title: A practical approach to a viral detection pipeline using existing viral and non-viral sequence resources.
abstract: 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.
authors.affiliation: Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, NJ, USA;
authors.forename: Kavitha
authors.initials: K
authors.lastname: Bekkari
authors.affiliation: High Performance Computing, Merck & Co., Inc., Rahway, NJ, USA; and.
authors.forename: Joseph
authors.initials: J
authors.lastname: Shpungin
authors.affiliation: Genetically-Defined Diseases and Genomics, Bristol-Myers Squibb, Hopewell, NJ, USA john.thompson@bms.com.
authors.forename: John Ryan
authors.initials: JR
authors.lastname: Thompson
mesh_terms: D057205:Automation, Laboratory; D001688:Biological Products / Q000032:analysis*; D001702:Biopharmaceutics / Q000379:methods* / Q000592:standards; D019295:Computational Biology; D004279:DNA, Viral / Q000235:genetics*; D030541:Databases, Genetic; D004340:Drug Contamination / Q000517:prevention & control*; D005189:False Positive Reactions; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards; D006801:Humans; D012367:RNA, Viral / Q000235:genetics*; D015203:Reproducibility of Results; D014773:Virology / Q000379:methods* / Q000592:standards; D014780:Viruses / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D057188:Workflow
chemical_list: D001688:Biological Products; D004279:DNA, Viral; D012367:RNA, Viral
keywords: Adventitious virus detection; High throughput sequencing; Virus contamination; Virus detection in samples