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, veae083. 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 amountEarly 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
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 ResearchConceptsVariant frequenciesAmplicon-based sequencingCommunity settingsVirus variantsEpidemiological estimatesEnglish populationGenomic surveillanceSARS-CoV-2Variant dynamicsSARS-CoV-2 pandemicOmicron variantClinical surveillanceVariantsNational levelEnglandSARS-CoV-2 Omicron variantDecision-makingPopulationIndividual testsPhylogenyReduce testingSurveillanceWastewater sitesDynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States
Hill V, Koch R, Bialosuknia S, Ngo K, Zink S, Koetzner C, Maffei J, Dupuis A, Backenson P, Oliver J, Bransfield A, Misencik M, Petruff T, Shepard J, Warren J, Gill M, Baele G, Vogels C, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer L, Armstrong P, Ciota A, Grubaugh N. Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States. Current Biology 2023, 33: 2515-2527.e6. PMID: 37295427, PMCID: PMC10316540, DOI: 10.1016/j.cub.2023.05.047.Peer-Reviewed Original ResearchVariant-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 ResearchToward a global virus genomic surveillance network
Hill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Toward a global virus genomic surveillance network. Cell Host & Microbe 2023, 31: 861-873. PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.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
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 levelThe 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 profilesLineagesVariantsMaking genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.
Campbell K, Gifford RJ, Singer J, Hill V, O'Toole A, Rambaut A, Hampson K, Brunker K. Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. PLoS Pathogens 2022, 18: e1010023. PMID: 35500026, DOI: 10.1371/journal.ppat.1010023.Peer-Reviewed Original ResearchRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022, 603: 679-686. PMID: 35042229, PMCID: PMC8942855, DOI: 10.1038/s41586-022-04411-y.Peer-Reviewed Original ResearchGenomic 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.Assignment 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 syndromeSpatiotemporal 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