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Human virome in nasopharynx and tracheal secretion samples
Pós-Graduação em Biologia MicrobianaSouza, Larissa da Costa; Blawid, Rosana; Pós-Graduação em Biologia MolecularSilva, João Marcos Fagundes; Pós-Graduação em Biologia MicrobianaNagata, Tatsuya.
Affiliation
  • Pós-Graduação em Biologia MicrobianaSouza, Larissa da Costa; Universidade de Brasília. Departamento de Biologia Celular. Pós-Graduação em Biologia MicrobianaSouza, Larissa da Costa. Brasília. BR
  • Blawid, Rosana; Universidade Federal Rural de Pernambuco. Departamento de Agronomia. Recife. BR
  • Pós-Graduação em Biologia MolecularSilva, João Marcos Fagundes; Universidade de Brasília. Departamento de Biologia Celular. Pós-Graduação em Biologia MolecularSilva, João Marcos Fagundes. Brasília. BR
  • Pós-Graduação em Biologia MicrobianaNagata, Tatsuya; Universidade de Brasília. Departamento de Biologia Celular. Pós-Graduação em Biologia MicrobianaNagata, Tatsuya. Brasília. BR
Mem. Inst. Oswaldo Cruz ; 114: e190198, 2019. tab, graf
Article in English | LILACS | ID: biblio-1040605
Responsible library: BR1.1
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.
Subject(s)


Full text: Available Collection: International databases Database: LILACS Main subject: Parvoviridae / Picornaviridae / Trachea / Nasopharynx / Coronaviridae / Herpesviridae Type of study: Practice guideline / Prognostic study Limits: Humans Language: English Journal: Mem. Inst. Oswaldo Cruz Journal subject: Tropical Medicine / Parasitology Year: 2019 Document type: Article Affiliation country: Brazil Institution/Affiliation country: Universidade Federal Rural de Pernambuco/BR / Universidade de Brasília/BR

Full text: Available Collection: International databases Database: LILACS Main subject: Parvoviridae / Picornaviridae / Trachea / Nasopharynx / Coronaviridae / Herpesviridae Type of study: Practice guideline / Prognostic study Limits: Humans Language: English Journal: Mem. Inst. Oswaldo Cruz Journal subject: Tropical Medicine / Parasitology Year: 2019 Document type: Article Affiliation country: Brazil Institution/Affiliation country: Universidade Federal Rural de Pernambuco/BR / Universidade de Brasília/BR
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