1745. Deep Sequencing for the Detection of Viruses in Multiple Sclerosis Brain Specimens
Session: Poster Abstract Session: Viral Infections; Pathogenesis and Epidemiology
Saturday, October 5, 2013
Room: The Moscone Center: Poster Hall C
Background: Multiple sclerosis (MS) is a demyelinating disease of unknown origin that affects the central nervous system of about 400,000 individuals in the U.S.A. Epidemiological studies have previously suggested an infectious component to the disease.  If a triggering infection persists or leaves traces of a pathogen's RNA within demyelinated brain, then these sequences should be identifiable in the afflicted tissue with a “deep sequencing” approach.  This approach can be used to discover novel pathogens in the absence of a culture system.

Methods: Deep sequencing of RNA extracted from 28 frozen brain specimens (14 primary progressive MS and 14 normal control) and 5 acute demyelinating brain FFPE biopsy specimens was performed using the Illumina HiSeq 2000.  The resulting single end 50-bp sequences were aligned to a non-redundant panviral database that includes 1.2 million sequences from 2,480 viral species. Normalized viral sequence hit rates (HR) were compared between the groups using the Mann-Whitney test.

Results: Metagenomic analysis of the 50-80 million reads per brain specimens revealed highly significant (p < 0.001) HR differences for 6 retroviral taxa, including several human endogenous retroviruses (HERV-K, HERV-W, and HERV-15).  A significant HR difference between the groups was also observed to the Lysine-tRNA primer binding site of the betaretrovirus MPMV (P = 0.018) and other retroviruses that use host Lysine-tRNA as their reverse transcription primer.  Reads mapping to this primer binding site were also present in the FFPE brain biopsy samples.

Conclusion: Deep sequencing can be used to detect viruses in frozen and fixed brain samples.  Endogenous retrovirus-like sequences are significantly increased in PPMS brain compared to normal controls, consistent with the findings of some other studies.  The identification of sequencing reads that map to MPMV/6A suggests that a endogenous or exogenous retrovirus, using a Lysine-tRNA primer, is present in the PPMS and acute demyelinating brain samples.

Benjamin Chan, Ph.D.1, Ted Wilson1, Kael F Fischer, PhD2 and John Kriesel, MD3, (1)University of Utah, Salt Lake City, UT, (2)Pathology, University of Utah School of Medicine, Salt Lake City, UT, (3)Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT


B. Chan, None

T. Wilson, None

K. F. Fischer, None

J. Kriesel, None

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