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LIM/46 - Laboratório de Parasitologia Médica, Hospital das Clínicas, Faculdade de Medicina
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- Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil(2021) ADELINO, Talita Emile Ribeiro; GIOVANETTI, Marta; FONSECA, Vagner; XAVIER, Joilson; ABREU, Alvaro Salgado de; NASCIMENTO, Valdinete Alves do; DEMARCHI, Luiz Henrique Ferraz; OLIVEIRA, Marluce Aparecida Assuncao; SILVA, Vinicius Lemes da; MELLO, Arabela Leal e Silva de; CUNHA, Gabriel Muricy; ABRANTES, Jayra Juliana Paiva Alves; WATANABE, Luiz Takao; REGO, Marta Ferreira da Silva; NARDY, Vanessa Brandao; AGUIAR, Shirlei Ferreira de; SANTOS, Fabiana Cristina Pereira dos; QUEIROZ, Alice Louize Nunes; NUNES, Bruno Tardelli Diniz; MARTINS, Livia Caricio; NUNES, Marcio Roberto Teixeira; SANTOS, Roselene Hans; SALLES, Flavia Cristina da Silva; CLARO, Ingra Morales; JESUS, Jaqueline Goes de; CANDIDO, Darlan da Silva; FABBRI, Cintia Marcela; GONZALEZ, Claudia; SAEZ, Lisseth; CHEN-GERMAN, Maria; BARRERA, Jaime Lagos; RAMIREZ-GONZALEZ, Jose Ernesto; OLIVEIRA, Elaine Cristina de; CAMPOS, Josefina; FALLER, Noelia Morel; VILLALOBOS, Marta Eugenia Viquez; KASLIN, Roberto; CISNEROS, Silvia Paola Salgado; ABURJAILE, Flavia Figueira; AMARAL, Carolina Dourado; FREIRE, Danielle Bandeira Costa de Sousa; CRUZ, Laura Nogueira; MATTOS, Daniel; CHAMON JUNIOR, Jorge Antonio; 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 Sa; BEZERRA, Rafael dos Santos; FALCAO, Melissa Barreto; CARVALHO, Rodrigo Dias de Oliveira; IANI, Felipe Campos de Melo; FILIPPIS, Ana Maria Bispo de; ABREU, Andre Luiz de; JESUS, Ronaldo de; ALBUQUERQUE, Carlos Frederico Campelo de; RICO, Jairo Mendez; SAID, Rodrigo Fabiano do Carmo; SILVA, Joscelio Aguiar; MOURA, Noely Fabiana Oliveira de; LEITE, Priscila; FRUTUOSO, Livia Carla Vinhal; HADDAD, Simone Kashima; MARTINEZ, Alexander; BARRETO, Fernanda Khouri; VAZQUEZ, Cynthia Carolina; CUNHA, Rivaldo Venancio da; ARAUJO, Emerson Luiz Lima; TOSTA, Stephane Fraga de Oliveira; FABRI, Allison de Araujo; CHALHOUB, Flavia Lowen Levy; LEMOS, Poliana da Silva; BRUYCKER-NOGUEIRA, Fernanda De; LICHS, Gislene Garcia de Castro; ZARDIN, Marina Castilhos Souza Umaki; SEGOVIA, Fatima Maria Cardozo; GONCALVES, Crhistinne Cavalheiro Maymone; GRILLO, Zoraida Del Carmen Fernandez; SLAVOV, Svetoslav Nanev; PEREIRA, Luiz Augusto; MENDONCA, Ana Flavia; PEREIRA, Felicidade Mota; MAGALHAES, Jurandy Junior Ferraz de; SANTOS JUNIOR, Agenor de Castro Moreira dos; LIMA, Maricelia Maia de; NOGUEIRA, Rita Maria Ribeiro; GOES-NETO, Aristoteles; 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; LOURENCO, Jose; ALCANTARA, Luiz Carlos Junior; CERQUEIRA, Erenilde Marques de; GRAF, Tiago; RAMALHO, Walter; NAVEGANTES, Wildo; REIS, Renato Barbosa; DUARTE, Clara Guerra; PEREIRA, Maira Alves; SILVA, Paulo Eduardo de Souza da; SOUZA, Raoni Almeida de; PAUVOLID-CORREA, Alex; PAIVA, Anne Aline Pereira de; FRITSCH, Hegger Machado; MARES-GUIA, Maria Angelica; TORRES, Maria Celeste; LIMA, Mauricio Teixeira; SEQUEIRA, Patricia; MARQUES, William de Almeida; JESUS, Jorlan Fernandes de; NAVECA, Felipe Gomes; SILVA, Alessandra Lima; PINTO, Anne Cybelle; JAISWAL, Arun Kumar; LOPES, Elisson 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 Guimaraes; SANTOS, Beatriz Senra Alvares da Silva; BUENO, Bruna Lopes; SIQUEIRA, Isadora Cristina de; VALLVE, Lourdes Farre; BORBA, Melina Mosquera Navarro; MAZZETTO, Alix Sandra; AGUIAR, Francisco de Assis Araujo; GOMES, Irenio da SilvaBrazil 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.
- Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus in Araraquara, São Paulo State(2024) SOUZA, Caio Santos de; CALEIRO, Giovana Santos; CLARO, Ingra Morales; JESUS, Jaqueline Goes de; COLETTI, Thais Moura; SILVA, Camila Alves Maia da; COSTA, Angela Aparecida; INENAMI, Marta; RIBEIRO, Andreia C.; FELIX, Alvina Clara; PAULA, Anderson Vicente de; FIGUEIREDO, Walter M.; LUNA, Expedito Jose de Albuquerque; SABINO, Ester C.; ROMANO, Camila M.Dengue virus (DENV) is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of Sao Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we sequenced 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for serotype 1, for genotype V and its main lineages. Within the last ten years, there have been at least three introductions of genotype V in Araraquara, distributed in two main lineages (L Ia and L Ib, and L II). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding the emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region.
- Characterization of insect-specific Culex flavivirus (Flaviviridae) nucleotide sequences in mosquitoes from urban parks in Sao Paulo, Brazil(2022) COLETTI, Thais de Moura; ROMANO, Camila Malta; URBINATTI, Paulo Roberto; TEIXEIRA, Renildo Souza; PEDROSA, Leila Weiss de Almeida; NARDI, Marcello Schiavo; NATAL, Delsio; COSTA, Antonio Charlys da; JESUS, Jaqueline Goes de; CLARO, Ingra Morales; SABINO, Ester Cerdeira; WITKIN, Steven S.; MARRELLI, Mauro Toledo; FERNANDES, Licia NatalBackground: Despite their worldwide occurrence, the distribution and role of insect-specific flaviviruses (ISFs) remain unclear. Methods: We evaluated the presence of ISFs in mosquitoes collected in Sao Paulo, Brazil, using reverse transcription and semi-nested polymerase chain reaction (PCR). Some of the positive samples were subjected to nanopore sequencing. Results: Twelve mosquito pools (2.8%) tested positive for flavivirus infection. Nanopore sequencing was successfully performed on six samples. Phylogenetic analysis grouped these sequences into genotype 2 of Culex flavivirus (CxFV). Conclusions: The identification of CxFV genotype 2 at new locations in Sao Paulo highlights the importance of understanding the role of ISFs in mosquito vector competence.
- Importation and early local transmission of COVID-19 in Brazil, 2020(2020) JESUS, Jaqueline Goes de; SACCHI, Claudio; CANDIDO, Darlan da Silva; CLARO, Ingra Morales; SALE, Flavia Cristina Silva; MANULI, Erika Regina; SILVA, Daniela Bernardes Borges da; PAIVA, Terezinha Maria de; PINHO, Margarete Aparecida Benega; SANTOS, Katia Correa de Oliveira; HILL, Sarah Catherine; AGUIAR, Renato Santana; ROMERO, Filipe; SANTOS, Fabiana Cristina Pereira dos; GONCALVES, Claudia Regina; TIMENETSKY, Maria do Carmo; QUICK, Joshua; CRODA, Julio Henrique Rosa; OLIVEIRA, Wanderson de; RAMBAUT, Andrew; PYBUS, Oliver G.; LOMAN, Nicholas J.; SABINO, Ester Cerdeira; FARIA, Nuno RodriguesWe conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil.
- Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020(2021) CLARO, Ingra Morales; SALES, Flavia Cristina da Silva; RAMUNDO, Mariana Severo; CANDIDO, Darlan S.; SILVA, Camila A. M.; JESUS, Jaqueline Goes de; MANULI, Erika R.; OLIVEIRA, Cristina Mendes de; SCARPELLI, Luciano; CAMPANA, Gustavo; PYBUS, Oliver G.; SABINO, Ester Cerdeira; FARIA, Nuno Rodrigues; LEVI, Jose EduardoIn December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in Sao Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.
- Molecular characterization and sequecing analysis of SARS-CoV-2 genome in Minas Gerais, Brazil(2022) FERREIRA, Giulia Magalhaes; CLARO, Ingra Morales; GROSCHE, Victoria Riquena; CANDIDO, Darlan; JOSE, Diego Pandelo; ROCHA, Esmenia Coelho; COLETTI, Thais de Moura; MANULI, Erika Regina; JR, Nelson Gaburo; FARIA, Nuno Rodrigues; SABINO, Ester Cerdeira; JESUS, Jaqueline Goes de; JARDIM, Ana Carolina GomesThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in Wuhan, China, is the causative agent of the coronavirus disease 2019 (COVID-19). Since its first notification in Sa similar to o Paulo state (SP) on 26th February 2020, more than 22,300,000 cases and 619,000 deaths were reported in Brazil. In early pandemic, SARS-CoV-2 spread locally, however, over time, this virus was disseminated to other regions of the country. Herein, we performed genomic sequencing and phylogenetic analysis of SARS-CoV-2 using 20 clinical samples of COVID-19 confirmed cases from 9 cities of Minas Gerais state (MG), in order to evaluate the molecular properties of circulating viral strains in this locality from March to May 2020. Our analyses demonstrated the circulation of B.1 lineage isolates in the investigated locations and nucleotide substitutions were observed into the genomic regions related to important viral structures. Additionally, sequences generated in this study clustered with isolates from SP, suggesting a dissemination route between these two states. Alternatively, monophyletic groups of sequences from MG and other states or country were observed, indicating independent events of virus introduction. These results reinforce the need of genomic surveillance for understand the ongoing spread of emerging viral pathogens.
- Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2(2021) VOGELS, Chantal B. F.; BREBAN, Mallery I.; OTT, Isabel M.; ALPERT, Tara; PETRONE, Mary E.; WATKINS, Anne E.; KALINICH, Chaney C.; EARNEST, Rebecca; ROTHMAN, Jessica E.; JESUS, Jaqueline Goes de; CLARO, Ingra Morales; FERREIRA, Giulia Magalhaes; CRISPIM, Myuki A. E.; SINGH, Lavanya; TEGALLY, Houriiyah; ANYANEJI, Ugochukwu J.; HODCROFT, Emma B.; MASON, Christopher E.; KHULLAR, Gaurav; METTI, Jessica; DUDLEY, Joel T.; MACKAY, Matthew J.; NASH, Megan; WANG, Jianhui; LIU, Chen; HUI, Pei; MURPHY, Steven; NEAL, Caleb; LASZLO, Eva; LANDRY, Marie L.; MUYOMBWE, Anthony; DOWNING, Randy; RAZEQ, Jafar; OLIVEIRA, Tulio de; FARIA, Nuno R.; SABINO, Ester C.; NEHER, Richard A.; FAUVER, Joseph R.; GRUBAUGH, Nathan D.With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath Coronavirus Disease 2019 (COVID-19) PCR assay because a key deletion in these viruses, spike Delta 69-70, would cause a ""spike gene target failure"" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Delta 69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Delta 3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Delta 3675-3677 as the primary target and spike Delta 69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
- Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019(2020) JESUS, Jaqueline Goes de; DUTRA, Karina Rocha; SALES, Flavia Cristina da Silva; CLARO, Ingra Morales; TERZIAN, Ana Carolina; CANDIDO, Darlan da Silva; HILL, Sarah C.; THEZE, Julien; TORRES, Celeste; D'AGOSTINI, Tatiana Lang; FELIX, Alvina Clara; REIS, Andreia F. Negri; ALCANTAR, Luiz Carlos Junior; ABREU, Andre L. de; CRODA, Julio H. R.; OLIVEIRA, Wanderson K. de; FILIPIS, Ana Maria Bispo de; CAMIS, Maria do Carmo Rodrigues dos Santos; ROMANO, Camila Malta; LOMAN, Nick J.; PYBUS, Oliver G.; SABINO, Ester Cerdeira; NOGUEIRA, Mauricio L.; FARIA, Nuno RodriguesBACKGROUND Despite efforts to mitigate the impact of dengue virus (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. Sao 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 generated20 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 Sao Jose 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.
- Lessons from a Multilaboratorial Task Force for Diagnosis of a Fatal Toxoplasmosis Outbreak in Captive Primates in Brazil(2023) SCHIFFLER, Francine Bittencourt; PEREIRA, Asheley Henrique Barbosa; MOREIRA, Silvia Bahadian; ARRUDA, Igor Falco; MOREIRA, Filipe Romero Rebello; D'ARC, Mirela; CLARO, Ingra Morales; PISSINATTI, Thalita de Abreu; CAVALCANTE, Liliane Tavares de Faria; MIRANDA, Thamiris dos Santos; COSENTINO, Matheus Augusto Calvano; OLIVEIRA, Renata Carvalho de; FERNANDES, Jorlan; ASSIS, Matheus Ribeiro da Silva; OLIVEIRA, Jonathan Goncalves de; SILVA, Thayssa Alves Coelho da; GALLIEZ, Rafael Mello; FAFFE, Debora Souza; JESUS, Jaqueline Goes de; SILVA, Marise Sobreira Bezerra da; BEZERRA, Matheus Filgueira; FERREIRA, Orlando da Costa; TANURI, Amilcar; CASTINEIRAS, Terezinha Marta; AGUIAR, Renato Santana; FARIA, Nuno Rodrigues; ALMEIDA, Alzira Paiva de; PISSINATTI, Alcides; SABINO, Ester Cerdeira; AMENDOEIRA, Maria Regina Reis; LEMOS, Elba Regina Sampaio de; UBIALI, Daniel Guimaraes; SANTOS, Andre F. A.Toxoplasmosis is an important zoonotic disease caused by the parasite Toxoplasma gondii and is especially fatal for neotropical primates. In Brazil, the Ministry of Health is responsible for national epizootic surveillance, but some diseases are still neglected. Here, we present an integrated investigation of an outbreak that occurred during the first year of the COVID-19 pandemic among eleven neotropical primates housed at a primatology center in Brazil. After presenting non-specific clinical signs, all animals died within four days. A wide range of pathogens were evaluated, and we successfully identified T. gondii as the causative agent within four days after necropsies. The liver was the most affected organ, presenting hemorrhage and hepatocellular necrosis. Tachyzoites and bradyzoite cysts were observed in histological examinations and immunohistochemistry in different organs; in addition, parasitic DNA was detected through PCR in blood samples from all specimens evaluated. A high prevalence of Escherichia coli was also observed, indicating sepsis. This case highlights some of the obstacles faced by the current Brazilian surveillance system. A diagnosis was obtained through the integrated action of researchers since investigation for toxoplasmosis is currently absent in national guidelines. An interdisciplinary investigation could be a possible model for future epizootic investigations in animals.