2024
Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022
da Silva L, Alcantara L, Fonseca V, Frias D, Zardin M, de Castro Lichs G, Esposito A, Xavier J, Fritsch H, Lima M, de Oliveira C, de Arruda L, de Mello Almeida Maziero L, Barretos E, Oshiro P, Menezes E, de Freitas Cardoso L, Lemos E, Lourenço J, de Albuquerque C, do Carmo Said R, Rosewell A, Demarchi L, Croda J, Giovanetti M, Gonçalves C. Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022. Viruses 2024, 16: 1143. PMID: 39066305, PMCID: PMC11281713, DOI: 10.3390/v16071143.Peer-Reviewed Original ResearchConceptsNext-generation sequencingPrison populationIncarcerated populationsOvercrowded cellsGenome sequenceGenomic characteristicsPrisonGenomic surveillanceEnclosed populationMato GrossoAverage coverageIsolation protocolSARS-CoV-2RT-qPCR testSARS-CoV-2 surveillanceRT-qPCRSequenceFrequent transferEpidemiological monitoringLimited healthcare accessGenomeCellsOmicron variant
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 mobilizationDengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies
de Arruda L, Giovanetti M, Fonseca V, Zardin M, de Castro Lichs G, Asato S, Esposito A, Müller M, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, de Mello Almeida Maziero L, Frias D, Neves D, da Silva L, Barretos E, Oshiro P, Goday B, dos Santos J, Kashima S, de Albuquerque C, do Carmo Said R, Rosewell A, Demarchi L, Croda J, Alcantara L, Gonçalves C. Dengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies. Viruses 2023, 15: 1790. PMID: 37766197, PMCID: PMC10536684, DOI: 10.3390/v15091790.Peer-Reviewed Original ResearchConceptsInforming public health actionOn-site training programDiverse viral lineagesPublic health actionPublic health strategiesMultiple introduction eventsSecretary of HealthMonitoring viral evolutionHealth strategiesHealth actionsGenome sequenceGenomic analysisDynamics of dengue virusTraining programIntroduction eventsGenomic surveillanceViral transmission patternsViral lineagesPublic healthHealthMato GrossoEpidemiological dataViral evolutionPreventive measuresSurveillance activitiesUnveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil
de Mello Almeida Maziero L, Giovanetti M, Fonseca V, Zardin M, de Castro Lichs G, de Rezende Romera G, Tsuha D, Frias D, Escandolhero V, Demarchi L, Castilho L, Barbosa K, Tebet D, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, Kashima S, do Carmo Said R, Rosewell A, Croda J, Alcantara L, Gonçalves C. Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil. Viruses 2023, 15: 1604. PMID: 37515290, PMCID: PMC10386548, DOI: 10.3390/v15071604.Peer-Reviewed Original ResearchConceptsGenomic surveillanceWhole-genome sequencingMultiple introduction eventsGenome sequencePublic health interventionsGenomic dataGenomic monitoringIntroduction eventsPublic health responseGenomic landscapeDispersal dynamicsPhylodynamic analysesPublic health laboratoriesHealth interventionsMato GrossoHealth responseTransmissible variantsSignificant burdenCentral Public Health LaboratoryOmicron variantVariantsHealth laboratoriesSequenceMidwest region of BrazilViral strainsPhylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay
Sanabria G, Sequera G, Aguirre S, Méndez J, dos Santos P, Gustafson N, Godoy M, Ortiz A, Cespedes C, Martínez G, García-Basteiro A, Andrews J, Croda J, Walter K. Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay. Nature Communications 2023, 14: 303. PMID: 36658111, PMCID: PMC9849832, DOI: 10.1038/s41467-023-35813-9.Peer-Reviewed Original ResearchConceptsIncident tuberculosis casesTB control programsTuberculosis casesRecent transmissionTransmission clustersNew infectionsProspective genomic surveillanceTransmission riskM. tuberculosisMycobacterium tuberculosisGenomic surveillanceMycobacterium tuberculosis complex genomeTuberculosisOutside prisonTransmission linkageControl programsInfectionIncidence
2022
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
Giovanetti M, Slavov S, Fonseca V, Wilkinson E, Tegally H, Patané J, Viala V, San E, Rodrigues E, Santos E, Aburjaile F, Xavier J, Fritsch H, Adelino T, Pereira F, Leal A, Iani F, de Carvalho Pereira G, Vazquez C, Sanabria G, Oliveira E, Demarchi L, Croda J, dos Santos Bezerra R, Paola Oliveira de Lima L, Martins A, Renata dos Santos Barros C, Marqueze E, de Souza Todao Bernardino J, Moretti D, Brassaloti R, de Lello Rocha Campos Cassano R, Mariani P, Kitajima J, Santos B, Proto-Siqueira R, Cantarelli V, Tosta S, Nardy V, Reboredo de Oliveira da Silva L, Gómez M, Lima J, Ribeiro A, Guimarães N, Watanabe L, Barbosa Da Silva L, da Silva Ferreira R, da Penha M, Ortega M, de la Fuente A, Villalba S, Torales J, Gamarra M, Aquino C, Figueredo G, Fava W, Motta-Castro A, Venturini J, do Vale Leone de Oliveira S, Gonçalves C, do Carmo Debur Rossa M, Becker G, Giacomini M, Marques N, Riediger I, Raboni S, Mattoso G, Cataneo A, Zanluca C, Duarte dos Santos C, Assato P, Allan da Silva da Costa F, Poleti M, Lesbon J, Mattos E, Banho C, Sacchetto L, Moraes M, Grotto R, Souza-Neto J, Nogueira M, Fukumasu H, Coutinho L, Calado R, Neto R, Bispo de Filippis A, Venancio da Cunha R, Freitas C, Peterka C, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said R, Campelo de A e Melo C, Almiron M, Lourenço J, de Oliveira T, Holmes E, Haddad R, Sampaio S, Elias M, Kashima S, Junior de Alcantara L, Covas D. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nature Microbiology 2022, 7: 1490-1500. PMID: 35982313, PMCID: PMC9417986, DOI: 10.1038/s41564-022-01191-z.Peer-Reviewed Original ResearchConceptsVariants of concernSARS-CoV-2 variantsLocal transmission clustersSARS-CoV-2 epidemicSARS-CoV-2COVID-19 casesTransmission clustersVirus transmission dynamicsSustained transmissionMultiple importationsMultiple viral lineagesGenomic epidemiologyGenomic surveillanceReal-time spreadTransmission dynamicsEpidemicViral lineagesHigher numberPandemicRestriction measuresEpidemiologyVariants
2021
Evolutionary 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