2023
Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil
de Oliveira L, de Rezende I, Navarini V, Marchioro S, Torres A, Croda J, Croda M, Gonçalves C, Xavier J, de Castro E, Lima M, Iani F, Adelino T, Aburjaile F, Demarchi L, Taira D, Zardin M, Fonseca V, Giovanetti M, Andrews J, Alcantara L, Simionatto S. Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil. Frontiers In Public Health 2023, 11: 1195779. PMID: 37965526, PMCID: PMC10641392, DOI: 10.3389/fpubh.2023.1195779.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 lineagesIntroduction eventsCharacterization of SARS-CoV-2Nanopore sequencing platformSARS-CoV-2 positive samplesMultiple SARS-CoV-2 variantsMultiple introduction eventsPhylogenetic reconstructionPhylogenetic dataGenome sequenceSequencing platformsGenomic characterizationSARS-CoV-2Genomic surveillanceSARS-CoV-2 variantsLineagesMato GrossoMortality rateViral dynamicsIndigenous populationCo-circulationPrevalence of malesMidwestern BrazilPositive samplesIndigenous mobilization
2022
Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Frontiers In Medicine 2022, 9: 826746. PMID: 35265640, PMCID: PMC8899026, DOI: 10.3389/fmed.2022.826746.Peer-Reviewed Original ResearchPopulation genomic approachesStandard phylogenetic approachesGenome sequencing dataHaplotype networkGenomic approachesPhylogenetic approachTajima's DHigh-quality consensus sequencesGenetic diversityPopulation geneticsGenomic variationConsensus sequenceLineage expansionSequencing dataSARS-CoV-2 diversityGenetic characterizationLineage identificationDiversity landscapeInfection pathwaySARS-CoV-2 lineagesRecurrent mutationsGISAID databaseSARS-CoV-2DiversityPathogens
2021
COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis
Lee M, Sallah YH, Petrone M, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert TD, Grubaugh ND, Gupta S. COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. JMIRx Med 2021, 2: e31503. PMID: 35014989, PMCID: PMC8722526, DOI: 10.2196/31503.Peer-Reviewed Original ResearchSARS-CoV-2 infectionPeak disease severityCOVID-19 outcomesChart reviewMean ageDisease severityHigher comorbidity burdenRetrospective chart reviewSARS-CoV-2 RNACohort of veteransGeneral US populationNon-white raceCOVID-19 infectionManual chart reviewSARS-CoV-2Multivariate regression analysisO2 requirementsNon-white veteransSARS-CoV-2 lineagesComorbidity burdenVirologic factorsD614G substitutionMultiple SARS-CoV-2 lineagesVirologic characteristicsClinical outcomesThe alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice
Bayarri-Olmos R, Johnsen L, Idorn M, Reinert L, Rosbjerg A, Vang S, Hansen C, Helgstrand C, Bjelke J, Bak-Thomsen T, Paludan S, Garred P, Skjoedt M. The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. ELife 2021, 10: e70002. PMID: 34821555, PMCID: PMC8635972, DOI: 10.7554/elife.70002.Peer-Reviewed Original ResearchConceptsK18-hACE2 miceTransgenic hACE2 miceFaster disease progressionAlpha/B.SARS-CoV-2 isolatesVariants of concernSARS-CoV-2 lineagesHACE2 miceConvalescent individualsCOVID-19 casesDisease progressionEnzyme 2Low doseB.1.1.7 variantAntibody neutralizationHuman angiotensinInoculation dosesMonoclonal antibodiesNew COVID-19 casesACE-2Lower inoculation dosesWinter 2021MiceN501Y variantsSeverityMultiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus J, Claro I, Ferreira G, Crispim MAE, Network B, Singh L, Tegally H, Anyaneji UJ, Africa N, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLOS Biology 2021, 19: e3001236. PMID: 33961632, PMCID: PMC8133773, DOI: 10.1371/journal.pbio.3001236.Peer-Reviewed Original ResearchEvolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil
Resende P, Delatorre E, Gräf T, Mir D, Motta F, Appolinario L, da Paixão A, da Fonseca Mendonça A, Ogrzewalska M, Caetano B, Wallau G, Docena C, dos Santos M, de Almeida Ferreira J, Sousa E, da Silva S, Fernandes S, Vianna L, da Costa Souza L, Ferro J, Nardy V, Santos C, Riediger I, do Carmo Debur M, Croda J, Oliveira W, Abreu A, Bello G, Siqueira M. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Frontiers In Microbiology 2021, 11: 615280. PMID: 33679622, PMCID: PMC7925893, DOI: 10.3389/fmicb.2020.615280.Peer-Reviewed Original ResearchPublic health interventionsHealth interventionsEarly pandemic phaseContinuous genomic surveillanceSARS-CoV-2 lineagesEffective reproductive numberLow prevalenceModerate prevalenceViral transmissionSARS-CoV-2 genomePandemic phaseWhole viral genomeGenomic surveillanceDissemination patternsAir travel restrictionsPrevalenceReproductive numberInterventionRio de JaneiroViral genomeBrazilian strainsPhylodynamic analysisPrevious studiesEpidemic dynamics
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