2024
DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specific
2023
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.Peer-Reviewed Original ResearchConceptsChronic infectionEvolutionary ratesGenetic diversityIntrahost evolutionDistinct genotypesHigher viral genome copiesVirus evolutionary ratesSARS-CoV-2 evolutionUntreated chronic infectionAdvantageous mutationsNucleotide substitutionsViral genome copiesDivergent variantsInfection hypothesisVariant emergenceViral populationsInfectious virusInfectionHallmark changesGenome copiesDifferent genotypesDiversityGenotypesTemporal dynamicsEvolution
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
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
2017
Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding Episode
Grubaugh ND, Fauver JR, Rückert C, Weger-Lucarelli J, Garcia-Luna S, Murrieta RA, Gendernalik A, Smith DR, Brackney DE, Ebel GD. Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding Episode. Cell Reports 2017, 19: 709-718. PMID: 28445723, PMCID: PMC5465957, DOI: 10.1016/j.celrep.2017.03.076.Peer-Reviewed Original ResearchConceptsGenetic diversityNovel virus variantsWNV genetic diversityMost genetic diversityComplex evolutionary forcesVirus populationsEvolutionary forcesWest Nile virusGenetic driftInfection phenotypesWNV variantsIndividual mosquitoesIntrahost variantsVirus variantsTransmission cyclePopulation levelMosquitoesDiversityContinuous threatNile virusVariantsArthropodsChikungunya virusVirusLarge epidemics
2016
Genetic 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