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
45 resultados
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- Wuhan large pig roundworm virus identified in human feces in Brazil(2018) LUCHS, Adriana; LEAL, Elcio; KOMNINAKIS, Shirley Vasconcelos; MILAGRES, Flavio Augusto de Padua; BRUSTULIN, Rafael; TELES, Maria da Aparecida Rodrigues; GILL, Danielle Elise; DENG, Xutao; DELWART, Eric; SABINO, Ester Cerdeira; COSTA, Antonio Charlys daWe report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98-99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.
- 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.
- Detection of human norovirus using next generation sequencing: Strain diversity and expanding whole-genome sequences availability from Brazil(2020) TINKER, R.; COSTA, A. C. Da; LEAL, E.; TAHMASEBI, R.; MILAGRES, F.; BRUSTULIN, R.; TELES, M. D. A. R.; LOBATO, M. C. A. B. S.; CHAGAS, R. T. Das; ABRAO, M. D. F. N. D. S.; SOARES, C. V. D. D. A.; DENG, X.; DELWART, E.; SABINO, E. C.; LUCHS, A.
- 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.
- Human sapovirus GI.2 and GI.3 from children with acute gastroenteritis in northern Brazil(2019) CILLI, Audrey; LUCHS, Adriana; LEAL, Elcio; GILL, Danielle; MILAGRES, Flavio Augusto de Padua; KOMNINAKIS, Shirley Vasconcelos; BRUSTULIN, Rafael; TELES, Maria da Aparecida Rodrigues; LOBATO, Marcia Cristina Alves Brito Sayao; CHAGAS, Rogerio Togisaki das; ABRAO, Maria de Fatima Neves dos Santos; SOARES, Cassia Vitoria de Deus Alves; DENG, Xutao; DELWART, Eric; SABINO, Ester Cerdeira; COSTA, Antonio Charlys daHuman sapoviruses (HSaV) are considered important causative agents of acute gastroenteritis in humans worldwide. However, knowledge of the genetic characteristics of the whole genome of HSaV in Brazil is limited. Here we report the complete genome sequences of six HSaVs GI.2 and two GI.3 strains obtained from children with acute gastroenteritis in the Northern region of Brazil. Next generation sequencing was used to obtain the full genome and molecular characterization of the genome was performed. Phylogenetic analysis of the genome was also performed. Only one complete HSaV GI.2 genome characterization in the country precedes that of the present study. This is the first complete genome sequence of genotype GI.3 in Brazil. The data obtained in this investigation can contribute to the augmentation of the database on the molecular diversity of HSaVs strains circulating in Brazil, and to the improvement of current typing protocols.
- 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.
- Identification of bacteriophages in the vagina of pregnant women: a descriptive study(2021) COSTA, A. C. da; MORON, A. F.; FORNEY, L. J.; LINHARES, I. M.; SABINO, E.; COSTA, S. F.; MENDES-CORREA, M. C.; WITKIN, S. S.Objective To determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women. Design Descriptive, observational cohort study. Setting Sao Paulo, Brazil. Population Pregnant women at 21-24 weeks' gestation. Methods Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analysed for phages by metagenomic sequencing. Main outcome measures Identification of phage families, genera and species. Results Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), three families in 20 women (18.7%), two families in 31 women (29.1%) and one family in 31 women (29.1%). The most common phage species detected wereBacillusphages in 48 (43.6%),Escherichiaphages in 45 (40.9%),Staphylococcusphages in 40 (36.4%),Gokushovirusin 33 (30.0%) andLactobacillusphages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina. Conclusions Multiple phages are present in the vagina of most mid-trimester pregnant women. Tweetable abstract Bacteriophages are present in the vagina of most pregnant women.
- Detection of RNA-Dependent RNA Polymerase of Hubei Reo-Like Virus 7 by Next-Generation Sequencing in Aedes aegypti and Culex quinquefasciatus Mosquitoes from Brazil(2019) RIBEIRO, Geovani de Oliveira; MONTEIRO, Fred Julio Costa; REGO, Marlisson Octavio da S.; RIBEIRO, Edcelha Soares D'Athaide; CASTRO, Daniela Funayama de; CASEIRO, Marcos Montani; MARINHO, Robson dos Santos Souza; KOMNINAKIS, Shirley Vasconcelos; WITKIN, Steven S.; DENG, Xutao; DELWART, Eric; SABINO, Ester Cerdeira; COSTA, Antonio Charlys da; LEAL, ElcioAdvancements in next-generation sequencing and bioinformatics have expanded our knowledge of the diversity of viruses (pathogens and non-pathogens) harbored by mosquitoes. Hubei reo-like virus 7 (HRLV 7) was recently detected by the virome analysis of fecal samples from migratory birds in Australia. We now report the detection of RNA-dependent RNA polymerase sequences of HRLV 7 in pools of Aedes aegypti and Culex quinquefasciatus mosquitoes species from the Brazilian Amazon forest. Phylogenetic inferences indicated that all HRLV 7 strains fall within the same independent clade. In addition, HRLV 7 shared a close ancestral lineage with the Dinovernavirus genus of the Reoviridae family. Our findings indicate that HRLV 7 is present in two species of mosquitoes.
- 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.
- Detection and characterization of Ilheus and Iguape virus genomes in historical mosquito samples from Southern Brazil(2020) CUNHA, Mariana Sequetin; LUCHS, Adriana; COSTA, Antonio Charlys da; RIBEIRO, Geovani de Oliveira; SANTOS, Fabiana Cristina Pereira dos; NOGUEIRA, Juliana Silva; KOMNINAKIS, Shirley Vasconcelos; MARINHO, Robson dos Santos Souza; WITKIN, Steven S.; VILLANOVA, Fabiola; DENG, Xutao; SABINO, Ester Cerdeira; DELWART, Eric; LEAL, Elcio; NOGUEIRA, Mauricio Lacerda; MAIORKA, Paulo CesarIn Brazil, flaviviruses have caused massive outbreaks. Surveillance programs designed to monitor virus activity in vectors provides a system for mapping disease distribution and for identifying specific vector species for targeted control. The present study aimed to describe the detection, whole genome characterization and phylogenetic analysis of Ilheus virus (ILHV) and Iguape virus (IGUV) strains obtained from historical mosquito's samples. Twelve isolates of pooled mosquito specimens (inoculated in neonate mouse brain) collected in the state of Sao Paulo, Brazil, in 1993, 1994 and 1997 were investigated. Viral RNA was extracted and analyzed by qRT-PCR using Flavivirus genus-specific primers. Positive samples were sequenced and underwent phylogenetic analyses. Flavivirus was detected in 50% of the specimens. Positive samples were successfully Sanger sequenced. Three Anopholes cruzii pools collected in 1994 were positive for IGUV. One Culex sp. pool, one Anopheles triannulatus pool, and one Coquillettidia juxtamansonia pool, collected in 1994, were positive for ILHV. Metagenomic sequencing successfully characterize one ILHV and four IGUV full genomes, and revealed a high degree of homology between the Brazilian ILHV and IGUV strains and isolates available in GenBank. Phylogenetic analysis of partial ILHV NS5 gene revealed three distinct lineages (clades), an indication of genetic heterogeneity in strains circulating in Brazil. Nucleotide insertions and a high-level of nucleotide diversity were observed in the NS1 protein and capsid region of IGUV strains, respectively. Detection of ILHV and IGUV in mosquitoes from Southeastern Brazil confirms the historical circulation of these viruses in this area. Furthermore, this first evidence of ILHV in Anopheles triannulatus suggests the potential importance of Anopheles mosquitoes in the IGUV transmission cycle. Genomic and phylogenetic analysis of these viruses provided insights into their diversity and evolution, which are important for the emergence patterns of flaviviruses and their evolutionary trends in Brazil, an endemic country for several arbovirus. in In-depth studies of ILHV and IGUV including vector competence and molecular studies are needed to shed light on their epidemiology and potential risk of future emergence.