Whole genome: next-generation sequencing as a virus safety test for biotechnological products

The availability of next-generation sequencing techniques is about to strongly modify the strategies of control of the viral safety of biologicals products. It is now possible to use the tools of metagenomics, which is the study of the microbial genetic sequences recovered directly from a given sample. In this setting, the sequence of all the nucleic acids species of the sample are determined and compared with those in databases. We describe the pipeline we are currently using and show comparison of its analytical sensitivity with that of polymerase chain reaction together with results of time course experiments in infected cells. We propose to test cell supernatants for viral genomes associated to capsids and testing cells for viral RNA transcripts as the hallmark for virus replication, and we suggest rules of interpretation of the results. We also discuss the applicability of next-generation sequencing for the control of raw materials.