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 settings
2023
Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics
Hollingsworth B, Grubaugh N, Lazzaro B, Murdock C. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLOS Pathogens 2023, 19: e1011588. PMID: 37651317, PMCID: PMC10470969, DOI: 10.1371/journal.ppat.1011588.Peer-Reviewed Original ResearchConceptsInsect-specific virusesPopulation structureMosquito viromeFine-scale genetic variationMosquito ecologyDiversity of virusesMosquito population structureMovement ratesMultiple spatial scalesViral ecologyGenetic variationHost genomeDisease ecologyCryptic aspectsVirome studiesEcologyViral discoveryViral phylogenyMosquito control programsViromeGenomeGenomic epidemiologySpatial scalesPhylogenyRelevant timescalesDevelopment 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 sitesNonsystematic 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 ResearchGenomic 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 ResearchMeSH KeywordsAedesAnimalsEvolution, MolecularGenomicsHumansMosquito VectorsZika VirusZika Virus InfectionConceptsHuman 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
2022
Global disparities in SARS-CoV-2 genomic surveillance
Brito A, Semenova E, Dudas G, Hassler G, Kalinich C, Kraemer M, Ho J, Tegally H, Githinji G, Agoti C, Matkin L, Whittaker C, Howden B, Sintchenko V, Zuckerman N, Mor O, Blankenship H, de Oliveira T, Lin R, Siqueira M, Resende P, Vasconcelos A, Spilki F, Aguiar R, Alexiev I, Ivanov I, Philipova I, Carrington C, Sahadeo N, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije K, Perkins M, van Kerkhove M, Hill S, Sabino E, Pybus O, Dye C, Bhatt S, Flaxman S, Suchard M, Grubaugh N, Baele G, Faria N. Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications 2022, 13: 7003. PMID: 36385137, PMCID: PMC9667854, DOI: 10.1038/s41467-022-33713-y.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 genomic surveillanceMiddle-income countriesHigh-income countriesGenomic surveillanceSARS-CoV-2Global pandemic preparednessPublic health responseCOVID-19 casesPandemic preparednessHealth responseMolecular testsSocioeconomic inequalitiesTurnaround timeIncome countriesSurveillanceGlobal disparitiesDaysGenomic sequencingVaccineCombining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota
Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications Biology 2022, 5: 439. PMID: 35545661, PMCID: PMC9095641, DOI: 10.1038/s42003-022-03347-3.Peer-Reviewed Original Research
2021
Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDC
M. S, Flaherty E, Alpert T, Carlson S, Fasulo L, Earnest R, White EB, Dickens N, Brito AF, Grubaugh ND, Hadler JL, Sosa LE. Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2021, 27: 2669-2672. PMID: 34545794, PMCID: PMC8462310, DOI: 10.3201/eid2710.211196.Peer-Reviewed Original Research
2020
Real-time public health communication of local SARS-CoV-2 genomic epidemiology
Kalinich CC, Jensen CG, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF, Fauver JR, Grubaugh ND, Brito AF. Real-time public health communication of local SARS-CoV-2 genomic epidemiology. PLOS Biology 2020, 18: e3000869. PMID: 32822393, PMCID: PMC7467297, DOI: 10.1371/journal.pbio.3000869.Peer-Reviewed Original Research
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 threatsMosquitoesFeverTravel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic
Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH, Network G, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic. Cell 2019, 178: 1057-1071.e11. PMID: 31442400, PMCID: PMC6716374, DOI: 10.1016/j.cell.2019.07.018.Peer-Reviewed Original ResearchPrecision epidemiology for infectious disease control
Ladner JT, Grubaugh ND, Pybus OG, Andersen KG. Precision epidemiology for infectious disease control. Nature Medicine 2019, 25: 206-211. PMID: 30728537, PMCID: PMC7095960, DOI: 10.1038/s41591-019-0345-2.Peer-Reviewed Original ResearchAn amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology 2019, 20: 8. PMID: 30621750, PMCID: PMC6325816, DOI: 10.1186/s13059-018-1618-7.Peer-Reviewed Original Research
2018
Genomic Insights into Zika Virus Emergence and Spread
Grubaugh ND, Faria NR, Andersen KG, Pybus OG. Genomic Insights into Zika Virus Emergence and Spread. Cell 2018, 172: 1160-1162. PMID: 29522736, DOI: 10.1016/j.cell.2018.02.027.Peer-Reviewed Original Research