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
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
2020
Accommodating 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 spreadDiversity