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 ResearchMeSH KeywordsDengueDengue VirusGenome, ViralGenotypeHigh-Throughput Nucleotide SequencingHumansRNA, ViralSerogroupWhole Genome SequencingConceptsAmplicon 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
2019
Endless 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 ResearchMeSH Keywords5' Untranslated RegionsAnimalsBirdsCrowsCulicidaeGenetic VariationGenome, ViralHigh-Throughput Nucleotide SequencingMutationRNA, ViralSerial PassageVirus ReplicationWest Nile virusConceptsUntranslated 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
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 ResearchMeSH KeywordsAnimalsAnophelesCricetinaeHigh-Throughput Nucleotide SequencingHumansMesocricetusPolymerase Chain ReactionRNA, ViralWest Nile virusConceptsEpstein-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