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bioRxiv · 10.1101/2021.01.27.428546

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

Melnick, M.·Prudencio, M.·Gonzales, P.·Larocca, T. J.·Dowell, R. D.·Song, Y.·Wuu, J.·Benatar, M.·Oskarsson, B.·Petrucelli, L.·Link, C. D.
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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.

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Melnick, M., Prudencio, M., Gonzales, P., Larocca, T. J., Dowell, R. D., Song, Y., Wuu, J., Benatar, M., Oskarsson, B., Petrucelli, L., Link, C. D.. 2021-01-30. Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood. https://doi.org/10.1101/2021.01.27.428546

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