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

Countermeasure development. Advancements in our capabilities to sequence viral genomes are changing the way we counteract global pandemics and acts of bioterrorism. There are two important aspects of countermeasure development that can benefit strongly from the availability of genome sequences and HT sequencing data: the detection of the infectious agent and the treatment of the disease caused by the agent. Taxonomic classification and detection through DNA/RNA-based inclusivity assays (i.e., using techniques such as PCR to detect the presence of a pathogen) can be designed using fragmented and incomplete genomes (e.g., SD and HQ sequences). Fully resolved ORFs (CC) further enable the development of immunological assays, such as enzyme-linked immunosorbent assays (ELISA) and immunofluorescence assays (IFA), for protein-based detection, and obtaining a complete genome opens the door to a plethora of additional downstream applications, including the design of exclusivity tests, the establishment of reverse genetics systems, and the design of robust forensics protocols. However, for effective development and testing of animal models, therapeutics, vaccines, and prophylactics, it is necessary to obtain a complete picture of the variability present within both the challenge stock and postinfection populations, thereby necessitating finished genomes. In these medical applications, it is also important to demonstrate the absence of adventitious agents.