Abstract
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 because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine 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.
Highlights
The standard method for rapidly detecting known human viruses in clinical samples is the polymerase chain reaction (PCR), in which short oligonucleotides are used to amplify and probe specific regions of viral genomes
The top hit in DisCVR was human rhinovirus (HRV)-A, which was the second hit in Kraken and CLARK but was not detected using real-time PCR (RT-PCR)
On a Linux operating systems CLARK and Kraken required more than 30 Gb of RAM to run samples against the respiratory dataset, whereas DisCVR ran with only 8 Gb
Summary
The standard method for rapidly detecting known human viruses in clinical samples is the polymerase chain reaction (PCR), in which short oligonucleotides are used to amplify and probe specific regions of viral genomes. The limitations of this technique include the targeting of a relatively small number of viruses per assay and a dependence on sequence conservation among viral strains. High-throughput sequencing (HTS) provides approaches to viral diagnosis that have much greater scope. Metagenomic analysis of HTS data can provide extensive viral genotyping information, as well as the characterization of complex multiple infections (Thorburn et al 2015). We have developed DisCVR, which is a fast, accurate and easy-to-use tool for detecting known human viruses in clinical samples
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