Metagenomic profiling, also called metagenomic shotgun sequencing (MSS) represents a powerful application made possible by the digital nature of next-generation sequencing technologies. In it, one basically sequences a sample isolate obtained from somewhere — a shovelful of dirt, a scoop of plankton, or anything else that contains living organisms. MSS has proven particularly useful to studies of the human microbiome, or in layman’s terms, all of the bacteria/viruses/fungi that live in our bodies.
Many such microbiota are beneficial or simply commensal (not doing harm) with us. Others, like methicillin-resistant Staphylococcus aureus (MRSA), can cause severe disease. Most efforts to chart the human microbiome have focused on bacteria, whose relatively stable genomes make them amenable to assay development. Viruses, in contrast, are somewhat under-studied. Part of that is due to the small size and highly variable nature of viral genomes.
A new study in Genome Research showcases a capture-based enrichment strategy to improve virome sequencing. The ViroCap panel was developed by Todd and Kristine Wylie, who happen to be colleagues of mine at the McDonnell Genome Institute. The panel enriches for nucleic acids from 34 families of DNA or RNA viruses that infect vertebrate hosts, beautifully illustrated in a figure from the paper (see above).
At the time of the ViroCap design, NCBI GenBank contained the sequenced genomes of around 440 viral species, for a total of about 1 Gbp (billion base pairs) of sequence. After considerable bioinformatics efforts, the authors produced a ~200 Mbp sequence target and worked with Nimblegen to have it designed.
Wylie TN, Wylie KM, Herter BN, & Storch GA (2015). Enhanced virome sequencing through solution-based capture enrichment. Genome research PMID: 26395152
Sourced through Scoop.it from: massgenomics.org