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Protocol for Generating Infectious RNA Viromes from Complex Biological Samples

  • Sonia Monteil-Bouchard
  • Sarah Temmam
  • Christelle DesnuesEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1838)

Abstract

This chapter proposes a simple, standardized protocol for generating RNA viromes from complex host-associated biological samples of various origins. Compared to other existing protocols to generate RNA viromes, this protocol preserves the infectivity of viral particles and allows for downstream applications such as viral characterization and isolation tests.

Key words

Virome Arthropods Metagenomics RNA viruses Sucrose density gradient Viral zoonosis 

Notes

Acknowledgments

This work was supported by a grant from the Agence Nationale de la Recherche number ANR-13-JSV6-0004 to CD.

References

  1. 1.
    Jones KE, Patel NG, Levy MA et al (2008) Global trends in emerging infectious diseases. Nature 451:990–993CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Angly FE, Felts B, Breitbart M et al (2006) The marine viromes of four oceanic regions. PLoS Biol 4:e368CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Djikeng A, Kuzmickas R, Anderson NG et al (2009) Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One 4(9):e7264CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Fancello L, Trape S, Robert C et al (2013) Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME J 7:359–369CrossRefPubMedGoogle Scholar
  5. 5.
    Rosario K, Breitbart M (2011) Exploring the viral world through metagenomics. Curr Opin Virol 1:289–297CrossRefPubMedGoogle Scholar
  6. 6.
    Whon TW, Kim MS, Roh SW et al (2012) Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere. J Virol 86:8221–8231CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Barzon L, Lavezzo E, Militello V et al (2011) Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12:7861–7884CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Belák S, Karlsson OE, Blomström AL et al (2013) New viruses in veterinary medicine, detected by metagenomic approaches. Vet Microbiol 165:95–101CrossRefPubMedGoogle Scholar
  9. 9.
    Blomström AL (2011) Viral metagenomics as an emerging and powerful tool in veterinary medicine. Vet Q 31(3):107–114CrossRefPubMedGoogle Scholar
  10. 10.
    Capobianchi MR, Giombini E (2013) Rozera G (2013) next-generation sequencing technology in clinical virology. Clin Microbiol Infect 19:15–22CrossRefPubMedGoogle Scholar
  11. 11.
    Chiu CY (2013) Viral pathogen discovery. Curr Opin Microbiol 16:468–478CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Temmam S, Davoust B, Berenger JM et al (2014) Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection? Int J Mol Sci 15:10377–10397CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Conceição-Neto N, Zeller M, Lefrère H et al (2015) Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep 5:16532CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Hall RJ, Wang J, Todd AK et al (2014) Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195:194–204CrossRefPubMedGoogle Scholar
  15. 15.
    Kohl C, Brinkmann A, Dabrowski PW et al (2015) Protocol for metagenomic virus detection in clinical specimens. Emerg Infect Dis 21(1):48–57CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Lewandowska DW, Zagordi O, Geissberger F-D et al (2017) Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. Microbiome 5:94CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Li L, Deng X, Mee ET et al (2015) Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 213:139–146CrossRefPubMedGoogle Scholar
  18. 18.
    Manso CF, Bibby DF, Mbisa JL (2017) Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples. Sci Rep 7:4173CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Rosseel T, Ozhelvaci O, Freimanis G et al (2015) Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 222:72–80CrossRefPubMedGoogle Scholar
  20. 20.
    Thurber RV, Haynes M, Breitbart M et al (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4(4):470–483CrossRefPubMedGoogle Scholar
  21. 21.
    Weynberg KD, Wood-Charlson EM, Suttle CA et al (2014) Generating viral metagenomes from the coral holobiont. Front Microbiol 5:206CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Temmam S, Monteil-Bouchard S, Robert C et al (2015) Host-associated metagenomics: a guide to generating infectious RNA Viromes. PLoS One 10(10):e0139810CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Froussard P (1993) rPCR: a powerful tool for random amplification of whole RNA sequences. PCR Methods Appl 2(3):185–190CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Sonia Monteil-Bouchard
    • 1
  • Sarah Temmam
    • 2
  • Christelle Desnues
    • 1
    Email author
  1. 1.Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Assistance-Publique des Hôpitaux de Marseille, Aix-Marseille Université, CNRS 7278, IRD 198, INSERM1095MarseilleFrance
  2. 2.Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut PasteurINSERM U1117ParisFrance

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