709. Deep Sequencing for the Detection of Viruses in Multiple Sclerosis Brain Specimens
Session: Abstracts: Virology
Friday, October 22, 2010
Background: Multiple sclerosis (MS) is a chronic demyelinating disease of unknown cause, which affects the brain and spinal cord of about 400,000 individuals in the U.S. Viruses have long been suspected as causative agents in MS based on the epidemiology of the disease including geographic patterns, isolated outbreaks, and migration studies.

Methods: Fifty frozen specimens from the brains of deceased persons affected by MS were obtained along with 15 normal control brain specimens.  RNA was extracted and ribosomal RNAs were depleted.  The brain RNA extracts were subjected to quality control before sequencing on the Illumina GAII. 

Results: Seventeen MS and 11 control brain extracts were sequenced, yielding 4-10 million sequences ( “reads") each.  These 36 bp reads were compared with a non-redundant database derived from the 600,000+ viral sequences in GenBank organized into 7945 taxa.  An individual read successfully aligned to the viral database was considered to be a “hit”.  Taxon hit rates, normalized by the the number of sequences obtained for each specimen, were used to judge relative enrichment of viral sequence.  A control distribution for each viral taxon was created from the hit rates of the non-MS samples.  Each MS specimen hit rate for every viral taxon were compared to the control distribution.  One or more of the 17 MS specimens was enriched (p<0.001) for 65 different taxa from 24 viral families.  A previously unsuspected flavivirus (GB virus C) was amplified from one of the MS brains and its presence was confirmed by immunohistochemistry.

Conclusion: Deep sequencing with subtraction of ribosomal and human sequences is a promising technique for multiple sclerosis pathogen discovery.


Subject Category: V. Virology including clinical and basic studies of viral infections, including hepatitis

Speakers:
John D. Kriesel, MD , Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT
Maurine Hobbs, PhD , Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT
Brandt B. Jones, BS , Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT
Kael Fischer, PhD , Pathology, University of Utah School of Medicine, Salt Lake City, UT

Disclosures:

J. D. Kriesel, Yes
Idaho Technology, Inc.: Grant Investigator, Research grant

M. Hobbs, None

B. B. Jones, None

K. Fischer, None

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