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Souza LDC, Blawid R, Silva JMF, Nagata T. Human virome in nasopharynx and tracheal secretion samples. Mem Inst Oswaldo Cruz 2019; 114:e190198. [PMID: 31596309 PMCID: PMC6779266 DOI: 10.1590/0074-02760190198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/20/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of
Influenza began in 2000. Central public health laboratories use reverse
transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis
of respiratory viruses, but this protocol identifies only specific targets,
resulted in inconclusive diagnosis for many samples. Thus, high-throughput
sequencing (HTS) would be complementary method in the identification of
pathogens in inconclusive samples for RT-qPCR or other specific detection
protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in
negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR
collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016
and subjected to HTS. The results were confirmed by the multiplex PR21
RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families
Herpesviridae, Coronaviridae,
Parvoviridae and Picornaviridae, with
the emphasis on rhinoviruses. The presence of respiratory viruses in the
samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus,
enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as
well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency
of rhinovirus occurrence was confirmed in population in winter, showing its
relevance for public health.
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Affiliation(s)
- Larissa da Costa Souza
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Laboratório Central de Saúde Pública do Distrito Federal, Brasília, DF, Brasil
| | - Rosana Blawid
- Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, PE, Brasil
| | - João Marcos Fagundes Silva
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
| | - Tatsuya Nagata
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
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Guerrero-Latorre L, Romero B, Bonifaz E, Timoneda N, Rusiñol M, Girones R, Rios-Touma B. Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1334-1343. [PMID: 30248857 DOI: 10.1016/j.scitotenv.2018.07.213] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, hepatitis, meningitis, respiratory infections, among others. This study analyzes the presence of viruses in highly impacted surface waters of urban rivers using next-generation sequencing techniques. Three representative locations of urban rivers, receiving the main discharges from Quito sewerage system, were selected. Water samples of 500 mL were concentrated by skimmed-milk flocculation method and the viral nucleic acid was extracted and processed for high throughput sequencing using Illumina MiSeq. The results yielded very relevant data of circulating viruses in the capital of Ecuador. A total of 29 viral families were obtained, of which 26 species were associated with infections in humans. Among the 26 species identified, several were related to gastroenteritis: Human Mastadenovirus F, Bufavirus, Sapporovirus, Norwalk virus and Mamastrovirus 1. Also detected were: Gammapapillomavirus associated with skin infections, Polyomavirus 1 related to cases of kidney damage, Parechovirus A described as cause of neonatal sepsis with neurological affectations and Hepatovirus A, the etiologic agent of Hepatitis A. Other emergent viruses identified, of which its pathogenicity remains to be fully clarified, were: Bocavirus, Circovirus, Aichi Virus and Cosavirus. The wide diversity of species detected through metagenomics gives us key information about the public health risks present in the urban rivers of Quito. In addition, this study describes for the first time the presence of important infectious agents not previously reported in Ecuador and with very little reports in Latin America.
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Affiliation(s)
- Laura Guerrero-Latorre
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Brigette Romero
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Edison Bonifaz
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Natalia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Blanca Rios-Touma
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador.
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