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  • article 22 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.
  • 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 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.
  • article 2 Citação(ões) na Scopus
    SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains
    (2023) MENDES-CORREA, Maria Cassia; SALOMAO, Matias Chiarastelli; GHILARDI, Fabio; TOZETTO-MENDOZA, Tania Regina; VILLAS-BOAS, Lucy Santos; PAULA, Anderson Vicente de; PAIAO, Heuder Gustavo Oliveira; COSTA, Antonio Charlys da; LEAL, Fabio E.; FERRAZ, Andrea de Barros Coscelli; SALES, Flavia C. S.; CLARO, Ingra M.; FERREIRA, Noely E.; PEREIRA, Geovana M.; JR, Almir Ribeiro da Silva; FREIRE, Wilton; ESPINOZA, Evelyn Patricia Sanchez; MANULI, Erika R.; ROMANO, Camila M.; JESUS, Jaqueline G. de; SABINO, Ester C.; WITKIN, Steven S.
    Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.
  • article 31 Citação(ões) na Scopus
    SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil
    (2021) ROMANO, Camila Malta; FELIX, Alvina Clara; PAULA, Anderson Vicente de; JESUS, Jaqueline Goes de; ANDRADE, Pamela S.; CANDIDO, Darlan; OLIVEIRA, Franciane M. de; RIBEIRO, Andreia C.; SILVA, Francini C. da; INEMAMI, Marta; COSTA, Angela Aparecida; LEAL, Cibele O. D.; FIGUEIREDO, Walter Manso; PANNUTI, Claudio Sergio; SOUZA, William M. de; FARIA, Nuno Rodrigues; SABINO, Ester Cerdeira
    Reinfection by the severe acute respiratory syndrome coronavirus type 2 (SARS-COV-2) has been reported in many countries, suggesting that the virus may continue to circulate among humans despite the possibility of local herd immunity due to massive previous infections. The emergence of variants of concern (VOC) that are more transmissible than the previous circulating ones has raised particular concerns on the vaccines effectiveness and reinfection rates. The P.1 lineage was first identified in December 2020 in Manaus city and is now globally spread. We report the first case of reinfection of SARS-CoV-2 caused by the P.1 variant outside of Manaus. The potential of these new variants to escape naturally and vaccine-induced immunity highlights the need for a global vigilance.
  • article 0 Citação(ões) na Scopus
    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 Gomes
    The 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.