Current challenges to virus discovery by metatranscriptomics

Meta-transcriptomic next-generation sequencing has transformed virus discovery, dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of meta-transcriptomics for virus discovery faces important challenges. As this technology becomes more widely adopted, the proportion of viral sequences in public databases with incorrect (e.g. mis-assignment of host) or limited information (e.g. lacking taxonomic classification) is likely to grow, limiting their utility in bioinformatic pipelines for virus discovery. In addition, we currently lack the bioinformatic tools that can accurately identify viruses showing little or no sequence similarity to database viruses or those that represent likely reagent contaminants. Herein, we outline some of the challenges to effective meta-transcriptomic virus discovery as well as their potential solutions.

Automated summary

Meta-transcriptomic next-generation sequencing has revolutionized virus discovery by expanding our knowledge of the virosphere, but faces challenges such as errors and limitations in viral sequences in public databases, as well as the lack of bioinformatic tools to identify novel viruses accurately.