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 dataInfectionPhylogenetic insights into the transmission dynamics of arthropod-borne viruses
Hill V, Dellicour S, Giovanetti M, Grubaugh N. Phylogenetic insights into the transmission dynamics of arthropod-borne viruses. Nature Reviews Genetics 2025, 1-15. PMID: 40481331, PMCID: PMC12257617, DOI: 10.1038/s41576-025-00854-x.Peer-Reviewed Original ResearchArthropod-borne virusesPhylogenetic insightsPhylogenetic modelsGenomic surveillanceAnimal populationsVertebrate hostsBluetongue virusArthropod vectorsHuman clinical dataEpidemiological dynamicsVeterinary healthClimate changeComplex transmission cyclesClinical dataVirusTransmission cycleTemporal patternsEpidemiological dataComplication surveillancePhylogeneticallyCrimean-Congo haemorrhagic fever
2022
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota
Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications Biology 2022, 5: 439. PMID: 35545661, PMCID: PMC9095641, DOI: 10.1038/s42003-022-03347-3.Peer-Reviewed Original Research
2018
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
Gardner LM, Bóta A, Gangavarapu K, Kraemer MUG, Grubaugh ND. Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas. PLOS Neglected Tropical Diseases 2018, 12: e0006194. PMID: 29346387, PMCID: PMC5790294, DOI: 10.1371/journal.pntd.0006194.Peer-Reviewed Original ResearchConceptsZika virus transmissionRisk factorsZika virusLocal transmissionVirus transmissionZika virus epidemicTransmission of ZikaRegional socioeconomic factorsEpidemiological elementsIncidence rateEpidemiological dataZika casesRisk profileInfection modelRisk of spreadVirus epidemicLocal vector controlSocioeconomic factorsVector-Borne PathogensVirusEpidemicHealth risks
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