2024
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
Li K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesWhole-genome sequencingAmino acid changesSingle nucleotide polymorphismsPairs of substitutionsViral copiesEpistasis testsGenome sequenceGenetic variationSpike geneAcid changesViral genomeNucleotide polymorphismsSARS-CoV-2Detect interactionsHost factorsVirus copiesCopyInfection dynamicsRT-qPCRPolymorphismOmicron BASARS-CoV-2 infection
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 timescales
2016
Isolation of a Novel Insect-Specific Flavivirus from Culiseta melanura in the Northeastern United States
Misencik MJ, Grubaugh ND, Andreadis TG, Ebel GD, Armstrong PM. Isolation of a Novel Insect-Specific Flavivirus from Culiseta melanura in the Northeastern United States. Vector-Borne And Zoonotic Diseases 2016, 16: 181-190. PMID: 26807512, PMCID: PMC4779966, DOI: 10.1089/vbz.2015.1889.Peer-Reviewed Original ResearchConceptsInsect-specific flavivirusesOpen reading framePhylogenetic analysisDistinct evolutionary lineagesAmino acid sequence identityObvious geographic structureLimited genetic variationNovel insect-specific flavivirusEvolutionary lineagesHost associationsGeographic structureComplete genomeGenetic variationField-collected mosquitoesReading frameMelanura larvaeNucleotide sequenceSequence identityLarval stagesSampled populationsNortheastern United StatesGenus FlavivirusCalbertado virusNS5 geneViral sequences