2024
Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC
Grubaugh N, Torres-Hernández D, Murillo-Ortiz M, Dávalos D, Lopez P, Hurtado I, Breban M, Bourgikos E, Hill V, López-Medina E. Early Release - Dengue Outbreak Caused by Multiple Virus Serotypes and Lineages, Colombia, 2023–2024 - Volume 30, Number 11—November 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 2391-2395. PMID: 39378873, PMCID: PMC11521178, DOI: 10.3201/eid3011.241031.Peer-Reviewed Original ResearchA new lineage nomenclature to aid genomic surveillance of dengue virus
Hill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.Peer-Reviewed Original ResearchConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settingsNorth–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic
Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M. North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic. BMC Infectious Diseases 2024, 24: 751. PMID: 39075335, PMCID: PMC11288047, DOI: 10.1186/s12879-024-09658-6.Peer-Reviewed Original ResearchConceptsGenome sequenceCombination of genome sequencingTrace transmission pathwaysDengue virusHistorical climatic patternsHigh climatic suitabilityCo-circulationDengue virus serotype 2Transmission pathwaysPhylogenetic analysisVirus transmission pathwaysBiodiversity hotspotHistorical climate dataVirus lineagesDominican RepublicImpacts of climate changeLineagesClimatic suitabilityClimate dataRising temperaturePathwaySerotype 2Subtropical regionsTransmission dynamicsImpact of climatic factors
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
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