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 amount
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 sites
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
CLIMB-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