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 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
The 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 profilesLineagesVariants
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 introductionLineagesDiversityCLIMB-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