Zappile P, Harkins G, Lemey P, Baele G, Duerr R, Heguy A. Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron. PLOS Pathogens 2023, 19: e1011348. PMID: 37071654, PMCID: PMC10180688, DOI: 10.1371/journal.ppat.1011348.Peer-Reviewed Original ResearchAccelerated 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
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.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 spreadDiversityEarly Release - Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19 - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC
Biggerstaff M, Cowling B, Cucunubá Z, Dinh L, Ferguson N, Gao H, Hill V, Imai N, Johansson M, Kada S, Morgan O, Pastore y Piontti A, Polonsky J, Prasad P, Quandelacy T, Rambaut A, Tappero J, Vandemaele K, Vespignani A, Warmbrod K, Wong J, Group F. Early Release - Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19 - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2020, 26: e201074. PMID: 32917290, PMCID: PMC7588530, DOI: 10.3201/eid2611.201074.Peer-Reviewed Original ResearchThe 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-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