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. 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 diagnosticsCombining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
Lopes R, Pham K, Klaassen F, Chitwood M, Hahn A, Redmond S, Swartwood N, Salomon J, Menzies N, Cohen T, Grubaugh N. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Reports 2024, 43: 114451. PMID: 38970788, DOI: 10.1016/j.celrep.2024.114451.Peer-Reviewed Original Research
2021
Intrahost speciations and host switches played an important role in the evolution of herpesviruses
Brito AF, Baele G, Nahata KD, Grubaugh ND, Pinney JW. Intrahost speciations and host switches played an important role in the evolution of herpesviruses. Virus Evolution 2021, 7: veab025. PMID: 33927887, PMCID: PMC8062258, DOI: 10.1093/ve/veab025.Peer-Reviewed Original ResearchIntrahost speciationHost switchingHost switchesEvolutionary historyTree reconciliationTree reconciliation analysesEvolution of herpesvirusesViral phylogenyHost biogeographyDivergence timingTopological incongruenceCophylogenetic analysesReconciliation analysisHost evolutionPhylogenetic differencesSequence dataGenomic dataViral speciesPhylogenyTemporal incongruenceCospeciationSpeciationImportant roleHostIncongruence