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 transmissionAssignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O’Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone J, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood S, Aanensen D, Holmes E, Pybus O, Rambaut A. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution 2021, 7: veab064. PMID: 34527285, PMCID: PMC8344591, DOI: 10.1093/ve/veab064.Peer-Reviewed Original ResearchSARS-CoV-2 genomic dataSARS-CoV-2 genome sequencesPhylogenetic assignmentGenome sequenceGenomics communityGenomic dataPangolin toolOutbreak lineageGenomic epidemiologyVirus genomeLineagesTransmission lineagesGenomePangolinsSARS-CoV-2Nomenclature schemeComputational toolsVirusPangoSequenceSevere acute respiratory syndromeAcute respiratory syndrome