2020
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications 2020, 11: 5620. PMID: 33159066, PMCID: PMC7648063, DOI: 10.1038/s41467-020-19122-z.Peer-Reviewed Original ResearchConceptsGenetic diversityPopulation genetic diversityViral lineagesNon-migratory birdsViral genetic diversityMigratory bird flywaysWest Nile virusPathogen genomesDispersal historyGenome collectionMosquito dispersalBird flywaysWildlife healthLineagesPhylodynamic approachesLongitudinal gradientDispersalWNV lineagesNorth AmericaDiversityEnvironmental factorsTemporal variationComputational analysisAnalytical workflowHistorical reconstruction
2015
Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness
Grubaugh ND, Smith DR, Brackney DE, Bosco-Lauth AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD. Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness. PLOS Pathogens 2015, 11: e1004874. PMID: 25993022, PMCID: PMC4439088, DOI: 10.1371/journal.ppat.1004874.Peer-Reviewed Original ResearchConceptsRNA virus populationsWNV populationsBird speciesRNA virusesNatural selectionFitness gainsVirus populationsStrength of selectionWest Nile virusSpecies-specific mannerDistinct phenotypic consequencesAverage mutation frequencyExperimental evolutionMutational toleranceError-prone replicationCompetitive fitnessPopulation structureNext-generation sequencingPhenotypic consequencesGenetic compositionWild birdsSelective pressureSequencing dataDefective genomesDifferent hosts