2024
A 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 factorsDengueSeq: 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-specificTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Taylor-Salmon E, Hill V, Paul L, Koch R, Breban M, Chaguza C, Sodeinde A, Warren J, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán J, Santiago G, Adams L, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman F, Galán J, Huits R, Hamer D, Vogels C, Morrison A, Michael S, Grubaugh N. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nature Communications 2024, 15: 3508. PMID: 38664380, PMCID: PMC11045810, DOI: 10.1038/s41467-024-47774-8.Peer-Reviewed Original ResearchConceptsDengue virusDENV-3Rates of severe diseaseMosquito-borne viral diseasePublic health threatPattern of spreadSevere diseaseLocal surveillanceGenomic epidemiologyEpidemiological patternsVirus surveillanceSurveillanceHealth threatSerotypesDiseaseIncreased rateDengueViral diseasesVirusInfected travelersFrequent outbreaksEarly Release - Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022–April 2023 - Volume 30, Number 2—February 2024 - Emerging Infectious Diseases journal - CDC
Jones F, Morrison A, Santiago G, Rysava K, Zimler R, Heberlein L, Kopp E, , Saunders K, Baudin S, Rico E, Mejía-Echeverri Á, Taylor-Salmon E, Hill V, Breban M, Vogels C, Grubaugh N, Paul L, Michael S, Johansson M, Adams L, Munoz-Jordan J, Paz-Bailey G, Stanek D. Early Release - Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022–April 2023 - Volume 30, Number 2—February 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 376-379. PMID: 38232709, PMCID: PMC10826764, DOI: 10.3201/eid3002.231615.Peer-Reviewed Original Research
2021
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay
Beddingfield B, Hartnett J, Wilson R, Kulakosky P, Andersen K, Robles-Sikisaka R, Grubaugh N, Aybar A, Nunez M, Fermin C, Garry R. Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay. Viruses 2021, 13: 1771. PMID: 34578352, PMCID: PMC8473068, DOI: 10.3390/v13091771.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, ViralAntigens, ViralCross ReactionsDengueDengue VirusEnzyme-Linked Immunosorbent AssayEpitopesFemaleFlavivirusHumansImmunoassayImmunologic TestsModels, MolecularMutagenesis, Site-DirectedPregnancyViral Nonstructural ProteinsWest Nile virusYellow fever virusZika VirusZika Virus InfectionConceptsZIKV nonstructural protein 1Nonstructural protein 1Antigen capture ELISADengue virusZika virusMild self-limiting illnessSelf-limiting illnessNS1 proteinMajor birth defectsSevere neurological diseaseYellow fever virusAntigen capture immunoassaySt. Louis encephalitis virusPolyclonal antibodiesLouis encephalitis virusWest Nile virusSerious outcomesAffinity-purified polyclonal antibodiesRelated flavivirusesNeurological diseasesRefinement of approachesEncephalitis virusWidespread flavivirusFlavivirusesFever virusLying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
Brito AF, Machado LC, Oidtman RJ, Siconelli MJL, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, de Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, España GC, Huang AT, Cummings DAT, Baele G, Franca RFO, da Fonseca BAL, Perkins TA, Wallau GL, Grubaugh ND. Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nature Communications 2021, 12: 2619. PMID: 33976183, PMCID: PMC8113494, DOI: 10.1038/s41467-021-22921-7.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overAntibodies, ViralBrazilChildChild, PreschoolDengueDengue VirusDisease SusceptibilityEpidemicsEpidemiological MonitoringFemaleGenome, ViralHumansImmunity, HeterologousIncidenceInfantInfant, NewbornMaleMiddle AgedMolecular TypingMosquito VectorsPhylogeographySerotypingYoung AdultZika VirusZika Virus InfectionConceptsDengue virus serotype 1Zika epidemicZika virus epidemicDENV lineagesVirus serotype 1DENV infectionProtective immunityDENV transmissionDengue susceptibilityDengue virusViral spreadLow transmission levelsSerotype 1Virus epidemicMajor outbreaksModel mosquitoEpidemicInfectionDengueTransmission suitabilityDengue incidenceYearsDengue dynamicsOutbreakIncidenceAsynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Petrone ME, Earnest R, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND, Tapia L. Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nature Communications 2021, 12: 151. PMID: 33420058, PMCID: PMC7794562, DOI: 10.1038/s41467-020-20391-x.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAedesAnimalsChikungunya FeverChikungunya virusChildChild, PreschoolCommunicable Diseases, EmergingDengueDengue VirusDisease OutbreaksDominican RepublicEndemic DiseasesEpidemiological MonitoringFemaleHumansInfantInfant, NewbornMaleMosquito ControlMosquito VectorsSpatio-Temporal AnalysisYoung AdultZika VirusZika Virus InfectionConceptsDengue outbreakDisease outbreaksDengue fever casesOutbreak of chikungunyaMosquito-Borne VirusesFever casesFuture health crisesMosquito-borne disease outbreaksFuture outbreaksVirus transmissionAedes mosquitoesSustainable disease control measuresHealth crisisVirusDisease control measuresOutbreakChikungunyaConstant surveillanceZikaControl measuresDominican Republic
2019
Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks
Pollett S, Fauver JR, Berry I, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. The Journal Of Infectious Diseases 2019, 221: s308-s318. PMID: 31711190, PMCID: PMC11095994, DOI: 10.1093/infdis/jiz302.Peer-Reviewed Original ResearchConceptsGenomic epidemiologyVirus outbreakPublic health responsePublic health toolPublic health agenciesPublic health emergencyKey epidemiological questionsStructured surveillanceChikungunya virusHealth responseEpidemiologyVirus controlHealth toolsHealth agenciesWest NileHealth emergencyVirus genomic dataYellow feverEpidemiological questionsControl of mosquitoesOutbreakOngoing advancesVirus threatsMosquitoesFeverArbovirus coinfection and co-transmission: A neglected public health concern?
Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. Arbovirus coinfection and co-transmission: A neglected public health concern? PLOS Biology 2019, 17: e3000130. PMID: 30668574, PMCID: PMC6358106, DOI: 10.1371/journal.pbio.3000130.Peer-Reviewed Original ResearchConceptsImpact of coinfectionPublic health concernPublic healthEpidemiological synergyVirus coinfectionAedes aegypti mosquitoesClinical diseaseSuch coinfectionsZika virusCoinfectionOutbreaks of virusesHealth concernAegypti mosquitoesMultiple virusesTransmission dynamicsVirusHealthHumansMosquitoesDiseaseDengue