ViralORFeome: an integrated database to generate a versatile collection of viral ORFs

Pellet, J.; Tafforeau, L.; Lucas-Hourani, M.; Navratil, V.; Meyniel, L.; Achaz, G.; Guironnet-Paquet, A.; Aublin-Gex, A.; Caignard, G.; Cassonnet, P.; Chaboud, A.; Chantier, T.; Deloire, A.; Demeret, C.; Le Breton, M.; Neveu, G.; Jacotot, L.; Vaglio, P.; Delmotte, S.; Gautier, C.; Combet, C.; Deleage, G.; Favre, M.; Tangy, F.; Jacob, Y.; Andre, P.; Lotteau, V.; Rabourdin-Combe, C.; Vidalain, P. O.

Because of their small-sized genomes, most viruses exhibit a limited number of ORFs. Therefore, building a viral ORFeome collection covering a significant number of viral pathogens can appear like a manageable project. However, this eventually becomes a daunting task when considering virus strains and polymorphisms that affect viral proteins (Table 1) . Nonetheless, these variations cannot be neglected since they often determine virulence and/or host adaptation. For example, a unique amino acid mutation in the polymerase of poliovirus can alter its processivity, turning a highly pathogenic virus into an attenuated strain that can eventually be used as a vaccine (14) . Similarly, a Semliki Forest virus strain encoding an nsP2 protein, with a single amino acid mutation in its nuclear localization signal, is impaired for the control of type I interferon response and strongly attenuated in vivo (15) . Thus, specific care must be taken when cloning a virus ORFeome, since an accurate identification of the strain that is used as a template is absolutely critical, both in terms of genotype and phenotype. For this reason, wild-type virus strains corresponding to primary isolates will be generally preferred to culture-adapted laboratory strains that often exhibit an altered phenotype in vivo. Such biological samples are often difficult to obtain, since it requires access to patients, medical-care facilities and laboratories of an appropriate biosafety level. With such constraints to obtain suitable viral RNA or DNA templates, a collaborative effort between virology laboratories is needed to build a comprehensive viral ORFeome resource. This motivated the development of ViralORFeome 1.0, an open-access database and management system designed to assist academic laboratories in the development of a viral ORFeome collection using a recombination-based cloning technology.