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 settingsSARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity
Peña-Hernández M, Alfajaro M, Filler R, Moriyama M, Keeler E, Ranglin Z, Kong Y, Mao T, Menasche B, Mankowski M, Zhao Z, Vogels C, Hahn A, Kalinich C, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach B, Homer R, Pyle A, Martinez D, Grubaugh N, Israelow B, Iwasaki A, Wilen C. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nature Microbiology 2024, 9: 2038-2050. PMID: 39075235, DOI: 10.1038/s41564-024-01765-z.Peer-Reviewed Original ResearchBat coronavirusesRelatives of SARS-CoV-2Upper airwayUpper airways of miceEpithelial cellsHuman nasal epithelial cellsAirways of miceMajor histocompatibility complex class I.SARS-CoV-2Nasal epithelial cellsHistocompatibility complex class I.Human bronchial epithelial cellsGenetic similarityBronchial epithelial cellsInnate immune restrictionCoronavirus replicationFunctional characterizationMolecular cloningReduced pathogenesisImpaired replicationBat virusCoronavirus pathogenesisPandemic potentialHigh-risk familiesImmune restrictionDengueSeq: 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 outbreaksIntranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract
Mao T, Kim J, Peña-Hernández M, Valle G, Moriyama M, Luyten S, Ott I, Gomez-Calvo M, Gehlhausen J, Baker E, Israelow B, Slade M, Sharma L, Liu W, Ryu C, Korde A, Lee C, Monteiro V, Lucas C, Dong H, Yang Y, Initiative Y, Gopinath S, Wilen C, Palm N, Dela Cruz C, Iwasaki A, Vogels C, Hahn A, Chen N, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Grubaugh N. Intranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319566121. PMID: 38648490, PMCID: PMC11067057, DOI: 10.1073/pnas.2319566121.Peer-Reviewed Original ResearchConceptsInterferon-stimulated genesRespiratory infectionsStrains of influenza A virusTreatment of respiratory viral infectionsRespiratory virus infectionsInfluenza A virusMouse model of COVID-19Respiratory viral infectionsNeomycin treatmentExpression of interferon-stimulated genesUpper respiratory infectionInterferon-stimulated gene expressionLower respiratory infectionsBroad spectrum of diseasesAdministration of neomycinRespiratory viral diseasesDisease to patientsUpper respiratory tractIntranasal deliveryCongenic miceIntranasal applicationNasal mucosaSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2A virusContribution of climate change to the spatial expansion of West Nile virus in Europe
Erazo D, Grant L, Ghisbain G, Marini G, Colón-González F, Wint W, Rizzoli A, Van Bortel W, Vogels C, Grubaugh N, Mengel M, Frieler K, Thiery W, Dellicour S. Contribution of climate change to the spatial expansion of West Nile virus in Europe. Nature Communications 2024, 15: 1196. PMID: 38331945, PMCID: PMC10853512, DOI: 10.1038/s41467-024-45290-3.Peer-Reviewed Original ResearchConceptsWest Nile virusEcological niche modelsExpansion of West Nile virusClimate changeWNV circulationNiche modelsNile virusMosquito-borne pathogensEffects of climate changeHuman population changeSpatial expansionContributions of climate changeWest Nile virus circulationEnvironmental changesPublic health threatHuman populationLand-useHuman influencePotential driversRisk of exposureLong-term trendsPopulation densityPopulation changeHealth threatClimateEarly 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
2023
Genomic epidemiology of West Nile virus in Europe
Koch R, Erazo D, Folly A, Johnson N, Dellicour S, Grubaugh N, Vogels C. Genomic epidemiology of West Nile virus in Europe. One Health 2023, 18: 100664. PMID: 38193029, PMCID: PMC10772404, DOI: 10.1016/j.onehlt.2023.100664.Peer-Reviewed Original ResearchSurvey of white-footed mice (Peromyscus leucopus) in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses
Earnest R, Hahn A, Feriancek N, Brandt M, Filler R, Zhao Z, Breban M, Vogels C, Chen N, Koch R, Porzucek A, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber H, Cantoni J, Pitzer V, Olarte Castillo X, Goodman L, Wilen C, Linske M, Williams S, Grubaugh N. Survey of white-footed mice (Peromyscus leucopus) in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses. Npj Viruses 2023, 1: 10. DOI: 10.1038/s44298-023-00010-4.Peer-Reviewed Original ResearchThe known unknowns of Powassan virus ecology
Brackney D, Vogels C. The known unknowns of Powassan virus ecology. Journal Of Medical Entomology 2023, 60: 1142-1148. PMID: 37862099, PMCID: PMC10645372, DOI: 10.1093/jme/tjad095.Peer-Reviewed Original ResearchDevelopment of an amplicon-based sequencing approach in response to the global emergence of mpox
Chen N, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak C, Sevinsky J, Libuit K, Park D, Hemarajata P, Garrigues J, Green N, Sierra-Patev S, Carpenter-Azevedo K, Huard R, Pearson C, Incekara K, Nishimura C, Huang J, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes J, Aquino C, Savino I, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa H, McHugh M, Maloney D, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton K, Churchwell G, Lee P, Pedrosa M, McGruder B, Schmedes S, Plumb M, Wang X, Barcellos R, Godinho F, Salvato R, Ceniseros A, Breban M, Grubaugh N, Gallagher G, Vogels C. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLOS Biology 2023, 21: e3002151. PMID: 37310918, PMCID: PMC10263305, DOI: 10.1371/journal.pbio.3002151.Peer-Reviewed Original ResearchConceptsPublic health laboratoriesHealth laboratoriesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Monkeypox virusRespiratory syndrome coronavirus 2Ongoing coronavirus disease 2019 (COVID-19) pandemicAnatomical body sitesAtypical clinical presentationCoronavirus disease 2019 (COVID-19) pandemicSyndrome coronavirus 2Course of infectionDisease 2019 pandemicRapid outbreak responseWhole-genome sequencingHuman monkeypox virusCT valuesClinical presentationViral loadCoronavirus 2Viral DNA concentrationsPathogen whole-genome sequencingZika virusClinical specimensBody sitesDynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States
Hill V, Koch R, Bialosuknia S, Ngo K, Zink S, Koetzner C, Maffei J, Dupuis A, Backenson P, Oliver J, Bransfield A, Misencik M, Petruff T, Shepard J, Warren J, Gill M, Baele G, Vogels C, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer L, Armstrong P, Ciota A, Grubaugh N. Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States. Current Biology 2023, 33: 2515-2527.e6. PMID: 37295427, PMCID: PMC10316540, DOI: 10.1016/j.cub.2023.05.047.Peer-Reviewed Original ResearchPhylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
Vogels C, Brackney D, Dupuis A, Robich R, Fauver J, Brito A, Williams S, Anderson J, Lubelczyk C, Lange R, Prusinski M, Kramer L, Gangloff-Kaufmann J, Goodman L, Baele G, Smith R, Armstrong P, Ciota A, Dellicour S, Grubaugh N. Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2218012120. PMID: 37040418, PMCID: PMC10120011, DOI: 10.1073/pnas.2218012120.Peer-Reviewed Original ResearchEnhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants
Moriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.Peer-Reviewed Original ResearchConceptsMHC-I expressionBreakthrough infectionsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variantsMajor histocompatibility complex class I expressionCell-mediated immunityInfluenza virus infectionSARS-CoV-2 VOCsMHC-I upregulationClass I expressionSARS-CoV-2T cell recognitionVirus infectionMHC II expressionSpike proteinEnhanced inhibitionInfectionCell recognitionCommon mutationsReinfectionE proteinAntibodiesViral genesSubvariantsExpressionNonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants
Petrone M, Lucas C, Menasche B, Breban M, Yildirim I, Campbell M, Omer S, Holmes E, Ko A, Grubaugh N, Iwasaki A, Wilen C, Vogels C, Fauver J. Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biology And Evolution 2023, 15: evad052. PMID: 36974986, PMCID: PMC10113931, DOI: 10.1093/gbe/evad052.Peer-Reviewed Original ResearchToward a global virus genomic surveillance network
Hill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Toward a global virus genomic surveillance network. Cell Host & Microbe 2023, 31: 861-873. PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.Peer-Reviewed Original ResearchAge-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose
Filardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.Peer-Reviewed Original ResearchConceptsBooster doseAntibody responseNeutralization titersVirus-specific IgG titersOlder adultsAntiviral humoral immunityPlasma antibody responsesHigh-risk populationSARS-CoV-2 spikeYears of ageAge-dependent impairmentHeterologous regimensBooster dosesBooster vaccineCoronaVac vaccineIgG titersProtective immunityHumoral immunityHumoral responseCoronaVacOmicron waveBooster strategyAge groupsEarly controlVaccineGenomic 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 virusPowassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDC
Hart C, Hassett E, Vogels C, Shapley D, Grubaugh N, Thangamani S. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2023, 29: 415-417. PMID: 36692472, PMCID: PMC9881768, DOI: 10.3201/eid2902.220410.Peer-Reviewed Original ResearchAccelerated 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