10 WAVLD ABSTRACT MartinBeer

World Association of Veterinary Laboratory Diagnosticians –16th International Symposium, Berlin, Germany, 5–8 June 2013
Metagenomics using Next Generation Sequencing Technology
Martin Beer*, Bernd Hoffmann and Dirk Höper
Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
Keywords: Next Generation Sequencing (NGS), metagenomics, viruses, Schmallenberg virus
In the past few years the next generation sequencing technology (NGS; high throughput sequencing
or deep sequencing) has made tremendous progress and now allows the rapid and reliable detection
of vast quantities of sequence information from purified pathogens or directly from sample materials.
Consequently, new possibilities for detecting and characterising novel pathogens, such as emerging
viruses, are now available to researchers in microbiology and also veterinary diagnostics.
Applying NGS can, in general, be divided into two different approaches: (1) the in-detail analysis and
characterisation of isolated pathogens allowing e.g. molecular epidemiology in an outbreak situation,
quasi-species analysis of selected viruses or the investigation of sequence variation in a very high
resolution by amplicon sequencing; (2) the undirected detection of sequence fragments in sample
materials using the so-called metagenomics approach.
A recent example of the discovery of a novel emerging virus using metagenomics is the detection of
Schmallenberg virus (SBV), a member of the Simbu serogroup within the genus Orthobunyavirus, in
2011 in Germany. Samples from cows with milk drop and fever were analysed following a protocol for
RNA and DNA preparation and subsequent NGS in a Genome Sequencer FLX instrument
(454/Roche). Using a newly developed software routine, all sequence fragments detected within the
sample material were compared with sequence databases, resulting in a few sequences showing a
high homology to viruses of the genus Orthobunyavirus. The information from NGS was used for the
development of SBV-specific real-time reverse-transcription polymerase chain reaction assays,
allowing the sensitive and specific direct detection of SBV genomes in diseased animals or malformed
lambs and calves.
With this presentation, the use of NGS for pathogen detection and characterisation will be
demonstrated, and the influence on future veterinary diagnostics and the important role of data
analysis will be discussed.