Human Virome in Nasopharynx and Tracheal Secretion Samples

Overview

Journal Mem Inst Oswaldo Cruz

Specialties Parasitology
Tropical Medicine

Date 2019 Oct 10

PMID 31596309

Citations 4

Authors

Larissa da Costa Souza

Rosana Blawid

Joao Marcos Fagundes Silva

Tatsuya Nagata

Affiliations

Soon will be listed here.

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.

Citing Articles

Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.

Ogunbayo A, Sabiu S, Nyaga M J Virol Methods. 2023; 314:114677.

PMID: 36657602 PMC: 10009504. DOI: 10.1016/j.jviromet.2023.114677.

Changes in the incidence and clinical manifestations of paediatric respiratory infections of viral aetiology during the SARS-CoV-2 pandemic.

Diaz Perez D, Reina J, Arcay R, Osona B Enferm Infecc Microbiol Clin (Engl Ed). 2022; 40(8):463-464.

PMID: 35624066 PMC: 9127700. DOI: 10.1016/j.eimce.2022.05.003.

[Impact of hygienic and social distancing measures against SARS-CoV-2 on respiratory infections caused by other viruses].

Reina J, Arcay R, Busquets M, Machado H Rev Esp Quimioter. 2021; 34(4):365-370.

PMID: 33887889 PMC: 8329571. DOI: 10.37201/req/017.2021.

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?.

Desforges M, Le Coupanec A, Dubeau P, Bourgouin A, Lajoie L, Dube M Viruses. 2019; 12(1).

PMID: 31861926 PMC: 7020001. DOI: 10.3390/v12010014.

References

Moreira L, Kamikawa J, Watanabe A, Carraro E, Leal E, Arruda E . Frequency of human rhinovirus species in outpatient children with acute respiratory infections at primary care level in Brazil. Pediatr Infect Dis J. 2011; 30(7):612-4. DOI: 10.1097/INF.0b013e31820d0de3. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Menzel P, Ng K, Krogh A . Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016; 7:11257. PMC: 4833860. DOI: 10.1038/ncomms11257. View

Allander T, Tammi M, Eriksson M, Bjerkner A, Tiveljung-Lindell A, Andersson B . Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A. 2005; 102(36):12891-6. PMC: 1200281. DOI: 10.1073/pnas.0504666102. View

Fawkner-Corbett D, Khoo S, Duarte C, Bezerra P, Bochkov Y, Gern J . Rhinovirus-C detection in children presenting with acute respiratory infection to hospital in Brazil. J Med Virol. 2015; 88(1):58-63. PMC: 4682890. DOI: 10.1002/jmv.24300. View

Morens D, Folkers G, Fauci A . The challenge of emerging and re-emerging infectious diseases. Nature. 2004; 430(6996):242-9. PMC: 7094993. DOI: 10.1038/nature02759. View

Jones M, Kapoor A, Lukashov V, Simmonds P, Hecht F, Delwart E . New DNA viruses identified in patients with acute viral infection syndrome. J Virol. 2005; 79(13):8230-6. PMC: 1143717. DOI: 10.1128/JVI.79.13.8230-8236.2005. View

Yongfeng H, Fan Y, Jie D, Jian Y, Ting Z, Lilian S . Direct pathogen detection from swab samples using a new high-throughput sequencing technology. Clin Microbiol Infect. 2010; 17(2):241-4. PMC: 7129681. DOI: 10.1111/j.1469-0691.2010.03246.x. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

10.

Leotte J, Trombetta H, Faggion H, Almeida B, Nogueira M, Vidal L . Impact and seasonality of human rhinovirus infection in hospitalized patients for two consecutive years. J Pediatr (Rio J). 2016; 93(3):294-300. PMC: 7094701. DOI: 10.1016/j.jped.2016.07.004. View

11.

Allander T, Andreasson K, Gupta S, Bjerkner A, Bogdanovic G, Persson M . Identification of a third human polyomavirus. J Virol. 2007; 81(8):4130-6. PMC: 1866148. DOI: 10.1128/JVI.00028-07. View

12.

Capobianchi M, Giombini E, Rozera G . Next-generation sequencing technology in clinical virology. Clin Microbiol Infect. 2013; 19(1):15-22. DOI: 10.1111/1469-0691.12056. View

13.

Thorburn F, Bennett S, Modha S, Murdoch D, Gunson R, Murcia P . The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol. 2015; 69:96-100. PMC: 4533236. DOI: 10.1016/j.jcv.2015.06.082. View

14.

Yozwiak N, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A . Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua. J Virol. 2010; 84(18):9047-58. PMC: 2937614. DOI: 10.1128/JVI.00698-10. View

15.

Zerbino D, Birney E . Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18(5):821-9. PMC: 2336801. DOI: 10.1101/gr.074492.107. View

16.

Bellei N, Carraro E, Perosa A, Watanabe A, Arruda E, Granato C . Acute respiratory infection and influenza-like illness viral etiologies in Brazilian adults. J Med Virol. 2008; 80(10):1824-7. PMC: 7166366. DOI: 10.1002/jmv.21295. View

17.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

18.

Hung H, Yang S, Chen C, Chiu C, Kuo C, Huang K . Molecular epidemiology and clinical features of rhinovirus infections among hospitalized patients in a medical center in Taiwan. J Microbiol Immunol Infect. 2018; 52(2):233-241. DOI: 10.1016/j.jmii.2018.08.009. View

19.

de Arruda E, Hayden F, McAuliffe J, DE SOUSA M, Mota S, McAuliffe M . Acute respiratory viral infections in ambulatory children of urban northeast Brazil. J Infect Dis. 1991; 164(2):252-8. DOI: 10.1093/infdis/164.2.252. View

20.

Nishizawa T, Okamoto H, Konishi K, Yoshizawa H, Miyakawa Y, Mayumi M . A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochem Biophys Res Commun. 1998; 241(1):92-7. DOI: 10.1006/bbrc.1997.7765. View