title: Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture.
abstract: Fetal bovine serum (FBS) and trypsin are reagents used in cell culture and have been the source of viral contamination of pharmaceutical products. We performed high throughput sequencing (HTS) of two pools of commercial batches of FBS and three commercial batches of trypsin. Taxonomies were assigned by comparing sequences of contigs and singletons to the entire NCBI nucleic acid and protein databases. The same major viral species were evidenced between batches of a given reagent but the proportion of viral reads among total reads varied markedly between samples (from 0.002% to 22.7%). In FBS, the sequences found were mainly from bovine viral diarrhea virus (BVDV) 1 to 3 and bovine parvovirus 3 (BPV3). The BVDV sequences derived from FBS showed only minor discrepancies with primers generally used for the screening of BVDV. Viral sequences in trypsin were mainly from porcine circovirus type 2. Other known viral sequences at lower read counts and potential new viral species (bovine parvovirus and bovine pegivirus) were evidenced. The load of some known and new viruses detected by HTS could be quantified by qPCR. Results of HTS provide a framework for evaluating the pertinence of control measures including the design of PCRs, bioassays and inactivation procedures.
authors.affiliation: Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France.
authors.forename: Léa
authors.initials: L
authors.lastname: Gagnieur
authors.affiliation: PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France.
authors.forename: Justine
authors.initials: J
authors.lastname: Cheval
authors.affiliation: PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France.
authors.forename: Marlène
authors.initials: M
authors.lastname: Gratigny
authors.affiliation: PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Hébert
authors.affiliation: PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France.
authors.forename: Erika
authors.initials: E
authors.lastname: Muth
authors.affiliation: Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France.
authors.forename: Marine
authors.initials: M
authors.lastname: Dumarest
authors.affiliation: Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France; PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France; Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie ENVA, INRA, ANSES, 7 avenue Général de Gaulle, F-94704 Maisons Alfort, France. Electronic address: marc.eloit@pasteur.fr.
authors.forename: Marc
authors.initials: M
authors.lastname: Eloit
mesh_terms: D000818:Animals; D002417:Cattle; D002478:Cells, Cultured; D001908:Diarrhea Viruses, Bovine Viral / Q000145:classification* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016133:Polymerase Chain Reaction; D011120:Polyomavirus / Q000145:classification* / Q000235:genetics
keywords: Fetal bovine serum; High throughput sequencing; Parvovirus; Pegivirus; Trypsin; Virus