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 dataInfectionClassification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach
Rancu I, Sobkowiak B, Warren J, Ciobanu N, Codreanu A, Crudu V, Colijn C, Cohen T, Chitwood M. Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach. Access Microbiology 2025, 7: 000964.v3. PMID: 40519974, PMCID: PMC12163731, DOI: 10.1099/acmi.0.000964.v3.Peer-Reviewed Original ResearchWhole-genome sequencing dataSequence dataTransmission inferenceMolecular epidemiological studiesMycobacterium tuberculosis strainsTuberculosis strainsHigh-burden settingsFraction of individualsCulture-positive diseaseStrainTransmission clustersFraction of casesLow-burden settingsSNPsForeign-born migrantsTransmission dynamicsSequenceTuberculosis casesMycobacteriaClustersNotified tuberculosis
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