Expansion of the metazoan virosphere: progress, pitfalls, and prospects

• Metagenomic discovery now contributes substantially to our view of virus evolution . • Serendipitous virus sequences from transcriptomes and genomes are under-utilised. • Small-RNA and strand-specific sequencing aid interpretation of viral metagenomes . • Barcode-switching and cryptic/unintended host material hamper robust host assignment. • Systematic host sampling is required to estimate the total number of animal viruses. Metagenomic sequencing has led to a recent and rapid expansion of the animal virome. It has uncovered a multitude of new virus lineages from under-sampled host groups, including many that break up long branches in the virus tree, and many that display unexpected genome sizes and structures. Although there are challenges to inferring the existence of a virus from a `virus-like sequence’, in the absence of an isolate the analysis of nucleic acid (including small RNAs) and sequence data can provide considerable confidence. As a consequence, this period of molecular natural history is helping to reshape our views of deep virus evolution.