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
12 resultados
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- 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.
- Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats(2024) COUTO, Roseane da Silva; RAMOS, Endrya do Socorro Foro; ABREU, Wandercleyson Uchoa; RODRIGUES, Luis Reginaldo Ribeiro; MARINHO, Luis Fernando; MORAIS, Vanessa dos Santos; VILLANOVA, Fabiola; PANDEY, Ramendra Pati; DENG, Xutao; DELWART, Eric; COSTA, Antonio Charlys da; LEAL, ElcioThe Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
- Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics(2020) TAHMASEBI, Roozbeh; LUCHS, Adriana; TARDY, Kaelan; HEFFORD, Philip Michael; TINKER, Rory J.; EILAMI, Owrang; MILAGRES, Flavio Augusto de Padua; BRUSTULIN, Rafael; TELES, Maria da Aparecida Rodrigues; MORAIS, Vanessa dos Santos; MOREIRA, Carlos Henrique Valente; BUCCHERI, Renata; ARAUJO, Emerson Luiz Lima; VILLANOVA, Fabiola; DENG, Xutao; SABINO, Ester Cerdeira; DELWART, Eric; LEAL, Elcio; COSTA, Antonio Charlys daHuman enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8% (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9% (55/251) of samples and mixed infections in 37.4% (94/251), with RVA/HAdV-F being the most frequent association (21.5%; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.
- Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA(2022) Himanshu; PRUDENCIO, Carlos R.; COSTA, Antonio Charlys da; LEAL, Elcio; CHANG, Chung-Ming; PANDEY, Ramendra PatiSince the discovery of antibiotics in the 20th century, they have been used to fight against infections. The overuse of antibiotics in the wider environment has resulted in the emergence of multidrug-resistant bacteria. In developing countries such as China and developed countries such as the USA, there is evidence of the high pervasiveness of antibiotic-resistant infections. However, the studies on the spread of antibiotic-resistant microorganisms that inform about the consequences are limited. The aim of our study was to analyze and compare antimicrobial resistance (AMR) identified in published research papers from that found in different food sources, which were published between 2012 and December 2021, covering most retail food items. Out of 132 research papers identified, 26 papers have met our strict criteria and are included in the qualitative and quantitative analysis. The selected papers led to 13,018 food samples, out of which 5000 samples were contaminated, including 2276 and 2724 samples from China and the USA, respectively. Meat, aquatic products, milk, and eggs show high to medium potential for AMR exposure to Gram-positive bacteria such as Staphylococcus, Enterococci, etc. and Gram-negative foodborne pathogens such as Campylobacter, Salmonella, Vibrio, etc. Most of the food samples show antibiotic resistance to beta-lactams, tetracycline, quinolones, and aminoglycosides. Retail food products such as meat, sea food, and some other food products, as well as AMR genetics and technically important bacteria, are proposed to be better merged with mitigation strategies and systematic One Health AMR surveillance to minimize the knowledge gaps and facilitate comprehensive AMR risk computation for the consumers.
- Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016(2021) LUCHS, Adriana; TARDY, Kaelan; TAHMASEBI, Roozbeh; MORILLO, Simone Guadagnucci; MILAGRES, Flavio Augusto de Padua; MORAIS, Vanessa dos Santos; BRUSTULIN, Rafael; TELES, Maria da Aparecida Rodrigues; AZEVEDO, Lais Sampaio de; SOUZA, Ellen Viana de; MEDEIROS, Roberta Salzone; SOUZA, Yasmin Franca Viana Pires de; ARAUJO, Emerson Luiz Lima; WITKIN, Steven S.; DENG, Xutao; DELWART, Eric; SABINO, Ester Cerdeira; LEAL, Elcio; COSTA, Antonio Charlys daThis study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.
- Detection of Hepatitis E Virus Genotype 3 in Feces of Capybaras (Hydrochoeris hydrochaeris) in Brazil(2023) CUNHA, Lia; LUCHS, Adriana; AZEVEDO, Lais S. S.; SILVA, Vanessa C. M.; LEMOS, Marcilio F. F.; COSTA, Antonio C. C.; COMPRI, Adriana P. P.; FRANCA, Yasmin; VIANA, Ellen; MALTA, Fernanda; MEDEIROS, Roberta S. S.; GUIDUCCI, Raquel; MORILLO, Simone G. G.; GOMES-GOUVEA, Michele S. S.; AMGARTEN, Deyvid; PINHO, Joao R. R.; MOREIRA, Regina C. C.Hepatitis E virus (HEV) is an emerging zoonotic pathogen associated with relevant public health issues. The aim of this study was to investigate HEV presence in free-living capybaras inhabiting urban parks in Sao Paulo state, Brazil. Molecular characterization of HEV positive samples was undertaken to elucidate the genetic diversity of the virus in these animals. A total of 337 fecal samples were screened for HEV using RT-qPCR and further confirmed by conventional nested RT-PCR. HEV genotype and subtype were determined using Sanger and next-generation sequencing. HEV was detected in one specimen (0.3%) and assigned as HEV-3f. The IAL-HEV_921 HEV-3f strain showed a close relationship to European swine, wild boar and human strains (90.7-93.2% nt), suggesting an interspecies transmission. Molecular epidemiology of HEV is poorly investigated in Brazil; subtype 3f has been reported in swine. This is the first report of HEV detected in capybara stool samples worldwide.
- Full genotype characterization of Brazilian canine G3P[3] strains during a 10-year survey (2012-2021) of rotavirus infection in domestic dogs and cats(2023) AZEVEDO, Lais Sampaio; COSTA, Fernanda Faria; GHANI, Monique Beerens Abdul; VIANA, Ellen; FRANCA, Yasmin; MEDEIROS, Roberta Salzone; GUIDUCCI, Raquel; MORILLO, Simone Guadagnucci; PRIMO, Dieli; LOPES, Ricardo Duarte; GOMES-GOUVEA, Michele Soares; COSTA, Antonio Charlys da; LUCHS, AdrianaThere is a dearth of information on the molecular epidemiology of rotaviruses in pets in Brazil. The aim of this study was to monitor rotavirus infections in household dogs and cats, determine full-genotype constellations, and obtain data on evolutionary relationships. Between 2012 and 2021, 600 fecal samples from dogs and cats (516 and 84, respectively) were collected at small animal clinics in Sao Paulo state, Brazil. Rotavirus screening was conducted using ELISA, PAGE, RT-PCR, sequencing, and phylogenetic analysis. Rotavirus type A (RVA) was detected in 0.5% (3/600) of the animals. No non-RVA types were detected. The three canine RVA strains were found to have a novel genetic constellation, G3-P[3] -I2-R3-C2-M3-A9-N2-T3-E3-H6, which has never been reported in dogs. As expected, all of the viral genes, except those encoding NSP2 and VP7, were closely related to the corresponding genes from canine, feline, and canine-like-human RVA strains. A novel N2 (NSP2) lineage was identified, grouping together Brazilian canine, human, rat and bovine strains, suggesting that genetic reassortment had occurred. Uruguayan G3 strains obtained from sewage contained VP7 genes that were phylogenetically close to those of the Brazilian canine strains, which suggests that these strains are widely distributed in pet populations in South American countries. For the NSP2 (I2), NSP3 (T3), NSP4 (E3), NSP5 (H6), VP1 (R3), VP3 (M3), and VP6 (I2) segments, phylogenetic analysis revealed possibly new lineages. The epidemiological and genetic data presented here point out the necessity for collaborative efforts to implement the One Health strategy in the field of RVA research and to provide an updated understanding of RVA strains circulating canines in Brazil.
- Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil and identification of potential genetic variants(2019) LUCHS, Adriana; COSTA, Antonio Charlys da; CILLI, Audrey; KOMNINAKIS, Shirley Cavalcante Vasconcelos; CARMONA, Rita de Cassia Compagnoli; BOEN, Lais; MORILLO, Simone Guadagnucci; SABINO, Ester Cerdeira; TIMENETSKY, Maria do Carmo Sampaio TavaresIn 2013, the equine-like G3P[8] DS-1-like rotavirus (RVA) strain emerged worldwide. In 2016, this strain was reported in northern Brazil. The aims of the study were to conduct a retrospective genetic investigation to identify the possible entry of these atypical strains in Brazil and to describe their distribution across a representative area of the country. From 2013 to 2017, a total of 4226 faecal samples were screened for RVA by ELISA, PAGE, RT-PCR and sequencing. G3P[8] represented 20.9 % (167/800) of all RVA-positive samples, further subdivided as equine-like G3P[8], DS-1-like (11.0 %; 88/800) and Wa-like G3P[8] (9.9%; 79/800). Six equine-like G3P[8] DS-1-like samples were selected for whole-genome investigation, confirming the backbone I2 R2 C2 M2 A2 N2 T2 E2 H2. During 2013-2014, Wa-like G3P[8] was predominant and no equine-like G3P[8] DS-1-like was detected. Equine-like G3P[8] DS-1-like was first identified in Parana in March/2015, suggesting that the strain entered Brazil through the Southern region. Equine-like G3P[8] rapidly spread across the area under surveillance and displayed a marked potential to replace Wa-like G3P[8] strains. Brazilian equine-like G3P[8] DS-1-like strains clustered with contemporary equine-like G3P[8] DS-1-like detected worldwide, but exhibited a distinct NSP2 genotype (N2) compared to the previously reported Amazon equine-like G3P[8] DS-1-like strain (N1). Two distinct NSP4 E2 genotype lineages were also identified. Taken together, these data suggest that different variants of equine-like G3P[8] DS-1-like strains might have been introduced into the country at distinct time points, and co-circulated in the period 2015-2017. The global emergence of equine-like G3P[8] DS-1-like strains, predominantly in countries using the Rotarix vaccine, raises the question of whether vaccines may be inducing selective pressures on zoonotic strains.
- Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis(2021) RAMOS, Endrya do Socorro Foro; RIBEIRO, Geovani de Oliveira; VILLANOVA, Fabiola; MILAGRES, Flavio Augusto de Padua; BRUSTULIN, Rafael; ARAUJO, Emerson Luiz Lima; PANDEY, Ramendra Pati; RAJ, V. Samuel; DENG, Xutao; DELWART, Eric; LUCHS, Adriana; COSTA, Antonio Charlys da; LEAL, ElcioMetagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.
- High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis(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; BERTANHE, Mayara; MARCATTI, Roberta; ARAUJO, Emerson Luiz Lima; WITKIN, Steven S.; DELWART, Eric; LUCHS, Adriana; COSTA, Antonio Charlys da; LEAL, ElcioEchoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey.