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

To alleviate any reliance on particular aspects of the different sequencing technologies, we have made two assumptions that should be valid in most viral sequencing projects. The first assumption is a basic understanding of the genomic structure of the virus being sequenced, including the expected size of the genome, the number of segments, and the number and distribution of major open reading frames (ORFs). Fortunately, genome structure is highly conserved within viral groups (6) , and although new viruses are constantly being uncovered, the discovery of a novel family or even genus remains relatively uncommon (7) . In the absence of such information, the defined standards can still be applied following further analysis to determine genome structure. The second assumption is that the genetic material of the virus being described can be accurately separated from the genomes of the host and/or other microbes, either physically or bioinformatically. Depending on the technology used, it is critical that the potential for crosscontamination of samples during the sample indexing/bar coding process and sequencing procedure be addressed with appropriate internal controls and procedural methods (8) .