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Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1746)

Abstract

Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.

Key words

CIM Monolithic chromatography Concentration Water virome NGS 
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Notes

Acknowledgments

The authors are grateful to the Slovenian Research Agency for the grant P4-0165 and to the FP7 EU project EMERAMB from the ERA-net action ARIMNet2. We are also grateful to Dr. Magda Tušek Žnidarič for her help with the transmission electron microscopy.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
  2. 2.Lek Pharmaceuticals d.d.MengesSlovenia
  3. 3.University of NottinghamNottinghamUK

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