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
2022
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study
Hay J, Kissler S, Fauver J, Mack C, Tai C, Samant R, Connolly S, Anderson D, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley J, Mason C, Nair M, Huang Y, DiFiori J, Ho D, Grubaugh N, Grad Y. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study. ELife 2022, 11: e81849. PMID: 36383192, PMCID: PMC9711520, DOI: 10.7554/elife.81849.Peer-Reviewed Original ResearchConceptsViral kineticsSARS-CoV-2 strainsAntibody titersViral reboundVaccination statusLonger clearance timeLower peak viral loadRetrospective cohort studyClearance timePeak viral loadSARS-CoV-2 variantsHigh antibody titersEffective immune responseRT-qPCR testingBooster vaccinationCohort studyEffect of ageViral loadHealth cohortSymptom statusImmune historyImmune responseInfection historyClearance rateInfectionLineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Baaijens J, Zulli A, Ott I, Nika I, van der Lugt M, Petrone M, Alpert T, Fauver J, Kalinich C, Vogels C, Breban M, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen B, Hanage W, Grubaugh N, Peccia J, Baym M. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biology 2022, 23: 236. PMID: 36348471, PMCID: PMC9643916, DOI: 10.1186/s13059-022-02805-9.Peer-Reviewed Original Research
2021
Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies
Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLOS Biology 2021, 19: e3001333. PMID: 34252080, PMCID: PMC8297933, DOI: 10.1371/journal.pbio.3001333.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionViral RNA concentrationClearance phaseAcute SARS-CoV-2 infectionReverse transcription-PCR testingPeak viral concentrationPersistent viral RNAPositive PCR testTranscription-PCR testingViral proliferationPublic health strategiesRNA concentrationViral concentrationInfection stagesCycle threshold valuesAcute infectionAsymptomatic individualsTest turnaround timeSymptomatic individualsClinical measuresHealth strategiesPatient progressPCR testingInfectionViral dynamicsStability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC
Ott IM, Strine MS, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL, . Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2021, 27: 1146-1150. PMID: 33754989, PMCID: PMC8007305, DOI: 10.3201/eid2704.204199.Peer-Reviewed Original Research
2020
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Team Y, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. PLOS Biology 2020, 18: e3000867. PMID: 33027248, PMCID: PMC7571696, DOI: 10.1371/journal.pbio.3000867.Peer-Reviewed Original ResearchMeSH KeywordsBetacoronavirusCase-Control StudiesClinical Laboratory TechniquesCoronavirus InfectionsCOVID-19COVID-19 TestingDNA PrimersHEK293 CellsHumansLimit of DetectionMultiplex Polymerase Chain ReactionNasopharynxPandemicsPneumonia, ViralReagent Kits, DiagnosticReverse Transcriptase Polymerase Chain ReactionRNA, ViralSARS-CoV-2United StatesConceptsSARS-CoV-2 RNAMultiplex RT-qPCRRT-qPCRSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testingSARS-CoV-2Quantitative reverse transcription PCRCycle threshold valuesReverse transcription-PCRRT-qPCR assaysDisease controlMultiplex RT-qPCR assayTranscription-PCRAssaysSingle assayLow copy numberMeasurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics
Peccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nature Biotechnology 2020, 38: 1164-1167. PMID: 32948856, PMCID: PMC8325066, DOI: 10.1038/s41587-020-0684-z.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 positive test resultsSARS-CoV-2 RNAPositive test resultsHospital admissionSpecimen collectionCOVID-19 hospital admissionsLocal hospital admissionsSARS-CoV-2 RNA concentrationsCoronavirus disease 2019 (COVID-19) outbreakRNA concentrationDisease 2019 outbreakClinical test resultsInfection surveillanceInfection dynamicsPositive testPopulation-wide levelCommunity infection dynamicsAdmissionNew HavenSex differences in immune responses that underlie COVID-19 disease outcomes
Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier J, Odio C, Farhadian S, Dela Cruz C, Grubaugh N, Schulz W, Ring A, Ko A, Omer S, Iwasaki A. Sex differences in immune responses that underlie COVID-19 disease outcomes. Nature 2020, 588: 315-320. PMID: 32846427, PMCID: PMC7725931, DOI: 10.1038/s41586-020-2700-3.Peer-Reviewed Original ResearchConceptsInnate immune cytokinesFemale patientsMale patientsImmune cytokinesDisease outcomeImmune responseCOVID-19COVID-19 disease outcomesPoor T cell responsesSARS-CoV-2 infectionSevere acute respiratory syndrome coronavirusAcute respiratory syndrome coronavirusSex-based approachModerate COVID-19Sex differencesRobust T cell activationT cell responsesWorse disease progressionWorse disease outcomesHigher plasma levelsNon-classical monocytesCoronavirus disease 2019T cell activationImmunomodulatory medicationsPlasma cytokinesSARS-CoV-2 infection of the placenta
Hosier H, Farhadian SF, Morotti RA, Deshmukh U, Lu-Culligan A, Campbell KH, Yasumoto Y, Vogels C, Casanovas-Massana A, Vijayakumar P, Geng B, Odio CD, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy AM, Aguilar G, Fardelmann KL, Harigopal M, Taylor HS, Pettker CM, Wyllie AL, Dela Cruz CS, Ring AM, Grubaugh ND, Ko AI, Horvath TL, Iwasaki A, Reddy UM, Lipkind HS. SARS-CoV-2 infection of the placenta. Journal Of Clinical Investigation 2020, 130: 4947-4953. PMID: 32573498, PMCID: PMC7456249, DOI: 10.1172/jci139569.Peer-Reviewed Case Reports and Technical NotesMeSH KeywordsAbortion, TherapeuticAbruptio PlacentaeAdultBetacoronavirusCoronavirus InfectionsCOVID-19FemaleHumansMicroscopy, Electron, TransmissionPandemicsPhylogenyPlacentaPneumonia, ViralPre-EclampsiaPregnancyPregnancy Complications, InfectiousPregnancy Trimester, SecondRNA, ViralSARS-CoV-2Viral LoadConceptsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2SARS-CoV-2 infectionRespiratory syndrome coronavirus 2SARS-CoV-2 invasionMaternal antibody responseSymptomatic COVID-19Second trimester pregnancySyndrome coronavirus 2Coronavirus disease 2019Materno-fetal interfaceDense macrophage infiltratesPlacental abruptionSevere preeclampsiaMacrophage infiltratesSevere morbidityTrimester pregnancyPregnant womenCoronavirus 2Antibody responseBackgroundThe effectsDisease 2019Histological examinationImmunohistochemical assaysPlacentaAnalytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets
Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nature Microbiology 2020, 5: 1299-1305. PMID: 32651556, PMCID: PMC9241364, DOI: 10.1038/s41564-020-0761-6.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 RTSevere acute respiratory syndrome coronavirusAcute respiratory syndrome coronavirusViral RNA copiesPublic health laboratoriesPublic health interventionsReverse transcription-PCR assaySARS-CoV-2 diagnostic testingDiagnostic assaysTranscription-PCR assaySARS-CoV-2 evolutionQuantitative reverse transcription-PCR assaysRapid diagnostic assaysHealth laboratoriesHealth interventionsDiagnostic testingRNA copiesPrimer-probe setsAssaysLow sensitivityCritical needAnalytical sensitivity
2019
Travel 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 ResearchEndless 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
2015
Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen Landscape
Grubaugh ND, Sharma S, Krajacich BJ, Fakoli LS, Bolay FK, Diclaro JW, Johnson WE, Ebel GD, Foy BD, Brackney DE. Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen Landscape. PLOS Neglected Tropical Diseases 2015, 9: e0003628. PMID: 25775236, PMCID: PMC4361501, DOI: 10.1371/journal.pntd.0003628.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusViral pathogensInfectious disease surveillance systemsViral nucleic acidsDisease surveillance systemsMosquito blood feedingMultiple viral pathogensRelevant concentrationsCanine distemper virusHigh riskInfectious diseasesDistemper virusHost bloodNext-generation sequencingQRT-PCRMosquito gutBloodBloodmeal ingestionSurveillance toolBlood feedingXenosurveillanceMosquito bloodmealsVirusVirus detectionNovel surveillance techniques