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 ResearchMeSH KeywordsAdultCOVID-19Epidemiological MonitoringFemaleGenome, ViralHumansMalePhylogenyPhylogeographyRNA, ViralRwandaSARS-CoV-2Travel-Related IllnessWhole Genome SequencingConceptsGenome 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 ResearchMeSH KeywordsCloud ComputingCOVID-19Epidemiological MonitoringGenome, ViralGenomicsHumansSARS-CoV-2Sequence Analysis, DNAUnited KingdomUser-Computer InterfaceWhole Genome Sequencing
2020
Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
Lu J, du Plessis L, Liu Z, Hill V, Kang M, Lin H, Sun J, François S, Kraemer M, Faria N, McCrone J, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, Bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus O, Ke C. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell 2020, 181: 997-1003.e9. PMID: 32359424, PMCID: PMC7192124, DOI: 10.1016/j.cell.2020.04.023.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremBetacoronavirusChinaCoronavirus InfectionsCOVID-19Epidemiological MonitoringHumansLikelihood FunctionsPandemicsPneumonia, ViralSARS-CoV-2TravelConceptsGenetic diversity of SARS-CoV-2Combination of metagenomic sequencingDiversity of SARS-CoV-2Genomic epidemiology of SARS-CoV-2Genetic diversityAmplicon approachPhylogenetic analysisMetagenomic sequencingPhylogenetic clusteringChina’s most populous province,Genetic variationEpidemiology of SARS-CoV-2Genomic epidemiologyIndependent introductionsSARS-CoV-2Molecular epidemiologyMolecular surveillanceGenomeLocal transmission chainsTransmission chainCentral ChinaSequenceSARS-CoV-2 infectionGuangdong Province