2023
Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages
Oliveira G, Vogels C, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros C, Agarwal R, Tsetsarkin K, Harris E, Ebel G, Wohl S, Grubaugh N, Andersen K. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages. PLOS Neglected Tropical Diseases 2023, 17: e0011055. PMID: 36753510, PMCID: PMC9907835, DOI: 10.1371/journal.pntd.0011055.Peer-Reviewed Original ResearchConceptsHuman primary cellsFitness differencesVirus lineagesRapid molecular evolutionPrimary cellsShort generation timeAmino acid sitesFitness changesHigh mutation ratePhenotypic evolutionMolecular evolutionPositive selectionMutation rateLineagesPhenotypic analysisPhenotypic changesRNA virusesGeneration timeRecombinant virusesAedes aegypti mosquitoesReplicative fitnessFitnessAegypti mosquitoesMosquitoesZika virus
2019
Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
Scroggs SLP, Grubaugh ND, Sena JA, Sundararajan A, Schilkey FD, Smith DR, Ebel GD, Hanley KA. Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts. MSphere 2019, 4: 10.1128/msphere.00291-19. PMID: 31243074, PMCID: PMC6595145, DOI: 10.1128/msphere.00291-19.Peer-Reviewed Original ResearchConceptsUntranslated regionSecondary structureBird speciesRNA genomeGenome cyclizationRNA virusesHost variationPrimary genomic sequenceWest Nile virusPrimary genome sequenceDS regionStructural diversityIntrahost genetic diversityVirus phenotypeComplex secondary structureVirus RNA genomeRNA secondary structureSerial passageSmall RNAsGenetic diversityNile virusGenome sequenceMutant lineagesGenomic sequencesNext-generation sequencing
2016
Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution
Grubaugh ND, Rückert C, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE. Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution. Virus Evolution 2016, 2: vew033. PMID: 28058113, PMCID: PMC5210029, DOI: 10.1093/ve/vew033.Peer-Reviewed Original ResearchSimilar selective pressuresMicro-evolutionary forcesGreat genetic plasticityArthropod-borne RNA virusesVirus populationsLong-term evolutionary trendsGenetic bottleneckSelective constraintsFlavivirus evolutionEcological nichesGenetic plasticitySelective pressureVertebrate hostsPopulation dynamicsArthropod-borne virusesRNA virusesEvolutionary trendsArthropod vectorsMolecular levelMechanistic explanationTransmission bottleneckHostHeterogeneous populationUnique rateRNAiGenetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching
Grubaugh ND, Weger-Lucarelli J, Murrieta RA, Fauver JR, Garcia-Luna SM, Prasad AN, Black WC, Ebel GD. Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching. Cell Host & Microbe 2016, 19: 481-492. PMID: 27049584, PMCID: PMC4833525, DOI: 10.1016/j.chom.2016.03.002.Peer-Reviewed Original ResearchConceptsRelative fitnessMosquito speciesLower relative fitnessWest Nile virusComplex virus populationsSignificant fitness costMosquito-borne RNA virusesHost switchingGenetic driftGenetic diversityAdaptive potentialPopulation expansionFitness costsAvian cellsDeleterious mutationsMutational diversityRNA virusesBridge vectorsViral populationsVirus populationsMosquito vectorsFitnessSpeciesDiversityNile virus
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