26 results on '"Giovanetti, Marta"'
Search Results
2. Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil.
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Iani, Felipe Campos de Melo, de Campos, Gabriel Montenegro, Adelino, Talita Emile Ribeiro, da Silva, Anielly Sarana, Kashima, Simone, Alcantara, Luiz Carlos Junior, Sampaio, Sandra Coccuzzo, Giovanetti, Marta, Elias, Maria Carolina, and Slavov, Svetoslav Nanev
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HEMORRHAGIC fever ,METAGENOMICS ,HEMORRHAGIC diseases ,LEPTOSPIRA interrogans ,YELLOW fever - Abstract
Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols. [ABSTRACT FROM AUTHOR]
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- 2024
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3. Epidemiological and Genomic Analysis of Asymptomatic SARS-CoV-2 Infections during the Delta and Omicron Epidemic Waves in São Paulo City, Brazil.
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Slavov, Svetoslav N., Lima, Alex R. J., Ribeiro, Gabriela, de Lima, Loyze P. O., Barros, Claudia R. dos S., Marqueze, Elaine C., Martins, Antonio J., Martininghi, Maiara, Palmieri, Melissa, Caldeira, Luiz A. V., da Silva, Fabiana E. V., Cacherik, Giselle, Nicolodelli, Aline L., Kashima, Simone, Giovanetti, Marta, Alcantara, Luiz Carlos Junior, Sampaio, Sandra C., and Elias, Maria C.
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SARS-CoV-2 Omicron variant ,GENOMICS ,SARS-CoV-2 ,BUS terminals ,EPIDEMICS - Abstract
We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of São Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the symptomatic individuals were excluded, and only asymptomatic cases were analyzed. During the Delta wave, a total of 4315 samples were collected, whereas 2372 samples were collected during the first Omicron wave. The incidence of the asymptomatic SARS-CoV-2 infection was 0.6% during the Delta wave and 0.8% during the Omicron wave. No statistical differences were found in the threshold amplification cycle. However, there was a statistical difference observed in the sublineage distribution between asymptomatic and symptomatic individuals. Our study determined the incidence of asymptomatic infection by monitoring individuals who remained symptom-free, thereby providing a reliable evaluation of asymptomatic SARS-CoV-2 carriage. Our findings reveal a relatively low proportion of asymptomatic cases, which could be attributed to our rigorous monitoring protocol for the presence of clinical symptoms. Investigating asymptomatic infection rates is crucial to develop and implement effective disease control strategies. [ABSTRACT FROM AUTHOR]
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- 2023
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4. Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil.
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Assato, Patricia Akemi, Clemente, Luan Gaspar, Giovanetti, Marta, Ribeiro, Gabriela, Lima, Alex Ranieri Jeronimo, Palmieri, Melissa, de Moraes, Leonardo Nazario, Kashima, Simone, Fukumasu, Heidge, Nogueira, Maurício Lacerda, Alcantara, Luiz Carlos Junior, Nicolodelli, Aline Lais, Martins, Antonio Jorge, Petry, Bruna, Banho, Cecilia Artico, Dos Santos Barros, Claudia Renata, Moncau-Gadbem, Cristina Tschorny, Moretti, Debora Botequio, De La Roque, Debora Glenda Lima, and Marqueze, Elaine Cristina
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COVID-19 pandemic ,SARS-CoV-2 Omicron variant ,INFECTIOUS disease transmission ,SARS-CoV-2 ,BUSINESS tourism ,COVID-19 - Abstract
São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city's different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide. [ABSTRACT FROM AUTHOR]
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- 2023
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5. Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
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Adelino, Talita ?mile Ribeiro, Giovanetti, Marta, Fonseca, Vagner, Xavier, Joilson, Abreu, ?lvaro Salgado de, Nascimento, Valdinete Alves do, Demarchi, Luiz Henrique Ferraz, Oliveira, Marluce Aparecida Assun??o, Silva, Vin?cius Lemos da, Mello, Arabela Leal e Silva de, Cunha, Gabriel Muricy, Santos, Roselene Hans, Oliveira, Elaine Cristina de, Chamon J?nior, Jorge Ant?nio, Iani, Felipe Campos de Melo, Filippis, Ana Maria Bispo de, Abreu, Andr? Luiz de, Jesus, Ronaldo de, Albuquerque, Carlos Frederico Campelo de, Rico, Jairo Mendez, Said, Rodrigo Fabiano do Carmo, Silva, Josc?lio Aguiar, Moura, Noely Fabiana Oliveira de, Leite, Priscila, Frutuoso, L?via Carla Vinhal, Haddad, Simone Kashima, Mart?nez, Alexander, Barreto, Fernanda Khouri, Vazquez, Cynthia Carolina, Cunha, Rivaldo Ven?ncio da, Ara?jo, Emerson Luiz Lima, Tosta, Stephane Fraga de Oliveira, Fabri, Allison de Ara?jo, Chalhoub, Fl?via Lowen Levy, Lemos, Poliana da Silva, Bruycker-Nogueira, Fernanda de, Lichs, Gislene Garcia de Castro, Zardin, Marina Castilho Souza Umaki, Segovia, F?tima Mar?a Cardozo, Gon?alves, Crhistinne Cavalheiro Maymone, Grillo, Zoraida Del Carmen Fernandez, Slavov, Svetoslav Nanev, Pereira, Luiz Augusto, Mendon?a, Ana Fl?via, Pereira, Felicidade Mota, Magalh?es, Jurandy J?nior Ferraz de, Santos J?nior, Agenor de Castro Moreira dos, Lima, Maric?lia Maia de, Nogueira, Rita Maria Ribeiro, G?es-Neto, Arist?teles, Azevedo, Vasco Ariston de Carvalho, Ramalho, Dario Brock, Oliveira, Wanderson Kleber, Macario, Eduardo Marques, Medeiros, Arnaldo Correia de, Pimentel, Victor, Holmes, Edward C, Oliveira, Tulio de, Louren?o, Jos?, Alcantara, Luiz Carlos Junior, Cerqueira, Erenilde Marques de, Graf, Tiago, Ramalho, Walter, Navegantes, Wildo, Reis, Renato Barbosa, Duarte, Clara Guerra, Pereira, Maria Alves, Silva, Paulo Eduardo de Souza da, Souza, Raoni Almeida de, Pauvolid-Corr?a, Alex, Paiva, Anne Aline Pereira de, Fritsch, Hegger Machado, Mares-Guia, Maria Ang?lica, Torres, Maria Celeste, Lima, Maur?cio Teixeira, Sequeira, Patr?cia, Marques, William de Almeida, Jesus, Jorlan Fernandes de, Naveca, Felipe Gomes, Silva, Alessandra Lima, Pinto, Anne Cybelle, Jaiswal, Arun Kumar, Lopes, ?lisson Nogueira, Costa, Francielly Morais Rodrigues da, Quintanilha-Peixoto, Gabriel, Soares, Gilson Carlos, Fonseca, Paula Luize Camargos, Souza, Renan Pedra de, Kato, Rodrigo Bentes, Santos, Rodrigo Profeta Silveira, Tiwari, Sandeep, Nogueira, Wylerson Guimar?es, Santos, Beatriz Senra ?lvares da Silva, Bueno, Bruna Lopes, Siqueira, Isadora Cristina de, Valle, Lourdes Farre, Borba, Melina Mosquera Navarro, Mazzetto, Alix Sandra, Aguiar, Francisco de Assis Ara?jo, Gomes, Irenio da Silva, Abrantes, Jayra Juliana Paiva Alves, Watanabe, Luiz Takao, Rego, Marta Ferreira da Silva, Nardy, Vanessa Brand?o, Aguiar, Shirlei Ferreira de, Santos, Fabiana Cristina Pereira dos, Queiroz, Alice Louize Nunes, Nunes, Bruno Tardelli Diniz, Martins, L?via Car?cio, Nunes, Marcio Roberto Teixeira, Salles, Fl?via Cristina da Silva, Claro, Ingra Morales, Jesus, Jaqueline Goes de, C?ndido, Darlan da Silva, Fabbri, Cintia Marcela, Gonz?lez, Claudia, Sa?z, Lisseth, Chen-Germ?n, Mar?a, Barrera, Jaime Lagos, Ram?rez-Gonz?lez, Jos? Ernesto, Campos, Josefina, Faller, Noelia Morel, Villalobos, Marta Eugenia V?quez, Kaslin, Roberto, Cisneros, Silvia Paola Salgado, Aburjaile, Fl?via Figueira, Amaral, Carolina Dourado, Freire, Danielle Bandeira Costa de Sousa, Cruz, Laura Nogueira, Mattos, Daniel, Landeira, Leandro Ferreira Lopes, Menezes, Mariane Talon de, Orioli, Ieda Maria, Ferraz, Ariane Coelho, Oliveira, Daiane Teixeira de, Reis, Alexandre Barbosa, Cota, Renata Guerra de S?, Bezerra, Rafael dos Santos, Falc?o, Melissa Barreto, and Carvalho, Rodrigo Dias de Oliveira
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0106 biological sciences ,0301 basic medicine ,Sequenciamento por Nanoporos ,Lineage (evolution) ,General Physics and Astronomy ,Dengue virus ,medicine.disease_cause ,01 natural sciences ,Dengue fever ,law.invention ,Dengue ,law ,Clade ,Phylogeny ,Molecular Epidemiology ,Multidisciplinary ,V?rus da Dengue / patogenicidade ,Varia??o Estrutural do Genoma ,Phylogenetics ,Transmission (mechanics) ,Geography ,Epidemiological Monitoring ,RNA, Viral ,Brazil ,Science ,Genome, Viral ,Real-Time Polymerase Chain Reaction ,010603 evolutionary biology ,Proof of Concept Study ,General Biochemistry, Genetics and Molecular Biology ,Article ,Dengue / virologia ,03 medical and health sciences ,medicine ,Humans ,Epidemics ,Retrospective Studies ,Whole genome sequencing ,Whole Genome Sequencing ,Genetic Variation ,Dengue / transmiss?o ,General Chemistry ,Dengue Virus ,medicine.disease ,Molecular Typing ,030104 developmental biology ,Evolutionary biology ,Feasibility Studies ,Nanopore sequencing ,Mobile Health Units - Abstract
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015–2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses., Here, the authors present results of the ZiBRA-2 project (https://www.zibra2project.org) which is an arbovirus surveillance project, across the Midwest of Brazil using a mobile genomics laboratory, combined with a genomic surveillance training program that targeted post-graduate students, laboratory technicians, and health practitioners in universities and laboratories.
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- 2021
6. Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil.
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Souza, Ueric José Borges de, Santos, Raíssa Nunes dos, Giovanetti, Marta, Alcantara, Luiz Carlos Junior, Galvão, Jucimária Dantas, Cardoso, Franciano Dias Pereira, Brito, Feliph Cássio Sobrinho, Franco, Ana Cláudia, Roehe, Paulo Michel, Ribeiro, Bergmann Morais, Spilki, Fernando Rosado, and Campos, Fabrício Souza
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CHIKUNGUNYA virus ,PLANT viruses ,VIRAL genomes ,CYTOSKELETAL proteins ,VIRAL transmission ,EPIDEMIOLOGY ,VIRAL mutation - Abstract
The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins' strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016–2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service. [ABSTRACT FROM AUTHOR]
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- 2022
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7. Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification.
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Souza, Juliana Vanessa Cavalcante, Santos, Hazerral de Oliveira, Leite, Anderson Brandão, Giovanetti, Marta, Bezerra, Rafael dos Santos, Carvalho, Eneas de, Bernardino, Jardelina de Souza Todão, Viala, Vincent Louis, Haddad, Rodrigo, Ciccozzi, Massimo, Alcantara, Luiz Carlos Junior, Sampaio, Sandra Coccuzzo, Covas, Dimas Tadeu, Kashima, Simone, Elias, Maria Carolina, and Slavov, Svetoslav Nanev
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EMERGING infectious diseases ,METAGENOMICS ,CHIKUNGUNYA ,ARBOVIRUS diseases ,DENGUE ,NUCLEOTIDE sequencing ,ARBOVIRUSES - Abstract
Viral metagenomics is increasingly being used for the identification of emerging and re-emerging viral pathogens in clinical samples with unknown etiology. The objective of this study was to shield light on the metavirome composition in clinical samples obtained from patients with clinical history compatible with an arboviral infection, but that presented inconclusive results when tested using RT-qPCR. The inconclusive amplification results might be an indication of the presence of an emerging arboviral agent that is inefficiently amplified by conventional PCR techniques. A total of eight serum samples with inconclusive amplification results for the routinely tested arboviruses—dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) obtained during DENV and CHIKV outbreaks registered in the state of Alagoas, Northeast Brazil between July and August 2021—were submitted to metagenomic next-generation sequencing assay using NextSeq 2000 and bioinformatic pipeline for viral discovery. The performed bioinformatic analysis revealed the presence of two arboviruses: DENV type 2 (DENV-2) and CHIKV with a high genome coverage. Further, the metavirome of those samples revealed the presence of multiple commensal viruses apparently without clinical significance. The phylogenetic analysis demonstrated that the DENV-2 genome belonged to the Asian/American genotype and clustered with other Brazilian strains. The identified CHIKV genome was taxonomically assigned as ECSA genotype, which is circulating in Brazil. Together, our results reinforce the utility of metagenomics as a valuable tool for viral identification in samples with inconclusive arboviral amplification. Viral metagenomics is one of the most potent methods for the identification of emerging arboviruses. [ABSTRACT FROM AUTHOR]
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- 2022
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8. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019
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Giovanetti, Marta, Faria, Nuno Rodrigues, Lourenço, José, Goes de Jesus, Jaqueline, Xavier, Joilson, Morales Claro, Ingra, Kraemer, Moritz U. G., Fonseca, Vagner, Dellicour, Simon, Thézé, Julien, da Silva Salles, Flavia, Gräf, Tiago, Paz Silveira, Paola, Alves do Nascimento, Valdinete, Costa de Souza, Victor, Campos de Melo Iani, Felipe, Castilho-Martins, Emerson Augusto, Nogueira Cruz, Laura, Wallau, Gabriel, Fabri, Allison, Levy, Flávia, Quick, Joshua, de Azevedo, Vasco, Santana Aguiar, Renato, De Oliveira, Tulio, Bôtto de Menezes, Camila, da Costa Castilho, Marcia, Terra, Tirza Matos, Souza da Silva, Marineide, Bispo de Filippis, Ana Maria, Luiz de Abreu, André, Kleber Oliveira, Wanderson, Croda, Julio, Campelo de Albuquerque, Carlos F., Nunes, Marcio R. T., Sabino, Ester Cerdeira, Loman, Nicholas, Naveca, Felipe Gomes, G.Pybus, Oliver, Alcantara, Luiz Carlos, Department of Infectious Diseases, Istituto Superiore di Sanita [Rome], University of Oxford [Oxford], Instituto Gonçalo Moniz, Partenaires INRAE, Universidade Federal de Minas Gerais, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), University of KwaZulu-Natal (UKZN), Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Distrito Federal, and Secretaria de em Saúde, Ministério da Saúde (SVS-MS), Brasília, Distrito Federal
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Microbiology (medical) ,Serotype ,lineage replacement ,lcsh:Arctic medicine. Tropical medicine ,Genotype ,lcsh:RC955-962 ,Lineage (evolution) ,[SDV]Life Sciences [q-bio] ,viruses ,030231 tropical medicine ,lcsh:QR1-502 ,Biology ,Dengue virus ,medicine.disease_cause ,Virus ,lcsh:Microbiology ,Dengue ,03 medical and health sciences ,0302 clinical medicine ,Phylogenetics ,Caribbean region ,parasitic diseases ,medicine ,Humans ,Phylogeny ,outbreak ,Outbreak ,Genetic Variation ,virus diseases ,Genomics ,Dengue Virus ,biochemical phenomena, metabolism, and nutrition ,Virology ,3. Good health ,genomic surveillance ,brazil ,dengue 2 ,RNA, Viral ,Original Article ,Brazil - Abstract
BACKGROUND: Despite efforts to mitigate the impact of DENV epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo state in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES: To understand the origin and dynamics of the 2019 DENV outbreak. METHODS: Here using portable nanopore sequencing we generated 20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of Sao Paulo state, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS: The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS: Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.
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- 2020
9. Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
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Giovanetti, Marta, Fonseca, Vagner, Wilkinson, Eduan, Tegally, Houriiyah, San, Emmanuel James, Althaus, Christian L, Xavier, Joilson, Slavov, Svetoslav Nanev, Viala, Vincent Louis, Lima, Alex Ranieri Jerônimo, Ribeiro, Gabriela, Souza-Neto, Jayme A, Fukumasu, Heidge, Coutinho, Luiz Lehmann, Cunha, Rivaldo Venancio da, Freitas, Carla, Melo, Carlos F Campelo de A e, Araújo, Wildo Navegantes de, Said, Rodrigo Fabiano Do Carmo, and Almiron, Maria
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SARS-CoV-2 Delta variant ,COVID-19 ,SARS-CoV-2 Omicron variant ,NATURAL immunity ,PANDEMICS ,FAILED states - Abstract
The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health. [ABSTRACT FROM AUTHOR]
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- 2022
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10. Dynamic Dispersion of HIV-1 Subtype C Toward Brazilian Northeastern Region.
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Oliveira, Rodrigo Cunha, Gräf, Tiago, Rego, Filipe Ferreira de Almeida, Silva, Gabriela Porto Santos Almeida, Giovanetti, Marta, and Monteiro Cunha, Joana Paixão
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The subtype C accounts for >50% of HIV type 1 (HIV-1) infections worldwide and it is currently the predominant viral form in South Brazil. Subtype C has been reported in all Brazilian regions; however, the phylogenetic relationship among strains circulating in those regions still remains unclear. This study aimed to investigate the origin and dynamic dispersion of HIV-1 subtype C toward Northeast Brazil. Our phylogenetic analysis suggests that most subtype C strains circulating in Brazil (99%) are descendant from the main lineage whose entrance in the country was previously described in the 1970s. According to the literature, additional introductions of subtype C were reported in the country through the Southeast region and in this study we identified another entry event that occurred most likely through the North region. Furthermore, our analysis suggests that the spread of subtype C to Brazilian Northeastern states occurred through multiple independent introductions of the main lineage that originated in South Brazil between mid-1980s and late 1990s. Despite the observation of eventual new HIV-1 subtype C introductions, our results highlight the predominance of a single lineage of this subtype in Brazil and the importance of South region in its dissemination throughout the country. [ABSTRACT FROM AUTHOR]
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- 2021
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11. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon
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Naveca, Felipe Gomes, Claro, Ingra, Giovanetti, Marta, de Jesus, Jaqueline Goes, Xavier, Joilson, Iani, Felipe Campos de Melo, do Nascimento, Valdinete Alves, de Souza, Victor Costa, Silveira, Paola Paz, Lourenço, José, Santillana, Mauricio, Kraemer, Moritz U. G., Quick, Josh, Hill, Sarah C., Thézé, Julien, Carvalho, Rodrigo Dias de Oliveira, Azevedo, Vasco, Salles, Flavia Cristina da Silva, Nunes, Marcio Roberto Teixeira, Lemos, Poliana da Silva, Candido, Darlan da Silva, Pereira, Glauco de Carvalho, Oliveira, Marluce Aparecida Assunção, Meneses, Cátia Alexandra Ribeiro, Maito, Rodrigo Melo, Cunha, Claudeth Rocha Santa Brígida, Campos, Daniela Palha de Sousa, Castilho, Marcia da Costa, Siqueira, Thalita Caroline da Silva, Terra, Tiza Matos, de Albuquerque, Carlos F. Campelo, da Cruz, Laura Nogueira, de Abreu, André Luis, Martins, Divino Valerio, Simoes, Daniele Silva de Moraes Vanlume, de Aguiar, Renato Santana, Luz, Sérgio Luiz Bessa, Loman, Nicholas, Pybus, Oliver G., Sabino, Ester C., Okumoto, Osnei, Alcantara, Luiz Carlos Junior, Faria, Nuno Rodrigues, and University of Oxford [Oxford]
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RNA viruses ,Viral Diseases ,Epidemiology ,[SDV]Life Sciences [q-bio] ,RC955-962 ,Filogeografia ,Pathology and Laboratory Medicine ,Geographical locations ,Disease Outbreaks ,Arctic medicine. Tropical medicine ,Zoonoses ,Medicine and Health Sciences ,Public and Occupational Health ,Genome Sequencing ,Phylogeny ,V?rus Chikungunya / gen?tica ,Boa Vista (RR) ,Chikungunya Virus ,virus diseases ,Genomics ,Infectious Diseases ,Medical Microbiology ,Viral Pathogens ,Epidemiological Monitoring ,Viruses ,Public aspects of medicine ,RA1-1270 ,Pathogens ,Brazil ,Research Article ,Neglected Tropical Diseases ,Alphaviruses ,Genome, Viral ,Research and Analysis Methods ,Microbiology ,Togaviruses ,parasitic diseases ,Genetics ,Genoma Viral ,Animals ,Humans ,Molecular Biology Techniques ,Sequencing Techniques ,Microbial Pathogens ,Molecular Biology ,Varia??o Gen?tica ,Whole Genome Sequencing ,Biology and life sciences ,Organisms ,Chikungunya Infection ,Computational Biology ,South America ,Monitoramento Epidemiol?gico ,Tropical Diseases ,Genome Analysis ,Genomic Libraries ,Filogenia ,Arbovirus / patogenicidade ,Chikungunya Fever ,People and places - Abstract
Background Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country. Methodology/Principal findings We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima. Conclusions/Significance This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region., Author summary Until the end of 2017, Brazil notified the highest number of infections caused by chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which suggests that approximately 39% of Roraima’s population was infected with CHIKV-ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data highlights the rapid spread of a less understood and poorly characterized CHIKV-ECSA genotype in Brazil. Investigations on potential associations between public health impact of CHIKV and genetic diversity of circulating strains are warranted to better evaluate its impact in Brazil and beyond.
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- 2019
12. Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil.
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Giovanetti, Marta, Augusto Pereira, Luiz, Santiago, Gilberto A., Fonseca, Vagner, García Mendoza, Maria Paquita, de Oliveira, Carla, de Moraes, Laise, Xavier, Joilson, Tosta, Stephane, Fristch, Hegger, de Castro Barbosa, Emerson, Strazza Rodrigues, Evandra, Figueroa-Romero, Dana, Padilla-Rojas, Carlos, Cáceres-Rey, Omar, Flávia Mendonça, Ana, de Bruycker Nogueira, Fernanda, Venancio da Cunha, Rivaldo, Bispo de Filippis, Ana Maria, and Freitas, Carla
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We used nanopore sequencing and phylogenetic analyses to identify a cosmopolitan genotype of dengue virus serotype 2 that was isolated from a 56-year-old male patient from the state of Goiás in Brazil. The emergence of a cosmopolitan genotype in Brazil will require risk assessment and surveillance to reduce epidemic potential. [ABSTRACT FROM AUTHOR]
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- 2022
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13. Genomic surveillance activities unveil the introduction of the SARS‐CoV‐2 B.1.525 variant of interest in Brazil: Case report.
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Pereira, Felicidade, Tosta, Stephane, Lima, Maricélia M., Reboredo de Oliveira da Silva, Luciana, Nardy, Vanessa B., Gómez, Marcela K. A., Lima, Jaqueline G., Fonseca, Vagner, Oliveira, Tulio, Lourenço, Jose, Alcantara, Luiz C., Giovanetti, Marta, and Leal, Arabela
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SARS-CoV-2 ,PANDEMICS - Abstract
The appearance of new variants of SARS‐CoV‐2 has recently challenged public health authorities with respect to tracking transmission and mitigating the impact in the evolving pandemic across countries. B.1.525 is considered a variant under investigation since it carries specific genetic signatures present in P.1, B.1.1.7, and B.1.351. Here we report genomic evidence of the first likely imported case of the SARS‐CoV‐2 B.1.525 variant, isolated in a traveler returning from Nigeria. [ABSTRACT FROM AUTHOR]
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- 2021
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14. Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil.
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Vasques Nonaka, Carolina Kymie, Miranda Franco, Marília, Gräf, Tiago, de Lorenzo Barcia, Camila Araújo, de Ávila Mendonça, Renata Naves, Felix de Sousa, Karoline Almeida, Costa Neiva, Leila Machado, Fosenca, Vagner, Almeida Mendes, Ana Verena, Santana de Aguiar, Renato, Giovanetti, Marta, de Freitas Souza, Bruno Solano, Nonaka, Carolina K V, Franco, Marília Miranda, de Sousa, Karoline Almeida Felix, Neiva, Leila M C, Mendes, Ana V A, and de Aguiar, Renato Santana
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SARS-CoV-2 ,REINFECTION ,COVID-19 ,EMERGING infectious diseases ,MEDICAL personnel - Abstract
Uncertainty remains about how long the protective immune responses against severe acute respiratory syndrome coronavirus 2 persists, and suspected reinfection in recovered patients has been reported. We describe a case of reinfection from distinct virus lineages in Brazil harboring the E484K mutation, a variant associated with escape from neutralizing antibodies. [ABSTRACT FROM AUTHOR]
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- 2021
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15. Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.
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Xavier, Joilson, Giovanetti, Marta, Fonseca, Vagner, Thézé, Julien, Gräf, Tiago, Fabri, Allison, Goes de Jesus, Jaqueline, Lima de Mendonça, Marcos Cesar, Damasceno dos Santos Rodrigues, Cintia, Mares-Guia, Maria Angélica, Cardoso dos Santos, Carolina, Fraga de Oliveira Tosta, Stephane, Candido, Darlan, Ribeiro Nogueira, Rita Maria, Luiz de Abreu, André, Kleber Oliveira, Wanderson, Campelo de Albuquerque, Carlos F., Chieppe, Alexandre, de Oliveira, Tulio, and Brasil, Patrícia
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CHIKUNGUNYA virus , *SOUTH Africans , *COMMUNICABLE diseases , *PUBLIC health surveillance , *VIRUS diseases , *COMPUTATIONAL biology , *ZIKA Virus Epidemic, 2015-2016 - Abstract
The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus’ rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. Our phylogenetic reconstructions indicated the circulation of the East-Central-South-African (ECSA) lineage in Rio de Janeiro. Time-measured phylogenetic analysis combined with CHIKV notified case numbers revealed the ECSA lineage was introduced in Rio de Janeiro around June 2015 (95% Bayesian credible interval: May to July 2015) indicating the virus was circulating unnoticed for 5 months before the first reports of CHIKV autochthonous transmissions in Rio de Janeiro, in November 2015. These findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases. [ABSTRACT FROM AUTHOR]
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- 2019
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16. Molecular identification of the emerging Human Gemykibivirus-2 (HuGkV-2) among Brazilian blood donors.
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Zucherato, Victória Simionatto, Giovanetti, Marta, Costa, Lara Okuyama Afonso, Krause, Luciana Maria Fontanari, Alves, Daiani Cristina Cilião, Moreira, Renata Maria Alencar, Pimentel, Barbara Maciel Sidou, Haddad, Rodrigo, Bitencourt, Hellen Tayaná, Ciccozzi, Massimo, Alcantara, Luiz Carlos Júnior, Kashima, Simone, Covas, Dimas Tadeu, and Slavov, Svetoslav Nanev
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BLOOD donors , *HUMAN DNA , *DNA viruses , *DNA - Abstract
Human gemykibivirus-2 (HuGkV-2) belonging to the Gemykibivirus genus (Genomoviridae family) is an emerging DNA virus which has been described as a component of the virome of a wide variety of samples including clinical ones. So far, the HuGkV-2 DNA prevalence in the human population as well as its clinical impact are completely unknown. The objective of this study was to investigate the HuGkV-2 DNA prevalence among Brazilian healthy blood donors from three different geographic regions. A total of 450 blood samples were screened for HuGkV-2 DNA (150 samples were from the Brazilian Amazon, 150 from Midwest Brazil and 150 from South Brazil). The overall HuGkV-2 DNA prevalence was 7.8 %. Considering the examined regions, the highest prevalence was observed in the Brazilian Amazon (city of Macapa, state of Amapa), 15.3 %, followed by the Midwest Brazil (city of Brasilia, Federal District) (6.0 %) and South Brazil (city of Santa Maria, Rio Grande do Sul State) (2.0 %). This study gives preliminary insights on the molecular prevalence of HuGkV-2 DNA among Brazilian blood donors, highlighting that the highest HuGkV-2 prevalence was recorded in the Brazilian Amazon. However, more studies regarding the prevalence, transmission routes and any possible clinical effects appear to be crucial in order to understand the impact of this emerging viral agent. • Human gemykibivirus-2 (HuGkV-2) is an emerging virus discovered by metagenomics. • HuGkV-2 DNA prevalence was estimated in Brazilian blood donors from three regions (Amazon, Central-West and South). • The Higher ighest HuGkV-2 DNA prevalence was estimated in the Brazilian Amazon, • More studies are needed to examine HuGkV-2 clinical significance and, transmission routes [ABSTRACT FROM AUTHOR]
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- 2023
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17. Merkel cell polyomavirus (MCPyV) DNA prevalence in Brazilian blood donors.
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Zucherato, Victoria Simionatto, da Costa, Perícles Natan Mendes, Giovanetti, Marta, Krause, Luciana Maria Fontanari, Alves, Daiani Cristina Cilião, Moreira, Renata Maria Alencar, Pimentel, Barbara Maciel Sidou, Haddad, Rodrigo, Bitencourt, Hellen Tayaná, Ciccozzi, Massimo, Alcantara, Luiz Carlos Júnior, Kashima, Simone, Covas, Dimas Tadeu, and Slavov, Svetoslav Nanev
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MERKEL cells , *BLOOD donors , *POLYOMAVIRUSES , *DNA , *MERKEL cell carcinoma - Abstract
Merkel cell polyomavirus (MCPyV) is an oncogenic virus that has been etiologically linked to Merkel cell carcinoma. Low levels of MCPyV DNA have been detected in blood donors with unclear impact on transfusion. The prevalence of MCPyV DNA in Brazilian blood donors is unclear. Therefore, the objective of this study was to evaluate the MCPyV DNA prevalence among Brazilian blood donors. We examined the presence of MCPyV DNA by real-time PCR (qPCR) in a total of 450 serum samples obtained from blood donors from three Brazilian regions (North, Central-West and South). The overall estimated MCPyV DNA prevalence was 1.1% (CI = 95%, 0.16–2.06%). Divided by region, in North Brazil (city of Macapa, state of Amapá) and South Brazil (city of Santa Maria, state of Rio Grande do Sul), the MCPyV prevalence was the same: 1.33% (CI = 95%, range 0.0–3.14%). In Central-West Brazil (city of Brasilia), the MCPyV prevalence was 0.6% (CI = 95%, 0.0–1.96%). All MCPyV positive samples showed a high cycle threshold (median Ct = 35.5), most probably related to the low viral load. More studies are necessary to unveil the impact of this oncogenic virus on transfusion medicine and if such exists, especially in regards of its infectivity and transmission potential. [ABSTRACT FROM AUTHOR]
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- 2023
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18. Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil.
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Iani, Felipe C.M., Giovanetti, Marta, Fonseca, Vagner, Souza, William M., Adelino, Talita E.R., Xavier, Joilson, Jesus, Jaqueline G., Pereira, Maira A., Silva, Marcos V.F., Costa, Alana V.B., Silva, Erniria C., Mendes, Márcia C.O., Filippis, Ana M.B., Albuquerque, Carlos F.C., Abreu, André L., Oliveira, Marluce A.A., Alcantara, Luiz C.J., and Faria, Nuno R.
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ZIKA virus , *ZIKA Virus Epidemic, 2015-2016 , *EPIDEMIOLOGY , *GENETIC epidemiology , *GENETIC variation , *ZIKA virus infections - Abstract
Autochthonous Zika virus (ZIKV) transmission in Brazil was first identified in April 2015 in Brazil, with the first ZIKV-associated microcephaly cases detected in October 2015. Despite efforts on understanding ZIKV transmission in Brazil, little is known about the virus epidemiology and genetic diversity in Minas Gerais (MG), the second most populous state in the country. We report molecular and genomic findings from the main public health laboratory in MG. Until January 2020, 26,817 ZIKV suspected infections and 86 congenital syndrome cases were reported in MG state. We tested 8552 ZIKV and microcephaly suspected cases. Ten genomes were generated on-site directly from clinical samples. A total of 1723 confirmed cases were detected in Minas Gerais, with two main epidemic waves; the first and larger epidemic wave peaked in March 2016, with the second smaller wave that peaked in March 2017. Dated molecular clock analysis revealed that multiple introductions occurred in Minas Gerais between 2014 and 2015, suggesting that the virus was circulating unnoticed for at least 16 months before the first confirmed laboratory case that we retrospectively identified in December 2015. Our findings highlight the importance of continued genomic surveillance strategies combined with traditional epidemiology to assist public health laboratories in monitoring and understanding the diversity of circulating arboviruses, which might help attenuate the public health impact of infectious diseases. • First positive ZIKV RT-qPCR cases in Minas Gerais were detected in December 2015. • Genomic surveillance detected at least three separate ZIKV introductions in Minas Gerais. • Genomic analysis suggests that ZIKV circulated silently several months before first detection. [ABSTRACT FROM AUTHOR]
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- 2021
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19. West Nile Virus in Brazil.
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Costa, Érica Azevedo, Giovanetti, Marta, Silva Catenacci, Lilian, Fonseca, Vagner, Aburjaile, Flávia Figueira, Chalhoub, Flávia L. L., Xavier, Joilson, Campos de Melo Iani, Felipe, da Cunha e Silva Vieira, Marcelo Adriano, Freitas Henriques, Danielle, Medeiros, Daniele Barbosa de Almeida, Guedes, Maria Isabel Maldonado Coelho, Senra Álvares da Silva Santos, Beatriz, Gonçalves Silva, Aila Solimar, de Pino Albuquerque Maranhão, Renata, da Costa Faria, Nieli Rodrigues, Farinelli de Siqueira, Renata, de Oliveira, Tulio, Ribeiro Leite Jardim Cavalcante, Karina, and Oliveira de Moura, Noely Fabiana
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WEST Nile virus ,PUBLIC health surveillance ,ERYTHROCYTES ,EPIDEMIOLOGICAL models - Abstract
Background: West Nile virus (WNV) was first sequenced in Brazil in 2019, when it was isolated from a horse in the Espírito Santo state. Despite multiple studies reporting serological evidence suggestive of past circulation since 2004, WNV remains a low priority for surveillance and public health, such that much is still unknown about its genomic diversity, evolution, and transmission in the country. Methods: A combination of diagnostic assays, nanopore sequencing, phylogenetic inference, and epidemiological modeling are here used to provide a holistic overview of what is known about WNV in Brazil. Results: We report new genetic evidence of WNV circulation in southern (Minas Gerais, São Paulo) and northeastern (Piauí) states isolated from equine red blood cells. A novel, climate-informed theoretical perspective of the potential transmission of WNV across the country highlights the state of Piauí as particularly relevant for WNV epidemiology in Brazil, although it does not reject possible circulation in other states. Conclusion: Our output demonstrates the scarceness of existing data, and that although there is sufficient evidence for the circulation and persistence of the virus, much is still unknown on its local evolution, epidemiology, and activity. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics with spill-over potential to humans. [ABSTRACT FROM AUTHOR]
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- 2021
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20. Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.
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Fabri, Allison Araújo, Rodrigues, Cintia Damasceno dos Santos, Santos, Carolina Cardoso dos, Chalhoub, Flávia Löwen Levy, Sampaio, Simone Alves, Faria, Nieli Rodrigues da Costa, Torres, Maria Celeste, Fonseca, Vagner, Brasil, Patricia, Calvet, Guilherme, Alcantara, Luiz Carlos Junior, Filippis, Ana Maria Bispo de, Giovanetti, Marta, and de Bruycker-Nogueira, Fernanda
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CHIKUNGUNYA virus ,EPIDEMICS ,ZIKA Virus Epidemic, 2015-2016 ,ARBOVIRUS diseases ,GENOTYPES ,VIRUS diversity ,VIRUS diseases - Abstract
The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016–2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016–2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework. [ABSTRACT FROM AUTHOR]
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- 2020
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21. Molecular frequency of human gemycircularvirus (GCYV) dna among blood donors from the Brazilian Amazon.
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Breno Zampieri Lima, Marlon, Giovana Pereira Daniel, Thuany, Tayaná Oliveira Bitencourt, Hellen, Carlos Junior Alcantara, Luiz, Haddad, Rodrigo, Kashima, Simone, Carolina Elias, Maria, Giovanetti, Marta, Coccuzzo Sampaio, Sandra, and Nanev Slavov, Svetoslav
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BLOOD donors , *DNA , *METAGENOMICS , *HUMAN beings - Abstract
• Gemycircularviruses are emerging group of viruses discovered by metagenomics in clinical samples. • The prevalence of Gemycircularvirus SL3 (GCYV-SL3) was estimated among Brazilian blood donors from the Brazilian Amazon. • The prevalence of GCYV-SL3 DNA was 1.7%. • More studies are needed to examine if GCYV-SL3 may impact transfusion safety. [ABSTRACT FROM AUTHOR]
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- 2024
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22. Neonatal surveillance for congenital Zika infection during the 2016 microcephaly outbreak in Salvador, Brazil: Zika virus detection in asymptomatic newborns.
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Oliveira, João V., Carvalho, Tereza C.X., Giovanetti, Marta, Jesus, Jaqueline G., Santos, Cleiton S., Pessoa, Lorena B., Magalhães Filho, Cláudio F.Q., Lima, Jéssica G.S., Carvalho, Daniel A.X., Figueiredo, Eduardo M., Biron, Ana Carolina, Santos, Daiana C., Viana, Paloma, Duarte, Alan O., Pessoa, Rosana, Souza, Gloryane B., Calcagno, Juan I., Lima, Fernanda W.M., Alcantara, Luiz C.J., and Siqueira, Isadora C.
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ZIKA virus infections , *ZIKA virus , *REVERSE transcriptase polymerase chain reaction - Abstract
Objective: To identify newborns with congenital Zika infection (CZI) at a maternity hospital in Salvador, Brazil, during the 2016 microcephaly outbreak.Methods: A prospective study enrolled microcephalic and normocephalic newborns with suspected CZI between January and December 2016. Serology (immunoglobulins IgM and IgG) and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) for the Zika virus were performed. Demographic and clinical characteristics of newborns with and without microcephaly were compared.Results: Of the 151 newborns enrolled, 32 (21.2%) were classified as microcephalic. The majority of these cases were born between January and May 2016. IgM and IgG Zika virus antibodies were detected in 5 (23.8%) and 17 (80.9%) microcephalic newborn blood samples, respectively. Six (24%) microcephalic newborns tested positive for Zika virus by RT-qPCR in urine or placenta samples. Thirteen (11.8%) normocephalic newborns also tested positive for Zika virus by PCR in urine, plasma, or placenta samples, while IgM antibodies against Zika were detected in 4 (4.2%) others.Conclusions: Identification of 17 normocephalic CZI cases, confirmed by IgM serology or RT-qPCR for Zika virus, provides evidence that CZI can present asymptomatically at birth. This finding highlights the need for prenatal and neonatal screening for Zika virus in endemic regions. [ABSTRACT FROM AUTHOR]- Published
- 2020
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23. HTLV-1aA introduction into Brazil and its association with the trans-Atlantic slave trade.
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Amoussa, Adjile Edjide Roukiyath, Wilkinson, Eduan, Giovanetti, Marta, de Almeida Rego, Filipe Ferreira, Araujo, Thessika Hialla A, de Souza Gonçalves, Marilda, de Oliveira, Tulio, and Alcantara, Luiz Carlos Junior
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HTLV , *VIRAL genetics , *PHYLOGENY , *SLAVE trade - Abstract
Introduction Human T-lymphotropic virus (HTLV) is an endemic virus in some parts of the world, with Africa being home to most of the viral genetic diversity. In Brazil, HTLV-1 is endemic amongst Japanese and African immigrant populations. Multiple introductions of the virus in Brazil from other epidemic foci were hypothesized. The long terminal repeat (LTR) region of HTLV-1 was used to infer the origin of the virus in Brazil, using phylogenetic analysis. Methods LTR sequences were obtained from the HTLV-1 database ( http://htlv1db.bahia.fiocruz.br ). Sequences were aligned and maximum-likelihood and Bayesian tree topologies were inferred. Brazilian specific clusters were identified and molecular-clock and coalescent models were used to estimate each cluster's time to the most recent common ancestor (tMRCA). Results Three Brazilian clusters were identified with a posterior probability ranged from 0.61 to 0.99. Molecular clock analysis of these three clusters dated back their respective tMRCAs between the year 1499 and the year 1668. Additional analysis also identified a close association between Brazilian sequences and new sequences from South Africa. Conclusion Our results support the hypothesis of a multiple introductions of HTLV-1 into Brazil, with the majority of introductions occurring in the post-Colombian period. Our results further suggest that HTLV-1 introduction into Brazil was facilitated by the trans-Atlantic slave trade from endemic areas of Africa. The close association between southern African and Brazilian sequences also suggested that greater numbers of the southern African Bantu population might also have been part of the slave trade than previously thought. [ABSTRACT FROM AUTHOR]
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- 2017
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24. Detection of encephalitis-causing viruses reveals predominance of chikungunya virus in the state of Bahia, Brazil.
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Sampaio, Maria Paula de Souza, do Rosário, Mateus Santana, Martins, Lorena Cunha, Trindade, Luiza Vieira Luedy, Francisco, Marcos Vinicius Lima de Oliveira, Costa, Bernardo Gratival Gouvea, Vasconcelos, Gessica Almeida, Lima, Italo Andrade Barbosa, Macêdo, Yasmin Santos Freitas, Carvalho, Fernanda Maria Lessa, de Santana, Marina Borges Rabelo, Khouri, Ricardo, Fritsch, Hegger, Xavier, Joilson, Fonseca, Vagner, Giovanetti, Marta, de Mello, Arabela Leal e Silva, Pereira, Felicidade Mota, Campos, Gubio Soares, and de Jesus, Pedro Antonio Pereira
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CHIKUNGUNYA virus , *WHOLE genome sequencing , *VIRAL antigens , *ENCEPHALITIS viruses , *ENTEROVIRUS diseases , *VARICELLA-zoster virus , *VIRAL encephalitis - Abstract
• The etiology of most encephalitis cases remained unknown. • Chikungunya virus was the predominant virus associated with encephalitis cases. • Chikungunya virus is a significant cause of encephalitis in Brazil. Encephalitis is a severe neurological syndrome for which herpesvirus and enteroviruses are the most common etiological agents. Arboviruses, a wildly diverse group of pathogens, are also critical epidemiological agents associated with encephalitis. In Brazil, little is known about the causative agents of encephalitis. We conducted a hospital surveillance for encephalitis between 2020 and 2022. Molecular (RT-PCR and qPCR) and serological (virus-specific IgM and viral antigens) techniques were performed in cerebrospinal fluid and serum samples obtained from study participants. In the 43 participants evaluated, the etiologic agent or the presence of IgM was detected in 16 (37.2%). Nine (20.9%) cases were positive for chikungunya virus (CHIKV), three (7.0%) for dengue virus, two (4.7%) for human adenovirus, one (2.3%) for varicella-zoster virus, and one (2.3%) for enterovirus. Whole-genome sequencing revealed that the CHIKV identified belongs to the East/Central/South African lineage. Herein, CHIKV is a common pathogen identified in encephalitis cases. Our results reinforce previous evidence that chikungunya represents a significant cause of encephalitis during CHIKV outbreaks and epidemics and add to existing information on the epidemiology of encephalitis in Brazil. [ABSTRACT FROM AUTHOR]
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- 2024
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25. Metavirome composition of Brazilian blood donors positive for the routinely tested blood-borne infections.
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Bezerra, Rafael dos Santos, Ximenez, João Paulo Bianchi, Giovanetti, Marta, Zucherato, Victoria Simionatto, Bitencourt, Hellen Tayaná, Zimmermann, Ana, Alcantara, Luiz Carlos Júnior, Covas, Dimas Tadeu, Kashima, Simone, and Slavov, Svetoslav Nanev
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BLOODBORNE infections , *BLOOD donors , *SUPERVISED learning , *TORQUE teno virus , *CHAGAS' disease , *NEUROSYPHILIS - Abstract
• Our study shows that the virome composition of blood donors positive for the routinely tested blood-borne infections can be related to the type of main infection. • The viral landscape of parenterally infected blood donors was shaped by the predominant identification of commensal viruses. • Region-specific emerging viruses with putative impact were also identified in the Brazilian Amazon. • Continuous metagenomic surveillance in blood donors is useful in the light of viruses which might pose threat to blood transfusion safety. Viral metagenomics is widely applied to characterize emerging viral pathogens but it can also reveal the virome composition in health and disease. The evaluation of the virome in healthy blood donors can provide important knowledge on possible transfusion threats. Currently, there is still a paucity of information regarding the virome of blood donors who test positive for routinely tested blood-borne infections. Such analysis may reveal co-infections which in turn appear to be crucial for transfusion medicine and for patient management. The aim of this study was to evaluate the metavirome in blood donors who tested positive for routinely tested blood-borne infections, the information for which is important for transfusion medicine and blood donor management. For this purpose, we analyzed 18 blood donations obtained from HIV and HBV-infected blood donors from the Brazilian Amazon (Amapa state) and 11 HIV, HBV, HCV, syphilis and Chagas disease - positive blood donations obtained from blood donors sampled in South Brazil (Rio Grande do Sul state). We additionally included a control group of 20 blood donors obtained from Southeast Brazil (State of São Paulo). Samples were assembled in pools and sequenced by the Illumina NovaSeq 6000 platform. To link a given virus with geographic region or type of blood donor, we performed supervised machine learning classification (fingerprint analysis). The virome of both locations was predominantly composed of commensal viruses. However, in HBV-infected blood donors from the Brazilian Amazon, the Human Pegivirus-1 (HPgV-1) reads were prevailing, while in HIV-infected donors from the same location, the torque teno virus (TTV) reads expressive abundance. In blood donors from South Brazil, the most abundant reads were classified as Human endogenous retrovirus K (HERV-K). Putative emerging viruses like the Human gemykibivirus-2 (HuGkV-2) were exclusively identified in samples from the Brazilian Amazon. The fingerprint analysis demonstrated that the HERV-K, TTV-7, 13, and 15 were statistically important for the infected blood donors, while TTV-5, 12 and 20 were linked to geographic localization. Our study revealed differences in the viral composition among blood donors who tested positive for routinely tested blood-borne infections from two different Brazilian regions and indicated the presence of putative emerging viruses in samples obtained from the Amazon. Together our results show that the presence of specific commensal viruses may be related donor infection status but additional investigations including larger study groups and samples from other Brazilian regions are needed to confirm this hypothesis. [ABSTRACT FROM AUTHOR]
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- 2022
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26. SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves.
- Author
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Alcantara, Luiz Carlos Junior, Nogueira, Elisson, Shuab, Gabriel, Tosta, Stephane, Fristch, Hegger, Pimentel, Victor, Souza-Neto, Jayme A., Coutinho, Luiz Lehmann, Fukumasu, Heidge, Sampaio, Sandra Coccuzzo, Elias, Maria Carolina, Kashima, Simone, Slavov, Svetoslav Nanev, Ciccozzi, Massimo, Cella, Eleonora, Lourenco, José, Fonseca, Vagner, and Giovanetti, Marta
- Subjects
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SARS-CoV-2 , *SARS-CoV-2 Omicron variant , *COVID-19 pandemic , *COVID-19 , *ANTIBODY formation , *EPIDEMICS , *ZIKA Virus Epidemic, 2015-2016 - Abstract
• Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. • Here we show how variants displacement have driven distinct epidemic waves in Brazil. • Genomic effort is pivotal to follow the evolution of this unpredictable virus. Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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