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 ResearchConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settings
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 sites
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 transmissionCLIMB-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 Research