Metagenomic Approaches to Disclose Disease-Associated Pathogens: Detection of Viral Pathogens in Honeybees

  • Fredrik Granberg
  • Oskar E. Karlsson
  • Sándor Belák
Part of the Methods in Molecular Biology book series (MIMB, volume 1247)


Metagenomic approaches have become invaluable for culture-independent and sequence-independent detection and characterization of disease-associated pathogens. Here, the sequential steps from sampling to verification of results are described for a metagenomic-based approach to detect potential pathogens in honeybees. The pre-sequencing steps are given in detail, but due to the rapid development of sequencing technologies, all platform-specific procedures, as well as subsequent bioinformatics analysis, are more generally described. It should also be noted that this approach could, with minor modifications, be adapted for other organisms and sample matrices.

Key words

Metagenomics Sequencing Unknown viruses Virus detection Diagnosis Unknown etiology 



The authors would especially like to thank Professor José Manuel Sánchez-Vizcaíno (Animal Health Department, Complutense University of Madrid, Madrid, Spain) and his research group for their contribution to the original paper on which this chapter was based. This work was supported by Epi-SEQ, a research project supported under the 2nd joint call for transnational research projects by EMIDA ERA-NET (FP7 project nr 219235); by the Award of Excellence (Excellensbidrag), provided to SB by the Swedish University of Agricultural Sciences (SLU); and by/executed in the framework of the EU project AniBioThreat (Grant Agreement: Home/2009/ISEC/AG/191) with the financial support from the Prevention of and Fight against Crime Programme of the European Union, European Commission—Directorate General Home Affairs. This publication reflects the views only of the authors, and the European Commission cannot be held responsible for any use, which may be made of the information contained therein. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Fredrik Granberg
    • 1
    • 2
  • Oskar E. Karlsson
    • 1
    • 2
  • Sándor Belák
    • 1
    • 2
    • 3
  1. 1.OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary MedicineUppsalaSweden
  2. 2.Department of Biomedical Sciences and Veterinary Public Health (BVF)Swedish University of Agricultural Sciences (SLU)UppsalaSweden
  3. 3.The National Veterinary Institute (SVA)UppsalaSweden

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