Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

Ladner, Jason T.; Beitzel, Brett; Chain, Patrick S. G.; Davenport, Matthew G.; Donaldson, Eric; Frieman, Matthew; Kugelman, Jeffrey; Kuhn, Jens H.; O’Rear, Jules; Sabeti, Pardis C.; Wentworth, David E.; Wiley, Michael R.; Yu, Guo-Yun; Sozhamannan, Shanmuga; Bradburne, Christopher; Palacios, Gustavo

Description of novel viruses. Despite the rapidly growing collection of viral sequences, the description of novel viruses is likely to remain an important aspect of viral genome sequencing (7, 15, 16) . This is true in part because viruses evolve rapidly and are capable of recombining to form novel genotypes (17, 18) . It is also true that most of the viruses that are currently circulating remain uncharacterized (15) . Particularly lacking are representatives from groups that are not currently known to infect humans or organisms of economic importance. It would be imprudent, however, to continue to ignore these uncharacterized reservoirs of diversity, because it is difficult to predict the source of future emerging diseases (19) (20) (21) . Additionally, with the current suite of primarily sequence similarity-based pathogen identification tools, the ability to detect novel pathogens is wholly dependent on highquality reference databases (22) . There is a trend toward requiring a complete genome sequence when a description of a novel virus is being published, and we agree that this is a good goal; however, the amount of time and resources required to complete the last 1 to 2% of a viral genome is often cost and time prohibitive for projects sequencing a large number of samples, and in most cases the very ends of the segments are not essential for proper identification and characterization. Therefore, for the majority of viral characterization projects, we recommend, at a minimum, a CC genome. This will ensure a complete description of the viral proteome and will allow accurate phylogenetic placement.