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 strains
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
2020
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microbial Genomics 2020, 6: mgen000418. PMID: 32735210, PMCID: PMC7641424, DOI: 10.1099/mgen.0.000418.Peer-Reviewed Original ResearchGenomic and Epidemiological Surveillance of Zika Virus in the Amazon Region
Giovanetti M, Faria N, Lourenço J, de Jesus J, Xavier J, Claro I, Kraemer M, Fonseca V, Dellicour S, Thézé J, da Silva Salles F, Gräf T, Silveira P, do Nascimento V, de Souza V, de Melo Iani F, Castilho-Martins E, Cruz L, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Aguiar R, de Oliveira T, de Menezes C, da Costa Castilho M, Terra T, da Silva M, de Filippis A, de Abreu A, Oliveira W, Croda J, de Albuquerque C, Nunes M, Sabino E, Loman N, Naveca F, Pybus O, Alcantara L. Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region. Cell Reports 2020, 30: 2275-2283.e7. PMID: 32075736, DOI: 10.1016/j.celrep.2020.01.085.Peer-Reviewed Original Research