2024
Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development
Klontz E, Chowdhury N, Holbrook N, Solomon I, Telford S, Aliota M, Vogels C, Grubaugh N, Helgager J, Hughes H, Velez J, Piantadosi A, Chiu C, Lemieux J, Branda J. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development. Viruses 2024, 16: 1653. PMID: 39599768, PMCID: PMC11599074, DOI: 10.3390/v16111653.Peer-Reviewed Original ResearchGenome sequenceDiversity of genomic sequencesHuman infectionsPCR assay designVirus genome sequencesAssay designIn silico analysisBiology of infectionViral genomic dataGenetic diversityGenomic dataSensitivity of PCRGenomeCladePCR assayHuman diseasesVirulent strainsPCR designPowassan virusSequenceImmunocompromised patientsPCRTick-borne virusesAssay developmentClinical diagnosticsPrevalence and Genetic Diversity of Deer Tick Virus (Powassan Virus, Lineage II) in Ixodes scapularis Ticks in Five Habitats at a Nature Reserve in Southern Maine, United States.
Robich R, Piantadosi A, Elias S, Cosenza D, Schneider E, Baxter L, LaFon E, Lubelczyk C, Meagher M, Vogels C, Smith R. Prevalence and Genetic Diversity of Deer Tick Virus (Powassan Virus, Lineage II) in Ixodes scapularis Ticks in Five Habitats at a Nature Reserve in Southern Maine, United States. American Journal Of Tropical Medicine And Hygiene 2024 PMID: 39406212, DOI: 10.4269/ajtmh.23-0643.Peer-Reviewed Original ResearchDeer tick virusHabitat typesGenetic diversityIxodes scapularis ticksInvasive vegetationAdult ticksLong-distance dispersalTick virusShort-range dispersalVirus prevalenceTick-borne encephalitis virusPhylogenetic analysisLineage IIHabitatPowassan virus lineage IIEnzootic fociNature ReserveNative vegetationTicksDeerNational Estuarine Research ReserveCompared to 0UnderstoryEncephalitis virusForestDengueSeq: 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
2023
Accelerated 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