ANTONIO CHARLYS DA COSTA
Projetos de Pesquisa
Unidades Organizacionais
LIM/52 - Laboratório de Virologia, Hospital das Clínicas, Faculdade de Medicina
LIM/46 - Laboratório de Parasitologia Médica, Hospital das Clínicas, Faculdade de Medicina
LIM/46 - Laboratório de Parasitologia Médica, Hospital das Clínicas, Faculdade de Medicina
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- Multiple clades of Husavirus in South America revealed by next generation sequencing(2021) RAMOS, Endrya do Socorro Foro; ROSA, Ulisses Alves; RIBEIRO, Geovani de Oliveira; VILLANOVA, Fabiola; MILAGRES, Flavio Augusto de Padua; BRUSTULIN, Rafael; MORAIS, Vanessa dos Santos; ARAUJO, Emerson Luiz Lima; PANDEY, Ramendra Pati; RAJ, V. Samuel; SABINO, Ester Cerdeira; DENG, Xutao; DELWART, Eric; LUCHS, Adriana; LEAL, Elcio; COSTA, Antonio Charlys daHusavirus (HuV) is an unclassified virus of the order Picornavirales that has already been identified worldwide in various locations. The genetic, epidemiological, and pathogenic characteristics are, however, little understood. In children with acute gastroenteritis, this study used next-generation sequencing to recognize unknown sources of viruses. In particular, 251 fecal samples obtained from individuals were sequenced in southern, northeastern, and northern Brazil. all samples were also analyzed using culture methods and parasitological tests to classify other enteric pathogens such as bacteria, parasites, and viruses. 1.9% of the samples tested positive for HuV, for a total of 5 positive children, with a mean age of 2 year, with three males and two females. Detailed molecular characterization of full genomes showed that Brazilian HuVs' nucleotide divergence is less than 11%. The genetic gap between Brazilian sequences and the closest HuV reported previously, on the other hand, is 18%. The study showed that Brazilian sequences are closely related to the HuV defined in Viet Nam in 2013, further characterization based on phylogenetics. At least two divergent clades of HuV in South America were also seen in the phylogenetic study.
- Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in Sao Paulo, Brazil(2011) SANABANI, Sabri Saeed; PASTENA, Evelyn Regina de Souza; COSTA, Antonio Charlys da; MARTINEZ, Vanessa Pouza; KLEINE-NETO, Walter; OLIVEIRA, Ana Carolina Soares de; SAUER, Mariana Melillo; BASSICHETTO, Katia Cristina; OLIVEIRA, Solange Maria Santos; TOMIYAMA, Helena Tomoko Iwashita; SABINO, Ester Cerdeira; KALLAS, Esper GeorgesBackground: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in Sao Paul, Brazil. Methodology: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed. Results: Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%). Conclusions: Our results confirm the existence of various HIV-1 subtypes circulating in Sao Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.
- Establishment and cryptic transmission of Zika virus in Brazil and the Americas(2017) FARIA, N. R.; QUICK, J.; CLARO, I. M.; THEZE, J.; JESUS, J. G. de; GIOVANETTI, M.; KRAEMER, M. U. G.; HILL, S. C.; BLACK, A.; COSTA, A. C. da; FRANCO, L. C.; SILVA, S. P.; WU, C. -H.; RAGHWANI, J.; CAUCHEMEZ, S.; PLESSIS, L. du; VEROTTI, M. P.; OLIVEIRA, W. K. de; CARMO, E. H.; COELHO, G. E.; SANTELLI, A. C. F. S.; VINHAL, L. C.; HENRIQUES, C. M.; SIMPSON, J. T.; LOOSE, M.; ANDERSEN, K. G.; GRUBAUGH, N. D.; SOMASEKAR, S.; CHIU, C. Y.; MUNOZ-MEDINA, J. E.; GONZALEZ-BONILLA, C. R.; ARIAS, C. F.; LEWIS-XIMENEZ, L. L.; BAYLIS, S. A.; CHIEPPE, A. O.; AGUIAR, S. F.; FERNANDES, C. A.; LEMOS, P. S.; NASCIMENTO, B. L. S.; MONTEIRO, H. A. O.; SIQUEIRA, I. C.; QUEIROZ, M. G. de; SOUZA, T. R. de; BEZERRA, J. F.; LEMOS, M. R.; PEREIRA, G. F.; LOUDAL, D.; MOURA, L. C.; DHALIA, R.; FRANCA, R. F.; MAGALHAES, T.; MARQUES JR., E. T.; JAENISCH, T.; WALLAU, G. L.; LIMA, M. C. de; NASCIMENTO, V.; CERQUEIRA, E. M. de; LIMA, M. M. de; MASCARENHAS, D. L.; MOURA NETO, J. P.; LEVIN, A. S.; TOZETTO-MENDOZA, T. R.; FONSECA, S. N.; MENDES-CORREA, M. C.; MILAGRES, F. P.; SEGURADO, A.; HOLMES, E. C.; RAMBAUT, A.; BEDFORD, T.; NUNES, M. R. T.; SABINO, E. C.; ALCANTARA, L. C. J.; LOMAN, N. J.; PYBUS, O. G.Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil(1). Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 20162). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease(3). However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.
- Epizootics due to Yellow Fever Virus in Sao Paulo State, Brazil: viral dissemination to new areas (2016-2017)(2019) CUNHA, Mariana Sequetin; COSTA, Antonio Charlys da; FERNANDES, Natalia Coelho Couto de Azevedo; GUERRA, Juliana Mariotti; SANTOS, Fabiana Cristina Pereira dos; NOGUEIRA, Juliana Silva; D'AGOSTINO, Leandro Guariglia; KOMNINAKIS, Shirley Vasconcelos; WITKIN, Steven S.; RESSIO, Rodrigo Albergaria; MAEDA, Adriana Yurika; VASAMI, Fernanda Gisele Silva; KAIGAWA, Ursula Mitsue Abreu; AZEVEDO, Lais Sampaio de; FACIOLI, Paloma Alana de Souza; MACEDO, Fernando Luiz Lima; SABINO, Ester Cerdeira; LEAL, Elcio; SOUZA, Renato Pereira deBeginning in late 2016 Brazil faced the worst outbreak of Yellow Fever in recent decades, mainly located in southeastern rural regions of the country. In the present study we characterize the Yellow Fever Virus (YFV) associated with this outbreak in Sao Paulo State, Brazil. Blood or tissues collected from 430 dead monkeys and 1030 pools containing a total of 5,518 mosquitoes were tested for YFV by quantitative RT-PCR, immunohistochemistry (IHC) and indirect immunofluorescence. A total of 67 monkeys were YFV-positive and 3 pools yielded YFV following culture in a C6/36 cell line. Analysis of five nearly full length genomes of YFV from collected samples was consistent with evidence that the virus associated with the Sao Paulo outbreak originated in Minas Gerais. The phylogenetic analysis also showed that strains involved in the 2016-2017 outbreak in distinct Brazilian states (i.e., Minas Gerais, Rio de Janeiro, Espirito Santo) intermingled in maximum-likelihood and Bayesian trees. Conversely, the strains detected in Sao Paulo formed a monophyletic cluster, suggesting that they were local-adapted. The finding of YFV by RT-PCR in five Callithrix monkeys who were all YFV-negative by histopathology or immunohistochemistry suggests that this YFV lineage circulating in Sao Paulo is associated with different outcomes in Callithrix when compared to other monkeys.
- Detailed characterization of Redondovirus in saliva of SARS-CoV-2-infected individuals in Sao Paulo, Brazil(2023) COSTA, Antonio Charlys da; MENDES-CORREA, Maria C.; TOZETTO-MENDOZA, Tania Regina; VILLAS-BOAS, Lucy S.; PAULA, Anderson Vicente de; PAIAO, Heuder Gustavo Oliveira; LEAL, Fabio E.; FERREIRA, Noely E.; HONORATO, Layla; LEAL, Elcio; GRANDI, Giuliano; MORAIS, Vanessa dos Santos; MANULI, Erika R.; SABINO, Ester C.; WITKIN, Steven S.BackgroundRedondovirus (ReDoV) is a DNA virus present in the respiratory tract of many healthy individuals. Since SARS-CoV-2, the virus responsible for COVID-19, also primarily infects the same site, we evaluated whether ReDoV was present at increased frequency in patients with COVID-19 and influenced infection parameters.MethodsSaliva samples were collected weekly from 59 individuals with COVID-19 and from 132 controls. ReDoV was detected by polymerase chain reaction and the genotypes were identified by metagenomics. Torque Teno Virus (TTV) in these samples were previously reported.ResultsReDoV was detected in saliva more frequently from COVID-19 patients (72.9%) than from controls (50.0%) (p = 0.0015). There were no associations between ReDoV detection and either continuous or intermittent SARS-CoV-2 shedding, the duration of SARS-CoV-2 detection in saliva, patients' sex or if infection was by the B1 or Gamma strain. The two ReDoV strains, Brisavirus and Vientovirus, were present in equivalent frequencies in ReDoV-positive COVID-19 patients and controls. Phylogenetic analysis suggested that the two ReDoV strains in Brazil were similar to strains previously detected on other continents.ConclusionReDoV expression in saliva is increased in males and females in Brazil with mild COVID-19 but its presence does not appear to influence properties of the SARS-CoV-2 infection.
- Disparity between scientific accomplishment and biotechnology availability in Brazil(2021) BRAZ, Lucia Maria Almeida; TAHMASEBI, Roozbeh; COSTA, Antonio Charlys da; WITKIN, Steven S.Despite being among the world's leaders in scientific output, Brazil ranks 66th among countries in the production of reagents and supplies needed for state-of-the-art scientific analyses. The production of needed reagents and equipment for experimental analyses and patient diagnostics is sorely lacking within Brazil and explicit in this pandemic period caused by SARS-CoV-2. A significant fraction of resources from Brazilian funding agencies is now being transferred to companies in other countries for the purchase of essential scientific-related products. Is this sustainable? Therefore it is necessary to draw the attention of all the world and Brazilian society about this situation
- Association between development of severe COVID-19 and a polymorphism in the CIAS1 gene that codes for an inflammasome component(2023) TOZETTO-MENDOZA, Tania R. R.; MENDES-CORREA, Maria Cassia; LINHARES, Iara Moreno; RAYMUNDI, Vanessa de Cassia; PAIAO, Heuder Gustavo de Oliveira; BARBOSA, Erick Matheus Garcia; LUNA-MUSCHI, Alessandra; HONORATO, Layla; CORREA, Giovanna Francisco; COSTA, Antonio Charlys da; COSTA, Silvia Figueiredo; WITKIN, Steven S. S.An elevated pro-inflammatory cytokine response is associated with severe life-threatening symptoms in individuals with Coronavirus Disease-2019 (COVID). The inflammasome is an intracellular structure responsible for generation of interleukin (IL)-1 & beta; and IL-18. NALP3, a product of the CIAS1 gene, is the rate-limiting component for inflammasome activity. We evaluated if a CIAS1 42 base pair length polymorphism (rs74163773) was associated with severe COVID. DNA from 93 individuals with severe COVID, 38 with mild COVID, and 98 controls were analyzed for this polymorphism. The 12 unit repeat allele is associated with the highest inflammasome activity. Five alleles, corresponding to 6, 7, 9, 12 or 13 repeat units, divided into 12 genotypes were identified. The frequency of the 12 unit repeat allele was 45.3% in those with severe disease as opposed to 30.0% in those with mild disease and 26.0% in controls (p < 0.0001, severe vs. controls). In contrast, the 7 unit repeat allele frequency was 30.1% in controls as opposed to 14.0% and 12.5% in those with severe or mild disease, respectively (p & LE; 0.0017). We conclude that individuals positive for the CIAS1 12 allele may be at elevated risk for development of severe COVID due to an increased level of induced pro-inflammatory cytokine production.
- Genomic and epidemiological monitoring of yellow fever virus transmission potential(2018) FARIA, N. R.; KRAEMER, M. U. G.; HILL, S. C.; JESUS, J. Goes de; AGUIAR, R. S.; IANI, F. C. M.; XAVIER, J.; QUICK, J.; PLESSIS, L. du; DELLICOUR, S.; THEZE, J.; CARVALHO, R. D. O.; BAELE, G.; WU, C. -H.; SILVEIRA, P. P.; ARRUDA, M. B.; PEREIRA, M. A.; PEREIRA, G. C.; LOURENCO, J.; OBOLSKI, U.; ABADE, L.; VASYLYEVA, T. I.; GIOVANETTI, M.; YI, D.; WEISS, D. J.; WINT, G. R. W.; SHEARER, F. M.; FUNK, S.; NIKOLAY, B.; FONSECA, V.; ADELINO, T. E. R.; OLIVEIRA, M. A. A.; SILVA, M. V. F.; SACCHETTO, L.; FIGUEIREDO, P. O.; REZENDE, I. M.; MELLO, E. M.; SAID, R. F. C.; SANTOS, D. A.; FERRAZ, M. L.; BRITO, M. G.; SANTANA, L. F.; MENEZES, M. T.; BRINDEIRO, R. M.; TANURI, A.; SANTOS, F. C. P. dos; CUNHA, M. S.; NOGUEIRA, J. S.; ROCCO, I. M.; COSTA, A. C. da; KOMNINAKIS, S. C. V.; AZEVEDO, V.; CHIEPPE, A. O.; ARAUJO, E. S. M.; MENDONCA, M. C. L.; SANTOS, C. C. dos; SANTOS, C. D. dos; MARES-GUIA, A. M.; NOGUEIRA, R. M. R.; SEQUEIRA, P. C.; ABREU, R. G.; GARCIA, M. H. O.; ABREU, A. L.; OKUMOTO, O.; KROON, E. G.; ALBUQUERQUE, C. F. C. de; LEWANDOWSKI, K.; PULLAN, S. T.; CARROLL, M.; OLIVEIRA, T. de; SABINO, E. C.; SOUZA, R. P.; SUCHARD, M. A.; LEMEY, P.; TRINDADE, G. S.; DRUMOND, B. P.; FILIPPIS, A. M. B.; LOMAN, N. J.; CAUCHEMEZ, S.; ALCANTARA, L. C. J.; PYBUS, O. G.The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
- Guapiacu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil(2021) RIBEIRO, Geovani de Oliveira; COSTA, Antonio Charlys da; GILL, Danielle Elise; RIBEIRO, Edcelha Soares D'Athaide; REGO, Marlisson Octavio da S.; MONTEIRO, Fred Julio Costa; VILLANOVA, Fabiola; NOGUEIRA, Juliana Silva; MAEDA, Adriana Yurika; SOUZA, Renato Pereira de; TAHMASEBI, Roozbeh; MORAIS, Vanessa S.; PANDEY, Ramendra Pati; RAJ, V. Samuel; SCANDAR, Sirle Abdo Salloum; VASAMI, Fernanda Gisele da Silva; D'AGOSTINO, Leandro Guaraglia; MAIORKA, Paulo Cesar; DENG, Xutao; NOGUEIRA, Mauricio Lacerda; SABINO, Ester Cerdeira; DELWART, Eric; LEAL, Elcio; CUNHA, Mariana SequetinClassical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiacu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3 ' UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
- First Detection of DS-1-like G1P[8] Double-gene Reassortant Rotavirus Strains on The American Continent, Brazil, 2013(2019) LUCHS, Adriana; COSTA, Antonio Charlys da; CILLI, Audrey; KOMNINAKIS, Shirley Cavalcante Vasconcelos; CARMONA, Rita de Cassia Compagnoli; MORILLO, Simone Guadagnucci; SABINO, Ester Cerdeira; TIMENETSKY, Maria do Carmo Sampaio TavaresEmergence of DS-1-like-G1P[8] rotavirus in Asia have been recently reported. We report for the first time the detection and the whole genome phylogenetic analysis of DS-1-like-G1P[8] strains in America. From 2013 to 2017, a total of 4226 fecal samples were screened for rotavirus by ELISA, PAGE, RT-PCR and sequencing. G1P[8] represented 3.7% (30/800) of all rotavirus-positive samples. DS-1-like-G1P[8] comprised 1.6% (13/800) detected exclusively in 2013, and Wa-like-G1P[8] comprised 2.1% (17/800) detected from 2013 to 2015. Whole genome sequencing confirmed the DS-1-like backbone I2-R2-C2-M2-A2-N2-T2-E2-H2. All genome segments of the Brazilian DS-1-like-G1P[8] strains clustered with those of Asian strains, and apart from African DS-1-like-G1P[8] strains. In addition, Brazilian DS-1-likeG1P[8] reassortants distantly clustered with DS-1-like backbone strains simultaneously circulating in the country, suggesting that the Brazilian DS-1-like-G1P[8] strains are likely imported from Asia. Two distinct NSP4 E2 genotype lineages were also identified, indicating the existence of a co-circulating pool of different DS-1-like G1P[8] strains. Surveillance systems must be developed to examine if RVA vaccines are still effective for the prevention against unusual DS-1-like-G1P[8] strains.