Virus genomics: what is being overlooked?

Viruses are diverse biological entities that influence all life. Even with limited genome sizes, viruses can manipulate, drive, steal from, and kill their hosts. The field of virus genomics, using sequencing data to understand viral capabilities, has seen significant innovations in recent years. However, with advancements in metagenomic sequencing and related technologies, the bottleneck to discovering and employing the virosphere has become the analysis of genomes rather than generation. With metagenomics rapidly expanding available data, vital components of virus genomes and features are being overlooked, with the issue compounded by lagging databases and bioinformatics methods. Despite the field moving in a positive direction, there are noteworthy points to keep in mind, from how software-based virus genome predictions are interpreted to what information is overlooked by current standards. In this review, we discuss conventions and ideologies that likely need to be revised while continuing forward in the study of virus genomics.