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Volumn 9, Issue 1, 2019, Pages

A method to identify respiratory virus infections in clinical samples using next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLUENZA; ISOLATION AND PURIFICATION; PROCEDURES; REPRODUCIBILITY; RESPIRATORY TRACT INFECTION; SEASON; VIROLOGY; VIRUS; VIRUS INFECTION;

EID: 85062011896     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-37483-w     Document Type: Article
Times cited : (34)

References (40)
  • 1
    • 84940376816 scopus 로고    scopus 로고
    • Planning for the Next Global Pandemic
    • Ross, A. G., Crowe, S. M. & Tyndall, M. W. Planning for the Next Global Pandemic. Int J Infect Dis 38, 89–94, 10.1016/j.ijid.2015.07.016S1201-9712(15)00183-6 (2015).
    • (2015) Int J Infect Dis , vol.38 , pp. 89-94
    • Ross, A.G.1    Crowe, S.M.2    Tyndall, M.W.3
  • 2
    • 85007185953 scopus 로고    scopus 로고
    • Planning for the unexpected: Ebola virus, Zika virus, what’s next?
    • Welfare, W. & Wright, E. Planning for the unexpected: Ebola virus, Zika virus, what’s next? Br J Hosp Med (Lond) 77, 704–707, 10.12968/hmed.2016.77.12.704 (2016).
    • (2016) Br J Hosp Med (Lond) , vol.77 , pp. 704-707
    • Welfare, W.1    Wright, E.2
  • 3
    • 0037085729 scopus 로고    scopus 로고
    • Real-time PCR in virology
    • COI: 1:CAS:528:DC%2BD38XisVaksbY%3D
    • Mackay, I. M., Arden, K. E. & Nitsche, A. Real-time PCR in virology. Nucleic Acids Res 30, 1292–1305 (2002).
    • (2002) Nucleic Acids Res , vol.30 , pp. 1292-1305
    • Mackay, I.M.1    Arden, K.E.2    Nitsche, A.3
  • 4
    • 0036080251 scopus 로고    scopus 로고
    • Viral agents as biological weapons and agents of bioterrorism
    • Bronze, M. S., Huycke, M. M., Machado, L. J., Voskuhl, G. W. & Greenfield, R. A. Viral agents as biological weapons and agents of bioterrorism. Am J Med Sci 323, 316–325, doi:S0002-9629(15)34447-5 (2002).
    • (2002) Am J Med Sci , vol.323 , pp. 316-325
    • Bronze, M.S.1    Huycke, M.M.2    Machado, L.J.3    Voskuhl, G.W.4    Greenfield, R.A.5
  • 5
    • 40449115382 scopus 로고    scopus 로고
    • A new arenavirus in a cluster of fatal transplant-associated diseases
    • Palacios, G. et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 358, 991–998, 10.1056/NEJMoa073785NEJMoa073785 (2008).
    • (2008) N Engl J Med , vol.358 , pp. 991-998
    • Palacios, G.1
  • 6
    • 57149120780 scopus 로고    scopus 로고
    • Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda
    • Towner, J. S. et al. Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 4, e1000212, 10.1371/journal.ppat.1000212 (2008).
    • (2008) PLoS Pathog , vol.4
    • Towner, J.S.1
  • 7
    • 85019741923 scopus 로고    scopus 로고
    • Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
    • Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 12, 1261–1276, 10.1038/nprot.2017.066nprot.2017.066 (2017).
    • (2017) Nat Protoc , vol.12 , pp. 1261-1276
    • Quick, J.1
  • 8
    • 79952524590 scopus 로고    scopus 로고
    • Viral metagenome analysis to guide human pathogen monitoring in environmental samples
    • Bibby, K., Viau, E. & Peccia, J. Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett Appl Microbiol 52, 386–392, 10.1111/j.1472-765X.2011.03014.x (2011).
    • (2011) Lett Appl Microbiol , vol.52 , pp. 386-392
    • Bibby, K.1    Viau, E.2    Peccia, J.3
  • 9
    • 84861571690 scopus 로고    scopus 로고
    • Application of enteric viruses for fecal pollution source tracking in environmental waters
    • Wong, K., Fong, T. T., Bibby, K. & Molina, M. Application of enteric viruses for fecal pollution source tracking in environmental waters. Environ Int 45, 151–164, 10.1016/j.envint.2012.02.009S0160-4120(12)00049-9 (2012).
    • (2012) Environ Int , vol.45 , pp. 151-164
    • Wong, K.1    Fong, T.T.2    Bibby, K.3    Molina, M.4
  • 10
    • 84861397655 scopus 로고    scopus 로고
    • Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China
    • Ge, X. et al. Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J Virol 86, 4620–4630, 10.1128/JVI.06671-11JVI.06671-11 (2012).
    • (2012) J Virol , vol.86 , pp. 4620-4630
    • Ge, X.1
  • 11
    • 64149083137 scopus 로고    scopus 로고
    • Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach
    • Nakamura, S. et al. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4, e4219, 10.1371/journal.pone.0004219 (2009).
    • (2009) PLoS One , vol.4
    • Nakamura, S.1
  • 12
    • 84857846563 scopus 로고    scopus 로고
    • Virus identification in unknown tropical febrile illness cases using deep sequencing
    • Yozwiak, N. L. et al. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6, e1485, 10.1371/journal.pntd.0001485PNTD-D-11-00551 (2012).
    • (2012) PLoS Negl Trop Dis , vol.6
    • Yozwiak, N.L.1
  • 13
    • 0033624497 scopus 로고    scopus 로고
    • Evaluation of BioStar FLU OIA assay for rapid detection of influenza A and B viruses in respiratory specimens
    • S1386653200000810
    • Hindiyeh, M. et al. Evaluation of BioStar FLU OIA assay for rapid detection of influenza A and B viruses in respiratory specimens. J Clin Virol 17, 119–126, doi:S1386653200000810 (2000).
    • (2000) J Clin Virol , vol.17 , pp. 119-126
    • Hindiyeh, M.1
  • 14
    • 77951842269 scopus 로고    scopus 로고
    • Rapid detection of influenza A pandemic (H1N1) 2009 virus neuraminidase resistance mutation H275Y by real-time reverse transcriptase PCR
    • Hindiyeh, M. et al. Rapid detection of influenza A pandemic (H1N1) 2009 virus neuraminidase resistance mutation H275Y by real-time reverse transcriptase PCR. J Clin Microbiol 48, 1884–1887, 10.1128/JCM.02540-09JCM.02540-09 (2010).
    • (2010) J Clin Microbiol , vol.48 , pp. 1884-1887
    • Hindiyeh, M.1
  • 15
    • 69149093400 scopus 로고    scopus 로고
    • In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses
    • Itoh, Y. et al. In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses. Nature 460, 1021–1025, 10.1038/nature08260nature08260 (2009).
    • (2009) Nature , vol.460 , pp. 1021-1025
    • Itoh, Y.1
  • 16
    • 0037232155 scopus 로고    scopus 로고
    • Simultaneous detection, subgrouping, and quantitation of respiratory syncytial virus A and B by real-time PCR
    • COI: 1:CAS:528:DC%2BD3sXhtFGmurw%3D
    • Hu, A., Colella, M., Tam, J. S., Rappaport, R. & Cheng, S. M. Simultaneous detection, subgrouping, and quantitation of respiratory syncytial virus A and B by real-time PCR. J Clin Microbiol 41, 149–154 (2003).
    • (2003) J Clin Microbiol , vol.41 , pp. 149-154
    • Hu, A.1    Colella, M.2    Tam, J.S.3    Rappaport, R.4    Cheng, S.M.5
  • 17
    • 33645903202 scopus 로고    scopus 로고
    • Characterization of human metapneumovirus infections in Israel
    • Regev, L. et al. Characterization of human metapneumovirus infections in Israel. J Clin Microbiol 44, 1484–1489, 10.1128/JCM.44.4.1484-1489.2006 (2006).
    • (2006) J Clin Microbiol , vol.44 , pp. 1484-1489
    • Regev, L.1
  • 18
    • 0034766782 scopus 로고    scopus 로고
    • Rapid detection of enterovirus RNA in cerebrospinal fluid specimens with a novel single-tube real-time reverse transcription-PCR assay
    • Verstrepen, W. A., Kuhn, S., Kockx, M. M., Van De Vyvere, M. E. & Mertens, A. H. Rapid detection of enterovirus RNA in cerebrospinal fluid specimens with a novel single-tube real-time reverse transcription-PCR assay. J Clin Microbiol 39, 4093–4096, 10.1128/JCM.39.11.4093-4096.2001 (2001).
    • (2001) J Clin Microbiol , vol.39 , pp. 4093-4096
    • Verstrepen, W.A.1    Kuhn, S.2    Kockx, M.M.3    Van De Vyvere, M.E.4    Mertens, A.H.5
  • 19
    • 38949154517 scopus 로고    scopus 로고
    • Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses
    • JCM.01739-0710.1128/JCM.01739-07
    • Lu, X. et al. Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses. J Clin Microbiol 46, 533–539, doi:JCM.01739-0710.1128/JCM.01739-07 (2008).
    • (2008) J Clin Microbiol , vol.46 , pp. 533-539
    • Lu, X.1
  • 20
    • 27744529987 scopus 로고    scopus 로고
    • Development of a real-time RT-PCR assay for detection and quantitation of parainfluenza virus 3
    • Hu, A. et al. Development of a real-time RT-PCR assay for detection and quantitation of parainfluenza virus 3. J Virol Methods 130, 145–148, 10.1016/j.jviromet.2005.06.014 (2005).
    • (2005) J Virol Methods , vol.130 , pp. 145-148
    • Hu, A.1
  • 21
    • 33847053190 scopus 로고    scopus 로고
    • Human respiratory coronavirus HKU1 versus other coronavirus infections in Italian hospitalised patients
    • Gerna, G. et al. Human respiratory coronavirus HKU1 versus other coronavirus infections in Italian hospitalised patients. J Clin Virol 38, 244–250, 10.1016/j.jcv.2006.12.008 (2007).
    • (2007) J Clin Virol , vol.38 , pp. 244-250
    • Gerna, G.1
  • 22
    • 0037410402 scopus 로고    scopus 로고
    • Rapid and quantitative detection of human adenovirus DNA by real-time PCR
    • Heim, A., Ebnet, C., Harste, G. & Pring-Akerblom, P. Rapid and quantitative detection of human adenovirus DNA by real-time PCR. J Med Virol 70, 228–239, 10.1002/jmv.10382 (2003).
    • (2003) J Med Virol , vol.70 , pp. 228-239
    • Heim, A.1    Ebnet, C.2    Harste, G.3    Pring-Akerblom, P.4
  • 23
    • 38149087985 scopus 로고    scopus 로고
    • High rate of human bocavirus and adenovirus coinfection in hospitalized Israeli children
    • Hindiyeh, M. Y. et al. High rate of human bocavirus and adenovirus coinfection in hospitalized Israeli children. J Clin Microbiol 46, 334–337, 10.1128/JCM.01618-07 (2008).
    • (2008) J Clin Microbiol , vol.46 , pp. 334-337
    • Hindiyeh, M.Y.1
  • 24
    • 0036308012 scopus 로고    scopus 로고
    • High TT virus load as an independent factor associated with the occurrence of hepatocellular carcinoma among patients with hepatitis C virus-related chronic liver disease
    • Tokita, H. et al. High TT virus load as an independent factor associated with the occurrence of hepatocellular carcinoma among patients with hepatitis C virus-related chronic liver disease. J Med Virol 67, 501–509, 10.1002/jmv.10129 (2002).
    • (2002) J Med Virol , vol.67 , pp. 501-509
    • Tokita, H.1
  • 25
    • 0031958794 scopus 로고    scopus 로고
    • Simultaneous detection and identification of human parainfluenza viruses 1, 2, and 3 from clinical samples by multiplex PCR
    • COI: 1:CAS:528:DyaK1cXivVWmtb8%3D, PID: 9574711
    • Echevarria, J. E., Erdman, D. D., Swierkosz, E. M., Holloway, B. P. & Anderson, L. J. Simultaneous detection and identification of human parainfluenza viruses 1, 2, and 3 from clinical samples by multiplex PCR. J Clin Microbiol 36, 1388–1391 (1998).
    • (1998) J Clin Microbiol , vol.36 , pp. 1388-1391
    • Echevarria, J.E.1    Erdman, D.D.2    Swierkosz, E.M.3    Holloway, B.P.4    Anderson, L.J.5
  • 26
    • 14844286905 scopus 로고    scopus 로고
    • Design of a multiplex PCR for Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae and Chlamydophila pneumoniae to be used on sputum samples
    • Stralin, K., Backman, A., Holmberg, H., Fredlund, H. & Olcen, P. Design of a multiplex PCR for Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae and Chlamydophila pneumoniae to be used on sputum samples. APMIS 113, 99–111, 10.1111/j.1600-0463.2005.apm1130203.x (2005).
    • (2005) APMIS , vol.113 , pp. 99-111
    • Stralin, K.1    Backman, A.2    Holmberg, H.3    Fredlund, H.4    Olcen, P.5
  • 27
    • 33645114353 scopus 로고    scopus 로고
    • PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food
    • Alarcon, B., Vicedo, B. & Aznar, R. PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food. J Appl Microbiol 100, 352–364, 10.1111/j.1365-2672.2005.02768.x (2006).
    • (2006) J Appl Microbiol , vol.100 , pp. 352-364
    • Alarcon, B.1    Vicedo, B.2    Aznar, R.3
  • 28
    • 0028948030 scopus 로고
    • PCR Amplification and Direct Sequencing of gyrB Genes with Universal Primers and Their Application to the Detection and Taxonomic Analysis of Pseudomonas putida Strains
    • COI: 1:CAS:528:DyaK2MXosFGmsb4%3D, PID: 16535156
    • Yamamoto, S. & Harayama, S. PCR Amplification and Direct Sequencing of gyrB Genes with Universal Primers and Their Application to the Detection and Taxonomic Analysis of Pseudomonas putida Strains. Appl Environ Microbiol 61, 3768 (1995).
    • (1995) Appl Environ Microbiol , vol.61 , pp. 3768
    • Yamamoto, S.1    Harayama, S.2
  • 29
    • 84887156629 scopus 로고    scopus 로고
    • Detection of influenza C virus by a real-time RT-PCR assay
    • Pabbaraju, K. et al. Detection of influenza C virus by a real-time RT-PCR assay. Influenza Other Respir Viruses 7, 954–960, 10.1111/irv.12099 (2013).
    • (2013) Influenza Other Respir Viruses , vol.7 , pp. 954-960
    • Pabbaraju, K.1
  • 30
    • 0342680132 scopus 로고    scopus 로고
    • Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR
    • COI: 1:CAS:528:DC%2BD3cXitVels7s%3D, PID: 10699020
    • Aguilar, J. C. et al. Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR. J Clin Microbiol 38, 1191–1195 (2000).
    • (2000) J Clin Microbiol , vol.38 , pp. 1191-1195
    • Aguilar, J.C.1
  • 31
    • 84892778088 scopus 로고    scopus 로고
    • Viral aetiology of acute lower respiratory tract illness in hospitalised paediatric patients of a tertiary hospital: one year prospective study
    • Singh, A. K. et al. Viral aetiology of acute lower respiratory tract illness in hospitalised paediatric patients of a tertiary hospital: one year prospective study. Indian J Med Microbiol 32, 13–18, 10.4103/0255-0857.124288IndianJMedMicrobiol_2014_32_1_13_124288 (2014).
    • (2014) Indian J Med Microbiol , vol.32 , pp. 13-18
    • Singh, A.K.1
  • 32
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359, 10.1038/nmeth.1923nmeth.1923 (2012).
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 33
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821–829, 10.1101/gr.074492.107gr.074492.107 (2008).
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 34
    • 40349087269 scopus 로고    scopus 로고
    • Metagenomic analysis of human diarrhea: viral detection and discovery
    • Finkbeiner, S. R. et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4, e1000011, 10.1371/journal.ppat.1000011 (2008).
    • (2008) PLoS Pathog , vol.4
    • Finkbeiner, S.R.1
  • 35
    • 0014622588 scopus 로고
    • A morphological study on the mechanism of diazoxide-hyperglycemia (clinical and experimental investigation)
    • COI: 1:STN:280:DyaE3c%2FmtlWrtw%3D%3D, PID: 4188182
    • Yoshinaga, T. A morphological study on the mechanism of diazoxide-hyperglycemia (clinical and experimental investigation). Endokrinologie 54, 410–422 (1969).
    • (1969) Endokrinologie , vol.54 , pp. 410-422
    • Yoshinaga, T.1
  • 36
    • 84941004024 scopus 로고    scopus 로고
    • Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains
    • Fernandez, M. et al. Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains. Front Microbiol 6, 871, 10.3389/fmicb.2015.00871 (2015).
    • (2015) Front Microbiol , vol.6 , pp. 871
    • Fernandez, M.1
  • 37
    • 0036095976 scopus 로고    scopus 로고
    • TTV, a new human virus with single stranded circular DNA genome
    • Hino, S. TTV, a new human virus with single stranded circular DNA genome. Rev Med Virol 12, 151–158, 10.1002/rmv.351 (2002).
    • (2002) Rev Med Virol , vol.12 , pp. 151-158
    • Hino, S.1
  • 38
    • 84960510387 scopus 로고    scopus 로고
    • New Phylogenetic Groups of Torque Teno Virus Identified in Eastern Taiwan Indigenes
    • Hsiao, K. L., Wang, L. Y., Lin, C. L. & Liu, H. F. New Phylogenetic Groups of Torque Teno Virus Identified in Eastern Taiwan Indigenes. PLoS One 11, e0149901, 10.1371/journal.pone.0149901PONE-D-16-00358 (2016).
    • (2016) PLoS One , vol.11
    • Hsiao, K.L.1    Wang, L.Y.2    Lin, C.L.3    Liu, H.F.4
  • 39
    • 0036007482 scopus 로고    scopus 로고
    • Analysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants
    • COI: 1:CAS:528:DC%2BD38XitFSrs78%3D
    • Peng, Y. H. et al. Analysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants. Arch Virol 147, 21–41 (2002).
    • (2002) Arch Virol , vol.147 , pp. 21-41
    • Peng, Y.H.1
  • 40
    • 33748300727 scopus 로고    scopus 로고
    • High torquetenovirus loads are correlated with bronchiectasis and peripheral airflow limitation in children
    • Pifferi, M. et al. High torquetenovirus loads are correlated with bronchiectasis and peripheral airflow limitation in children. Pediatr Infect Dis J 25, 804–808, 10.1097/01.inf.0000232723.58355.f400006454-200609000-00010 (2006).
    • (2006) Pediatr Infect Dis J , vol.25 , pp. 804-808
    • Pifferi, M.1


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