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Mejías-Molina C, Pico-Tomàs A, Martínez-Puchol S, Itarte M, Torrell H, Canela N, Borrego CM, Corominas L, Rusiñol M, Bofill-Mas S. Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals. Hum Genomics 2024; 18:10. [PMID: 38303015 PMCID: PMC10832175 DOI: 10.1186/s40246-024-00580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome. RESULTS The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression. CONCLUSIONS This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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Coutinho CRM, Cardoso JF, Siqueira JAM, Machado RS, Chagas Júnior WDD, Tavares FN, Gabbay YB. Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019). J Med Virol 2023; 95:e28873. [PMID: 37349989 DOI: 10.1002/jmv.28873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.
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Affiliation(s)
| | - Jedson Ferreira Cardoso
- Laboratório de Bioinformática-BIOINFO, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Jones Anderson Monteiro Siqueira
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Raiana Scerni Machado
- Programa de Pós-graduação em Medicina Tropical, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Wanderley Dias das Chagas Júnior
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
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Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses 2021; 13:v13122365. [PMID: 34960634 PMCID: PMC8704738 DOI: 10.3390/v13122365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/21/2023] Open
Abstract
Metagenomics 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.
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Luchs A, Tardy K, Tahmasebi R, Morillo SG, Milagres FADP, Morais VDS, Brustulin R, Teles MDAR, de Azevedo LS, de Souza EV, Medeiros RS, de Souza YFVP, Araújo ELL, Witkin SS, Deng X, Delwart E, Sabino EC, Leal E, da Costa AC. Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016. Arch Virol 2021; 166:3165-3172. [PMID: 34417874 DOI: 10.1007/s00705-021-05206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/30/2022]
Abstract
This 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.
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Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| | - Kaelan Tardy
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Simone Guadagnucci Morillo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | | | - Lais Sampaio de Azevedo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Ellen Viana de Souza
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Roberta Salzone Medeiros
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | | | - Emerson Luiz Lima Araújo
- Coordenação Geral de Laboratórios de Saúde Pública, Departamento de Articulação Estratégica de Vigilância em Saúde da Secretaria de Vigilância em Saúde do Ministério da Saúde do Brasil (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Elcio Leal
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.
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Luchs A. Comments on "Detection and identification of enteroviruses circulating in children with acute gastroenteritis in Pará State, Northern Brazil (2010-2011)". Virol J 2021; 18:133. [PMID: 34193190 PMCID: PMC8243610 DOI: 10.1186/s12985-021-01602-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
Investigation of human enterovirus (EV) in diarrheic fecal specimens is valuable to address EV diversity circulating worldwide. However, the detection of EV strains exclusively in fecal specimens must be interpreted cautiously. EV are well known causative agents associated with a spectrum of human diseases, but not acute gastroenteritis. EV isolation in stool samples could not necessarily be associated with diarrheic symptoms, as most EV infections appear to be asymptomatic, and healthy children could excrete EV in their stool. The diagnostic of EV is only confirmed when the neutralization test presents a significant increase in antibody titers (three times or more) in the paired serum samples (acute-phase and convalescent-phase) against the same EV serotype isolated in feces. In addition, patients suffering from acute gastroenteritis, even during an EV investigation, must be screened in parallel for gastroenteric viruses (i.e. norovirus and rotavirus) in order to clarify if the symptoms could be linked to other viral agent detected in their fecal samples. Surveillance of EV diversity among distinct patient groups, including diarrheic individuals, must be taken into consideration and can considerably increase the power of non-polio EV surveillance system in Brazil. More well-designed studies are necessary to further elucidate the role of EV in acute gastroenteritis.
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Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Adolfo Lutz Institute, Virology CenterAv. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
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Villanova F, Marcatti R, Bertanhe M, Morais VDS, Milagres FADP, Brustulin R, Araújo ELL, Tahmasebi R, Witkin SS, Deng X, Delwart E, Sabino EC, Abreu-Junior CH, Leal É, da Costa AC. New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples. Microorganisms 2021; 9:microorganisms9071349. [PMID: 34206387 PMCID: PMC8307838 DOI: 10.3390/microorganisms9071349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022] Open
Abstract
Squash mosaic virus (SqMV) is a phytovirus that infects great diversity of plants worldwide. In Brazil, the SqMV has been identified in the states of Ceará, Maranhão, Piauí, Rio Grande do Norte, and Tocantins. The presence of non-pathogenic viruses in animals, such as phytoviruses, may not be completely risk-free. Similarities in gene repertories between these viruses and viruses that affect animal species have been reported. The present study describes the fully sequenced genomes of SqMV found in human feces, collected in Tocantins, and analyzes the viral profile by metagenomics in the context of diarrhea symptomatology. The complete SqMV genome was obtained in 39 of 253 analyzed samples (15.5%); 97.4% of them belonged to children under 5 years old. There was no evidence that the observed symptoms were related to the presence of SqMV. Of the different virus species detected in these fecal samples, at least 4 (rotavirus, sapovirus, norovirus, parechovirus) are widely known to cause gastrointestinal symptoms. The presence of SqMV nucleic acid in fecal samples is likely due to recent dietary consumption and it is not evidence of viral replication in the human intestinal cells. Identifying the presence of SqMV in human feces and characterization of its genome is a relevant precursor to determining whether and how plant viruses interact with host cells or microorganisms in the human gastrointestinal tract.
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Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
| | - Roberta Marcatti
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Mayara Bertanhe
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo 05508-270, SP, Brazil
| | - Vanessa dos Santos Morais
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Flavio Augusto de Padua Milagres
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Rafael Brustulin
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, DF, Brazil;
| | - Roozbeh Tahmasebi
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Steven S. Witkin
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
- Correspondence:
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
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Multiple clades of Husavirus in South America revealed by next generation sequencing. PLoS One 2021; 16:e0248486. [PMID: 33755700 PMCID: PMC7987173 DOI: 10.1371/journal.pone.0248486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/28/2021] [Indexed: 11/19/2022] Open
Abstract
Husavirus (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.
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López GR, Martinez LM, Freyre L, Freire MC, Vladimirsky S, Rabossi A, Cisterna DM. Persistent Detection of Cosavirus and Saffold Cardiovirus in Riachuelo River, Argentina. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:64-73. [PMID: 33165867 DOI: 10.1007/s12560-020-09451-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/04/2020] [Indexed: 06/11/2023]
Abstract
Cosaviruses (CoSV) and Saffold cardiovirus (SAFV) are novel members of the Picornaviridae family. The Matanza-Riachuelo river basin covers a total area of 2200 km2 with approximately 60 km long. Its last section is called Riachuelo River. The aim of this study was to describe the circulation of both picornaviruses and their relationship with the environmental situation of the Riachuelo River using 274 samples collected from 2005 to 2015. CoSV and SAFV were investigated in samples available by two periods: 2005-2006 and 2014-2015 (103 and 101, respectively). Physicochemical and bacteriological parameters confirmed very high levels of human fecal contamination during the 11 years evaluated. CoSV was detected in 85.7% (66/77) and 65.4% (17/26) of the samples collected in 2005-2006 and 2014-2015 periods, respectively. Species A and D were identified, the first one being widely predominant: 74.1% (20/27) and 75.0% (3/4) in both periods. SAFV virus was detected in 47.1% (32/68) and 52.6% (10/19) in periods 2005-2006 and 2014-2015, respectively. SAFV-6 was the most identified genotype in the entire study, while SAFV-3 was predominant in 2005-2006. The contribution of genotypes 1, 2, 4 and 8 was minor. The high prevalence of CoSV and SAFV suggests that both viruses have been circulating in Argentina at least since 2005. Our results show that a watercourse with high rates of human fecal contamination can become a persistent source of new viruses which capacity to produce human diseases is unknown.
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Affiliation(s)
- Gabriela Riviello López
- Prefectura Naval Argentina, Av. Eduardo Madero 235 (1106ACC), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Leila Marina Martinez
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Freyre
- Prefectura Naval Argentina, Av. Eduardo Madero 235 (1106ACC), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Cecilia Freire
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sara Vladimirsky
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro Rabossi
- IIBBA-CONICET and FIL, Av. Patricias Argentinas 435 (1405BWE), Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel Marcelo Cisterna
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina.
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9
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Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil. Arch Virol 2021; 166:905-913. [PMID: 33462673 DOI: 10.1007/s00705-020-04944-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/13/2020] [Indexed: 01/24/2023]
Abstract
From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.
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10
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Schneider J, Engler M, Hofmann J, Selinka HC, Jones TC, Drosten C, Diedrich S, Corman VM, Böttcher S. Molecular detection of cosaviruses in a patient with acute flaccid paralysis and in sewage samples in Germany. Virus Res 2021; 297:198285. [PMID: 33548413 DOI: 10.1016/j.virusres.2020.198285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/02/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
Cosaviruses (CoSV) were first identified in stool samples collected from non-polio acute flaccid paralysis (AFP) cases and their healthy contacts in Pakistan in 2003. The clinical importance of CoSV remains unclear as data on epidemiology are scarce and no routine diagnostic testing is done. In this study, we characterized human CoSV (HCoSV) in a child with non-polio AFP and in sewage samples collected in Berlin, Germany. Using unbiased high-throughput sequencing and specific PCR, we characterized a HCoSV-D in stool samples of a three-year-old child hospitalized in Germany with non-polio AFP and travel history to Pakistan. The shedding pattern and absence of other relevant pathogens suggests that HCoSV-D may have been involved in the genesis of AFP. The HCoSV-RNA concentration was high, with 2.57 × 106 copies per mL fecal/suspension, decreasing in follow-up samples. To investigate the possibility of local circulation of HCoSV, we screened Berlin sewage samples collected between 2013 and 2018. Molecular testing of sewage samples has shown the presence of CoSV in several parts of the world, but until now not in Germany. Of our sewage samples, 54.3 % were positive for CoSV, with up to three viral species identified in samples. Phylogenetically, the German sequences clustered intermixed with sequences obtained globally. Together, these findings emphasize the need for further clinical, epidemiological, environmental, pathogenicity and phylogenetic studies of HCoSV.
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Affiliation(s)
- J Schneider
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - M Engler
- Department of Paediatrics, Sana Klinikum Offenbach GmbH, Starkenburgring 66, 63069, Offenbach am Main, Germany
| | - J Hofmann
- Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - H C Selinka
- German Environment Agency, Microbiological Risks, Corrensplatz 1, 14195, Berlin, Germany
| | - T C Jones
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - C Drosten
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany
| | - S Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
| | - V M Corman
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany.
| | - S Böttcher
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany.
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11
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Tahmasebi R, Luchs A, Tardy K, Hefford PM, Tinker RJ, Eilami O, de Padua Milagres FA, Brustulin R, Teles MDAR, Dos Santos Morais V, Moreira CHV, Buccheri R, Araújo ELL, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Charlys da Costa A. Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics. J Gen Virol 2020; 101:1280-1288. [PMID: 33044150 DOI: 10.1099/jgv.0.001500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human 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.
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Affiliation(s)
- Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Kaelan Tardy
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Rory J Tinker
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Owrang Eilami
- School of Medicine Social, Determinants of Health Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil
| | | | | | | | - Renata Buccheri
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, DF, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
| | - Xutao Deng
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
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12
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Lobo PS, Cardoso JF, Barata RR, Lemos PS, Guerra SFS, Soares LS, Nunes MRT, Mascarenhas JDP. Near-complete genome of cosavirus A from a child hospitalized with acute gastroenteritis, Brazil. INFECTION GENETICS AND EVOLUTION 2020; 85:104555. [PMID: 32931954 DOI: 10.1016/j.meegid.2020.104555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 11/25/2022]
Abstract
Acute gastroenteritis (AG) is responsible for 525,000 deaths worldwide in children under-5-years and is caused by the Human Cosavirus (HCoSV; family Picornaviridae, Genus Cosavirus). Although its health importance, a significant percentage of diarrhea cases (≈ 40 %) still of unknown etiology. In Brazil, few studies have reported HCoSV-A sequences analyzing partial 5' UTR. This study characterized the first near-complete genome of a Cosavirus A (strain AM326) from a child hospitalized with AG in Amazonas state, Northern Brazil. High throughput sequencing (HTS) was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of the Evandro Chagas Institute collected in 2017. Sequence reads were assembled by the De Novo approach using three distinct algorithmic (IDBA-UD, Spades, and MegaHit). The final contig was recovered from the HCoSV-AM326 sample revealing 7,735 nt in length (SRA number SRR12535029; GenBank MT023104) and the genetic characterization, as well as phylogenetic analysis demonstrated a new variant strain from Brazil, highlighting the association of HCoSV-A as a possible causative agent of AG. This finding demonstrates the importance of the metagenomic approach to elucidate cases of diarrhea without a defined etiology, as well as providing a better understanding about the virus genetics, evolution and epidemiology.
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Affiliation(s)
- Patrícia S Lobo
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Jedson F Cardoso
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Rafael R Barata
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Poliana S Lemos
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Sylvia F S Guerra
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Luana S Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Márcio R T Nunes
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Joana D P Mascarenhas
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil.
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13
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Tahmasebi R, da Costa AC, Tardy K, J. Tinker R, de Padua Milagres FA, Brustulin R, Rodrigues Teles MDA, Togisaki das Chagas R, de Deus Alves Soares CV, Sakurada Aranha Watanabe A, Salete Alencar C, Villanova F, Deng X, Delwart E, Luchs A, Leal É, Cerdeira Sabino E. Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil. Viruses 2020; 12:v12050508. [PMID: 32375411 PMCID: PMC7290489 DOI: 10.3390/v12050508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Human Adenovirus species C (HAdV-C) is the most common etiologic agent of respiratory disease. In the present study, we characterized the nearly full-length genome of one potential new HAdV-C recombinant strain constituted by Penton and Fiber proteins belonging to type 89 and a chimeric Hexon protein of types 1 and 89. By using viral metagenomics techniques, we screened out, in the states of Tocantins and Pará, Northern and North regions of Brazil, from 2010 to 2016, 251 fecal samples of children between 0.5 to 2.5 years old. These children were presenting acute diarrhea not associated with common pathogens (i.e., rotavirus, norovirus). We identified two HAdV-C strains in two distinct patients. Phylogenetic analysis performed using all complete genomes available at GenBank database indicated that one strain (HAdV-C BR-245) belonged to type 1. The phylogenetic analysis also indicated that the second strain (HAdV-C BR-211) was located at the base of the clade formed by the newly HAdV-C strains type 89. Recombination analysis revealed that strain HAdV-C BR-211 is a chimera in which the variable regions of Hexon gene combined HAdV-C1 and HAdV-C89 sequences. Therefore, HAdV-C BR-211 strain possesses a genomic backbone of type HAdV-C89 and a unique insertion of HAdV-C1 in the Hexon sequence. Recombination may play an important driving force in HAdV-C diversity and evolution. Studies employing complete genomic sequencing on circulating HAdV-C strains in Brazil are needed to understand the clinical significance of the presented data.
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Affiliation(s)
- Roozbeh Tahmasebi
- Polytechnic School of University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Antonio Charlys da Costa
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Kaelan Tardy
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Rory J. Tinker
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Flavio Augusto de Padua Milagres
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Rafael Brustulin
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil
| | - Maria da Aparecida Rodrigues Teles
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Rogério Togisaki das Chagas
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Cassia Vitória de Deus Alves Soares
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | | | - Cecilia Salete Alencar
- Central Laboratory Division-DLC-HCSP, Clinical Laboratory and LIM 03-Department of Pathology, Clinical Hospital, University of Sao Paulo Medical School, Sao Paulo 01246-000, Brazil;
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para 66075-000, Brazil;
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-000, Brazil;
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para 66075-000, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Ester Cerdeira Sabino
- Polytechnic School of University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
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14
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Rosa UA, Ribeiro GDO, Villanova F, Luchs A, Milagres FADP, Komninakis SV, Tahmasebi R, Lobato MCABS, Brustulin R, Chagas RTD, Abrão MDFNDS, Soares CVDDA, Tinker RJ, Pandey RP, Raj VS, Sabino EC, Deng X, Delwart E, Costa ACD, Leal É. First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil. Sci Rep 2019; 9:18599. [PMID: 31819139 PMCID: PMC6901473 DOI: 10.1038/s41598-019-55216-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/11/2019] [Indexed: 01/26/2023] Open
Abstract
Diarrhea remains one of the most common causes of deaths in children. Although many studies have investigated the prevalence of enteric pathogens around the globe some diarrheal episodes remain unexplained. It is possible that some yet-unidentified viral agents could be related to these cases of gastroenteritis. By using viral metagenomics techniques, we screened 251 fecal samples of children between 0.5 to 2.5-year-old with acute diarrhea not associated with common pathogens. These children live in rural areas and have different levels of contact with animals such as pigs, cows and bats. Here we report a complete genome of one mammalian orthoreovirus (MRV) type 3, denoted TO-151/BR, detected in a female child in the state of Tocantins (north of Brazil). Brazilian TO-151/BR strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strains. Phylogenetic analyses showed that other segments were more similar to MRV-3s of different geographic locations and hosts, including human and bats, highlighting genome reassortment and lack of host-specific barriers. This is the first report of MRV-3 in South America and a hypothesis of a silent long-term circulation of this virus in Brazil has been raised.
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Affiliation(s)
- Ulisses Alves Rosa
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil
| | | | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, 01246-000, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, 77001-090, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André, 09060-870, Brazil.,Retrovirology Laboratory, Federal University of São Paulo, São Paulo, 04023-062, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | | | - Rafael Brustulin
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, 77001-090, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Rogério Togisaki das Chagas
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | | | - Cassia Vitória de Deus Alves Soares
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Rory J Tinker
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, 131 029, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, 131 029, Haryana, India
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,LIM/46, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 01246-903, Brazil
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94143, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94143, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil.
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15
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Osundare FA, Opaleye OO, Akindele AA, Adedokun SA, Akanbi OA, Bock CT, Diedrich S, Böttcher S. Detection and Characterization of Human Enteroviruses, Human Cosaviruses, and a New Human Parechovirus Type in Healthy Individuals in Osun State, Nigeria, 2016/2017. Viruses 2019; 11:E1037. [PMID: 31703317 PMCID: PMC6893832 DOI: 10.3390/v11111037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Human enteroviruses and human parechoviruses are associated with a broad range of diseases and even severe and fatal conditions. For human cosaviruses, the etiological role is yet unknown. Little is known about the circulation of non-polio enteroviruses, human parechoviruses, and human cosaviruses in Nigeria. A total of 113 stool samples were collected from healthy individuals in Osun State between February 2016 and May 2017. RT-PCR assays targeting the 5' non-coding region (5' -NCR) were used to screen for human enteroviruses, human parechoviruses, and human cosaviruses. For human enteroviruses, species-specific RT-PCR assays targeting the VP1 regions were used for molecular typing. Inoculation was carried out on RD-A, CaCo-2, HEp-2C, and L20B cell lines to compare molecular and virological assays. Ten samples tested positive for enterovirus RNA with 11 strains detected, including CV-A13 (n = 3), E-18 (n = 2), CV-A20 (n = 1), CV-A24 (n = 1), EV-C99 (n = 1), and EV-C116 (n = 2). Three samples tested positive for human parechovirus RNA, and full genome sequencing on two samples allowed assignment to a new Parechovirus A type (HPeV-19). Thirty-three samples tested positive for cosavirus with assignment to species Cosavirus D and Cosavirus A based on the 5'-NCR region. Screening of stool samples collected from healthy individuals in Nigeria in 2016 and 2017 revealed a high diversity of circulating human enteroviruses, human parechoviruses, and human cosaviruses. Molecular assays for genotyping showed substantial benefits compared with those of cell-culture assays.
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Affiliation(s)
- Folakemi Abiodun Osundare
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo 230222, Nigeria; (F.A.O.); (O.O.O.); (A.A.A.); (S.A.A.); (O.A.A.)
- Science Laboratory Technology Department, Federal Polytechnic, Ede 232101, Nigeria
| | - Oladele Oluyinka Opaleye
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo 230222, Nigeria; (F.A.O.); (O.O.O.); (A.A.A.); (S.A.A.); (O.A.A.)
- Department of Infectious Diseases, Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany
| | - Akeem Abiodun Akindele
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo 230222, Nigeria; (F.A.O.); (O.O.O.); (A.A.A.); (S.A.A.); (O.A.A.)
| | - Samuel Adeyinka Adedokun
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo 230222, Nigeria; (F.A.O.); (O.O.O.); (A.A.A.); (S.A.A.); (O.A.A.)
| | - Olusola Anuoluwapo Akanbi
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo 230222, Nigeria; (F.A.O.); (O.O.O.); (A.A.A.); (S.A.A.); (O.A.A.)
- Department of Infectious Diseases, Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany
| | - Claus-Thomas Bock
- Department of Infectious Diseases, Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany
- Institute of Tropical Medicine, University of Tuebingen, 72074 Tuebingen, Germany
| | - Sabine Diedrich
- National Reference Center for Polioviruses and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | - Sindy Böttcher
- National Reference Center for Polioviruses and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
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16
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Okitsu S, Khamrin P, Takanashi S, Thongprachum A, Hoque SA, Takeuchi H, Khan MA, Hasan SMT, Iwata T, Shimizu H, Jimba M, Hayakawa S, Maneekarn N, Ushijima H. Molecular detection of enteric viruses in the stool samples of children without diarrhea in Bangladesh. INFECTION GENETICS AND EVOLUTION 2019; 77:104055. [PMID: 31629889 DOI: 10.1016/j.meegid.2019.104055] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/25/2019] [Accepted: 09/29/2019] [Indexed: 12/14/2022]
Abstract
A number of molecular epidemiological studies reported the detection of enteric viruses in asymptomatic children. The role of these viruses in an asymptomatic infection remains unclear. This study investigated the enteric viruses in the stool samples collected from children without diarrhea. Stool samples were collected during June to October 2016, from 227 children who lived in Matlab, Bangladesh. Seventeen enteric viruses, including rotavirus A, B, and C (RVA, RVB, and RVC), norovirus GI (NoV GI), norovirus GII (NoV GII), sapovirus (SaV), adenovirus (AdV), human astrovirus (HAstV), Aichivirus (AiV), human parechovirus (HPeV), enterovirus (EV), human bocavirus (HBoV), Saffold virus (SAFV), human cosavirus (HCoSV), bufavirus (BufV), salivirus (SalV), and rosavirus (RoV), were investigated by RT-PCR method. One hundred and eighty-two (80.2%; 182/227) samples were positive for some of these viruses, and 19.8% (45/227) were negative. Among the positive samples, 46.7% (85/182) were a single infection, and 53.3% (97/182) were coinfection with multiple viruses. The HCoSV was the most prevalent virus (41.4%), followed by EV (32.2%), NoV GII (25.6%), HPeV (8.8%), RVA (6.2%), AdV (5.7%), AiV (5.3%), SAFV (4.4%), and SaV (2.6%). Each of NoV GI, HAstV, HBoV, and BufV was detected at 0.4%. However, RVB, RVC, SalV, and RoV were not detected in this study. Phylogenetic analysis showed that diverse HCoSV species and genotypes were circulating in Bangladesh, and four strains of species A are proposed to be new genotypes. The data indicated that non-diarrheal Bangladeshi children were asymptomatically infected with wide varieties of enteric viruses.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Japan; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan.
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan
| | | | - Sheikh Ariful Hoque
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Haruko Takeuchi
- Department of Community and Global Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Md Alfazal Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - S M Tafsir Hasan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Japan
| | - Masamine Jimba
- Department of Community and Global Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Japan; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan
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17
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Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil. Viruses 2019; 11:v11060488. [PMID: 31146371 PMCID: PMC6630568 DOI: 10.3390/v11060488] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023] Open
Abstract
We characterized the 24 nearly full-length genomes of human parechoviruses (PeV) from children in the north of Brazil. The initial phylogenetic analysis indicated that 17 strains belonged to genotype 1, 5 to genotype 4, and 1 to genotype 17. A more detailed analysis revealed a high frequency of recombinant strains (58%): A total of 14 of our PeV-As were chimeric, with four distinct recombination patterns identified. Five strains were composed of genotypes 1 and 5 (Rec1/5); five strains shared a complex mosaic pattern formed by genotypes 4, 5, and 17 (Rec4/17/5); two strains were composed of genotypes 1 and 17 (Rec1/17); and two strains were composed of genotype 1 and an undetermined strain (Rec1/und). Coalescent analysis based on the Vp1 gene, which is free of recombination, indicated that the recombinant strains most likely arose in this region approximately 30 years ago. They are present in high frequencies and are circulating in different small and isolated cities in the state of Tocantins. Further studies will be needed to establish whether the detected recombinant strains have been replacing parental strains or if they are co-circulating in distinct frequencies in Tocantins.
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