Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Abstract

Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis (ALS) patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq data sets currently being generated.

The discovery of phages in the Substantia Nigra and its implication for Parkinson’s Disease

“…Next-generation sequencing becomes novel approach to identify and characterize virobiota in tissues 64 . Sequencing of viral mRNA fragments that encrypted in human transcriptome reveal viral involvement in human diseases 65 . Newly-developed bioinformatic approaches, viruSITE 66 and Virus-Track 64 are designed for mining the encrypted virome in transcriptome of host tissues.…”