Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing

Shasta D McClenahan; Christine Uhlenhaut; Philip R Krause

doi:10.1016/j.vaccine.2014.10.022

Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing

Vaccine. 2014 Dec 12;32(52):7115-21. doi: 10.1016/j.vaccine.2014.10.022. Epub 2014 Oct 27.

Authors

Shasta D McClenahan¹, Christine Uhlenhaut², Philip R Krause³

Affiliations

¹ Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
² Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany.
³ Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA. Electronic address: Philip.krause@fda.hhs.gov.

PMID: 25454874
DOI: 10.1016/j.vaccine.2014.10.022

Abstract

We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types, including cell culture substrates and vaccines.

Keywords: Adventitious agent; Cell substrate; Degenerate PCR; Massively parallel sequencing (MPS); Virus.

MeSH terms

Animals
Biological Products*
Cell Line*
Drug Contamination / prevention & control*
High-Throughput Nucleotide Sequencing / methods*
Indicators and Reagents*
Polymerase Chain Reaction / methods*
Technology, Pharmaceutical / methods*

Substances

Biological Products
Indicators and Reagents