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  • article 20 Citação(ões) na Scopus
    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 Silva
    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.
  • article 0 Citação(ões) na Scopus
    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.
  • article 1 Citação(ões) na Scopus
    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 Natal
    Background: 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.
  • bookPart 0 Citação(ões) na Scopus
    Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2
    (2023) VOGELS, C. B. F.; BREBAN, M. I.; OTT, I. M.; ALPERT, T.; PETRONE, M. E.; WATKINS, A. E.; KALINICH, C. C.; EARNEST, R.; ROTHMAN, J. E.; JESUS, J. G. de; CLARO, I. M.; FERREIR, G. M.; CRISPIM, M. A. E.; SINGH, L.; TEGALLY, H.; ANYANEJI, U. J.; HODCROF, E. B.; MASON, C. E.; KHULLAR, G.; METTI, J.; DUDLEY, J. T.; MACKAY, M. J.; NASH, M.; WANG, J.; LIU, C.; HUI, P.; MURPHY, S.; NEAL, C.; LASZLO, E.; LANDRY, M. L.; MUYOMBWE, A.; DOWNING, R.; RAZEQ, J.; OLIVEIRA, T. de; FARIA, N. R.; SABINO, E. C.; NEHER, R. A.; FAUVER, J. R.; GRUBAUGH, N. D.
    Broadly accessible and inexpensive surveillance methods are needed to track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOC) around the world. While sequencing is the gold standard to identify circulating SARS-CoV-2 variants, routine genomic surveillance is not available in many locations primarily due to a lack of resources and expertise. The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples conducted in this study is not research involving human patients. Multiplex-PCR products were purified by using AmpureXP beads, and quantification was carried out using the Qubit dsDNA High Sensitivity assay on the Qubit 3.0. © 2023 Jenny Stanford Publishing Pte. Ltd.
  • article 0 Citação(ões) na Scopus
    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.
  • article 104 Citação(ões) na Scopus
    First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease
    (2020) DOMINGUES, Renan Barros; MENDES-CORREA, Maria Cassia; LEITE, Fernando Brunale Vilela de Moura; SABINO, Ester Cerdeira; SALARINI, Diego Zanotti; CLARO, Ingra; SANTOS, Daniel Wagner; JESUS, Jaqueline Goes de; FERREIRA, Noely Evangelista; ROMANO, Camila Malta; SOARES, Carlos Augusto Senne
    The association between coronaviruses and central nervous system (CNS) demyelinating lesions has been previously shown. However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. SARS-COV-2 was previously detected in cerebrospinal fluid (CSF) sample of a patient with encephalitis. However, the virus identity was not confirmed by deep sequencing of SARS-COV-2 detected in the CSF. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74-100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs.
  • article 61 Citação(ões) na Scopus
    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 Rodrigues
    We 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.
  • article 43 Citação(ões) na Scopus
    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 Eduardo
    In 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.
  • article 879 Citação(ões) na Scopus
    Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
    (2021) FARIA, Nuno R.; MELLAN, Thomas A.; WHITTAKER, Charles; CLARO, Ingra M.; CANDIDO, Darlan da S.; MISHRA, Swapnil; CRISPIM, Myuki A. E.; SALES, Flavia C.; HAWRYLUK, Iwona; MCCRONE, John T.; HULSWIT, Ruben J. G.; FRANCO, Lucas A. M.; RAMUNDO, Mariana S.; JESUS, Jaqueline G. de; ANDRADE, Pamela S.; COLETTI, Thais M.; FERREIRA, Giulia M.; SILVA, Camila A. M.; MANULI, Erika R.; PEREIRA, Rafael H. M.; PEIXOTO, Pedro S.; KRAEMER, Moritz U.; GABURO JR., Nelson; CAMILO, Cecilia da C.; HOELTGEBAUM, Henrique; SOUZA, William M.; ROCHA, Esmenia C.; SOUZA, Leandro M. de; PINHO, Mariana C. de; ARAUJO, Leonardo J. T.; V, Frederico S. Malta; LIMA, Aline B. de; SILVA, Joice do P.; ZAULI, Danielle A. G.; FERREIRA, Alessandro C. de S.; SCHNEKENBERG, Ricardo P.; LAYDON, Daniel J.; WALKER, Patrick G. T.; SCHLUETER, Hannah M.; SANTOS, Ana L. P. dos; VIDAL, Maria S.; CARO, Valentina S. Del; FILHO, Rosinaldo M. F.; SANTOS, Helem M. dos; AGUIAR, Renato S.; PROENCA-MODENA, Jose L. P.; NELSON, Bruce; HAY, James A.; MONOD, Melodie; MISCOURIDOU, Xenia; COUPLAND, Helen; SONABEND, Raphael; VOLLMER, Michaela; GANDY, Axel; PRETE JR., Carlos A.; NASCIMENTO, Vitor H.; SUCHARD, Marc A.; BOWDEN, Thomas A.; POND, Sergei L. K.; WU, Chieh-Hsi; RATMANN, Oliver; FERGUSON, Neil M.; DYE, Christopher; LOMAN, Nick J.; LEMEY, Philippe; RAMBAUT, Andrew; FRAIJI, Nelson A.; CARVALHO, Maria do P. S. S.; PYBUS, Oliver G.; FLAXMAN, Seth; BHATT, Samir; SABINO, Ester C.
    Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
  • article 2 Citação(ões) na Scopus
    Impact of COVID-19 RT-PCR testing of asymptomatic health care workers on absenteeism and hospital transmission during the pandemic
    (2023) MENDES, Elisa Teixeira; NETO, Danilo Glauco Pereira Villagelin; FERREIRA, Giulia Magalhaes; VALENCA, Ian Nunes; LIMA, Maria Patelli Juliani Souza; FREITAS, Maria Fernanda Marciano Barros de; DONALISIO, Maria Rita; MELO, Marcio Cristiano; LAZARI, Carolina; GOES, Jacqueline; MORALES, Ingra; JARDIM, Ana Carolina Gomes; SANTOS, Pamela Andrade dos; FRANCO, Lucas Augusto Moyses; SABINO, Ester Cerdeiro; COSTA, Silvia Figueiredo
    Background: Reducing the transmission of SARS-CoV-2 from asymptomatic and pre-symptomatic patients is critical in controlling the circulation of the virus.Methods: This study evaluated the prevalence of Reverse transcription polymerase chain reaction (RT-PCR) positivity in serial tests in 429 asymptomatic health care workers (HCW) and its impact on absenteeism. HCW from a COVID-19 reference hospital were tested, screened, and placed on leave. A time-series seg-mented regression of weekly absenteeism rates was used, and cases of infection among hospitalized patients were analyzed. Viral gene sequencing and phylogenetic analysis were performed on samples from HCW who had a positive result.Results: A significant decrease in absenteeism was detected 3-4 weeks after the intervention at a time of increased transmission within the city. The prevalence of RT-PCR positivity among asymptomatic professio-nals was 17.3%. Phylogenetic analyses (59 samples) detected nine clusters, two of them strongly suggestive of intrahospital transmission with strains (75% B.1.1.28) circulating in the region during this period.Conclusions: Testing and placing asymptomatic professionals on leave contributed to control strategy for COVID-19 transmission in the hospital environment, and in reducing positivity and absenteeism, which directly influences the quality of care and exposes professionals to an extra load of stress.(c) 2022 Association for Professionals in Infection Control and Epidemiology, Inc.