TY - JOUR T1 - A Practical Approach to a Viral Detection Pipeline Using Existing Viral and Non-Viral Sequence Resources JF - PDA Journal of Pharmaceutical Science and Technology JO - PDA J Pharm Sci Technol SP - 595 LP - 601 DO - 10.5731/pdajpst.2014.01022 VL - 68 IS - 6 AU - Kavitha Bekkari AU - Joseph Shpungin AU - John Ryan Thompson Y1 - 2014/11/01 UR - http://journal.pda.org/content/68/6/595.abstract N2 - For public health safety, vaccines and other pharmaceutical products as well as the raw materials used in their manufacture need to be tested for adventitious virus contamination. The current standard of practice is to develop culture-based or polymerase chain reaction assays for the types of viruses one might expect based upon the source of reagents used. High-throughput sequencing technology is well-suited for building an unbiased strategy for the purpose of adventitious virus detection. We have developed an approach to automate curation of publically available nucleotide sequences, and have practically balanced the desire to capture all viral diversity while simultaneously reducing the use of partial viral sequences that represent the largest source of false positive results. In addition, we describe an effective workflow for virus detection that can process sequence data from all currently available High-throughput sequencing technologies and produce a report that summarizes the weight of sequence data in support of each detected virus. ER -