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
2301. Viral Kinetics of Sequential SARS-CoV-2 Infections
Kissler S, Hay J, Fauver J, Mack C, Tai C, Anderson D, Ho D, Grubaugh N, Grad Y. 2301. Viral Kinetics of Sequential SARS-CoV-2 Infections. Open Forum Infectious Diseases 2023, 10: ofad500.1923. PMCID: PMC10677142, DOI: 10.1093/ofid/ofad500.1923.Peer-Reviewed Original ResearchSARS-CoV-2 infectionFaster clearance timesViral clearance timeSecond infectionVaccination statusClearance timeViral kineticsFirst infectionAcute SARS-CoV-2 infectionPrior SARS-CoV-2 infectionVaccine doseDisease coursePatient characteristicsPrior infectionOropharyngeal swabsImmune responseInfection historySubsequent infectionSequential infectionUS populationViral variantsInfectionHost factorsConvenience sampleConflicting resultsViral kinetics of sequential SARS-CoV-2 infections
Kissler S, Hay J, Fauver J, Mack C, Tai C, Anderson D, Ho D, Grubaugh N, Grad Y. Viral kinetics of sequential SARS-CoV-2 infections. Nature Communications 2023, 14: 6206. PMID: 37798265, PMCID: PMC10556125, DOI: 10.1038/s41467-023-41941-z.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionFaster clearance timesPrior SARS-CoV-2 infectionViral clearance timeSecond infectionClearance timeViral kineticsFirst infectionAcute SARS-CoV-2 infectionVaccination statusAnterior naresOropharyngeal swabsImmune responseSubsequent infectionSequential infectionViral variantsInfectionHost factorsConvenience sampleSame variantRT-qPCR measurementsRelative abilityVaccinationSwabsIndividuals