2025
Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US
Chen N, Pham K, Chaguza C, Lopes R, Klaassen F, Kalinich C, Initiative Y, Kerantzas N, Pandya S, Ferguson D, Schulz W, Weinberger D, Pitzer V, Warren J, Grubaugh N, Hahn A. Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US. Viruses 2025, 17: 1020. PMID: 40733636, PMCID: PMC12299087, DOI: 10.3390/v17071020.Peer-Reviewed Original ResearchConceptsDominant lineageHost-pathogen dynamicsGenomic surveillance programsResponse to previous infectionsSequence dataVariant fitnessLineage replacementCopy numberDynamic fitness landscapesLineagesSARS-CoV-2Integrated analysisViral copy numberFitness landscapeReplacement dynamicsReproductive rateOmicron lineagesGrowth rateImmune escapeAntigen exposureVariant emergenceViral sheddingPrevious infectionEpidemiological dataInfection
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
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