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DisCVR: Rapid viral diagnosis from high-throughput sequencing data

By Maha Maabar, Andrew J. Davison, Fiona Thorburn, Rory Gunson, Massimo Palmarini, Joseph Hughes

Posted 23 Jan 2019
bioRxiv DOI: 10.1101/527127 (published DOI: 10.1093/ve/vez033)

High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories be-cause of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (22 nucleotide sequences) to k-mers from taxonomically labelled viral genomes. DisCVR was validated using published HTS data for 89 clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.

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