Human virome in nasopharynx and tracheal secretion samples
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 targ...
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| Format: | Article |
| Language: | English |
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Fundação Oswaldo Cruz (FIOCRUZ)
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| Series: | Memorias do Instituto Oswaldo Cruz |
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| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762019000100349&lng=en&tlng=en |
| _version_ | 1797758415239380992 |
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| author | Larissa da Costa Souza Rosana Blawid João Marcos Fagundes Silva Tatsuya Nagata |
| author_facet | Larissa da Costa Souza Rosana Blawid João Marcos Fagundes Silva Tatsuya Nagata |
| author_sort | Larissa da Costa Souza |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T18:29:38Z |
| format | Article |
| id | doaj.art-0d81009e6e7b4c27b5bbc67d4be0cd59 |
| institution | Directory Open Access Journal |
| issn | 1678-8060 |
| language | English |
| last_indexed | 2024-03-12T18:29:38Z |
| publisher | Fundação Oswaldo Cruz (FIOCRUZ) |
| record_format | Article |
| series | Memorias do Instituto Oswaldo Cruz |
| spelling | doaj.art-0d81009e6e7b4c27b5bbc67d4be0cd592023-08-02T08:19:32ZengFundação Oswaldo Cruz (FIOCRUZ)Memorias do Instituto Oswaldo Cruz1678-806011410.1590/0074-02760190198S0074-02762019000100349Human virome in nasopharynx and tracheal secretion samplesLarissa da Costa SouzaRosana BlawidJoão Marcos Fagundes SilvaTatsuya NagataBACKGROUND 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.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762019000100349&lng=en&tlng=enrespiratory viruspublic healthhigh-throughput sequencingRT-qPCR |
| spellingShingle | Larissa da Costa Souza Rosana Blawid João Marcos Fagundes Silva Tatsuya Nagata Human virome in nasopharynx and tracheal secretion samples Memorias do Instituto Oswaldo Cruz respiratory virus public health high-throughput sequencing RT-qPCR |
| title | Human virome in nasopharynx and tracheal secretion samples |
| title_full | Human virome in nasopharynx and tracheal secretion samples |
| title_fullStr | Human virome in nasopharynx and tracheal secretion samples |
| title_full_unstemmed | Human virome in nasopharynx and tracheal secretion samples |
| title_short | Human virome in nasopharynx and tracheal secretion samples |
| title_sort | human virome in nasopharynx and tracheal secretion samples |
| topic | respiratory virus public health high-throughput sequencing RT-qPCR |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762019000100349&lng=en&tlng=en |
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