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Beurdeley-Fehlbaum P, Pennington M, Hégerlé N, Albert M, Bennett A, Cheval J, Clark A, Cruveiller S, Desbrousses C, Frederick J, Gros E, Hunter K, Jaber T, Gaiser M, Jouffroy O, Lamamy A, Melkowski M, Moro J, Niksa P, Pillai S, Eloit M, Ruppach H. Evaluation of a viral transcriptome Next Generation Sequencing assay as an alternative to animal assays for viral safety testing of cell substrates. Vaccine 2023; 41:5383-5391. [PMID: 37468389 DOI: 10.1016/j.vaccine.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
The viral safety of biological products is ensured by tests throughout the production chain, and, for certain products, by steps in the manufacturing process enabling the elimination or inactivation of viruses. Current testing programs include sample inoculation in animals and embryonic eggs. Following the 3Rs principles of replacement, reduction, and refinement of animal-use methods, such techniques are intended to be replaced not only for ethical reasons but also because of their inherent technical limitations, their long turnaround times, and their limits in virus detection. Therefore, we have compared the limit and range of sensitivity of in vivo tests used for viral testing of cells with a transcriptomic assay based on Next Generation Sequencing (NGS). Cell cultures were infected with a panel of nine (9) viruses, among them only five (5) were detected, with variable sensitivity, by in vivo tests. The transcriptomic assay was able to detect one (1) infected cell among 103 to 107 non-infected cells for all viruses assessed, including those not detected by the conventional in vivo tests. Here we show that NGS extends the breath of detection of viral contaminants compared to traditional testing. Collectively, these results support the replacement of the conventional in vivo tests by an NGS-based transcriptomic assay for virus safety testing of cell substrates.
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Affiliation(s)
| | - Matthew Pennington
- KCAS Bioanalytical & Biomarker Services, 10830 S Clay Blair Blvd., Olathe, KS 66061, USA
| | | | | | - Amy Bennett
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | | | - Allison Clark
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | | | | | - Janalyn Frederick
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA.
| | - Edwige Gros
- PathoQuest, 11 rue Watt, 75013 Paris, France
| | - Kathryn Hunter
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | - Tareq Jaber
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | - Madison Gaiser
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA.
| | | | | | | | - Jennifer Moro
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | - Paula Niksa
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | - Shenba Pillai
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
| | - Marc Eloit
- PathoQuest, 11 rue Watt, 75013 Paris, France; Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 27 Avenue du Général Leclerc, 94704 Maisons-Alfort, France; Institut Pasteur, Université Paris Cité, Laboratoire de Découverte des Pathogènes, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Horst Ruppach
- Charles River Laboratories, Inc., 251 Ballardvale Street, 01887-1000 Wilmington, MA, USA
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Khan AS, Mallet L, Blümel J, Cassart JP, Knezevic I, Ng SHS, Wall M, Jakava-Viljanen M, Logvinoff C, Goios A, Neels P. Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals. Biologicals 2023; 83:101696. [PMID: 37478506 PMCID: PMC10522920 DOI: 10.1016/j.biologicals.2023.101696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023] Open
Abstract
Next-generation sequencing (NGS) has been proven to address some of the limitations of the current testing methods for adventitious virus detection in biologics. The International Alliance for Biological Standardization (IABS), the U.S. Food and Drug Administration (FDA), and the European Directorate for the Quality of Medicines and Healthcare (EDQM) co-organized the "3rd Conference on Next-generation Sequencing for Adventitious Virus Detection in Biologics for Humans and Animals", which was held on September 27-28, 2022, in Rockville, Maryland, U.S.A. The meeting gathered international representatives from regulatory and public health authorities and other government agencies, industry, contract research organizations, and academia to present the current status of NGS applications and the progress on NGS standardization and validation for detection of viral adventitious agents in biologics, including human and animal vaccines, gene therapies, and biotherapeutics. Current regulatory expectations were discussed for developing a scientific consensus regarding using NGS for detection of adventitious viruses. Although there are ongoing improvements in the NGS workflow, the development of reference materials for facilitating method qualification and validation support the current use of NGS for adventitious virus detection.
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Affiliation(s)
- Arifa S Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Laurent Mallet
- European Directorate for the Quality of Medicines and Healthcare, Strasbourg, France
| | | | | | - Ivana Knezevic
- Department of Health Product Policy and Standards, World Health Organization, Geneva, Switzerland
| | - Siemon H S Ng
- Notch Therapeutics, Vancouver, British Columbia, Canada
| | | | | | | | - Ana Goios
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Pieter Neels
- International Alliance for Biological Standardization, Geneva, Switzerland
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3
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Barone PW, Keumurian FJ, Neufeld C, Koenigsberg A, Kiss R, Leung J, Wiebe M, Ait-Belkacem R, Azimpour Tabrizi C, Barbirato C, Beurdeley P, Brussel A, Cassart JP, Cote C, Deneyer N, Dheenadhayalan V, Diaz L, Geiselhoeringer A, Gilleece MM, Goldmann J, Hickman D, Holden A, Keiner B, Kopp M, Kreil TR, Lambert C, Logvinoff C, Michaels B, Modrof J, Mullan B, Mullberg J, Murphy M, O'Donnell S, Peña J, Ruffing M, Ruppach H, Salehi N, Shaid S, Silva L, Snyder R, Spedito-Jovial M, Vandeputte O, Westrek B, Yang B, Yang P, Springs SL. Historical evaluation of the in vivo adventitious virus test and its potential for replacement with next generation sequencing (NGS). Biologicals 2023; 81:101661. [PMID: 36621353 DOI: 10.1016/j.biologicals.2022.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) collected historical data from 20 biopharmaceutical industry members on their experience with the in vivo adventitious virus test, the in vitro virus test, and the use of next generation sequencing (NGS) for viral safety. Over the past 20 years, only three positive in vivo adventitious virus test results were reported, and all were also detected in another concurrent assay. In more than three cases, data collected as a part of this study also found that the in vivo adventitious virus test had given a negative result for a sample that was later found to contain virus. Additionally, the in vivo adventitious virus test had experienced at least 21 false positives and had to be repeated an additional 21 times all while using more than 84,000 animals. These data support the consideration and need for alternative broad spectrum viral detection tests that are faster, more sensitive, more accurate, more specific, and more humane. NGS is one technology that may meet this need. Eighty one percent of survey respondents are either already actively using or exploring the use of NGS for viral safety. The risks and challenges of replacing in vivo adventitious virus testing with NGS are discussed. It is proposed to update the overall virus safety program for new biopharmaceutical products by replacing in vivo adventitious virus testing approaches with modern methodologies, such as NGS, that maintain or even improve the final safety of the product.
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Affiliation(s)
| | | | | | | | - Robert Kiss
- MIT Center for Biomedical Innovation, USA; UPSIDE Foods, USA
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4
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Dransart B, Dehghani H, Moore A. Product-safety considerations in allogeneic chimeric antigen-receptor T-cell process flows. Curr Opin Biotechnol 2022; 78:102797. [PMID: 36179407 DOI: 10.1016/j.copbio.2022.102797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/07/2022] [Accepted: 08/21/2022] [Indexed: 12/14/2022]
Abstract
Allogeneic chimeric antigen-receptor T-cell process flows comprise large-scale primary cultures incorporating traditional biologics processing steps such as cell expansion, with novel processing steps such as electroporation. In addition, these process flows begin with donor-derived peripheral blood mononuclear cells and generate single batches of product, which may be used to treat hundreds of patients. The corresponding unit operation-process safety considerations are individually diverse, and in combination are currently unique and rapidly evolving. The use of available regulations and the principles of quality by design are useful in designing appropriate control strategies into the process during development to ensure process safety.
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Affiliation(s)
- Bryan Dransart
- Allogene Therapeutics, 210 E. Grand Avenue, South San Francisco, CA 94080, USA
| | - Houman Dehghani
- Allogene Therapeutics, 210 E. Grand Avenue, South San Francisco, CA 94080, USA
| | - Alison Moore
- Allogene Therapeutics, 210 E. Grand Avenue, South San Francisco, CA 94080, USA.
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5
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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6
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Zhang Z, Chen J, Wang J, Gao Q, Ma Z, Xu S, Zhang L, Cai J, Zhou W. Reshaping cell line development and CMC strategy for fast responses to pandemic outbreak. Biotechnol Prog 2021; 37:e3186. [PMID: 34148295 DOI: 10.1002/btpr.3186] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
The global pandemic outbreak COVID-19 (SARS-COV-2), has prompted many pharmaceutical companies to develop vaccines and therapeutic biologics for its prevention and treatment. Most of the therapeutic biologics are common human IgG antibodies, which were identified by next-generation sequencing (NGS) with the B cells from the convalescent patients. To fight against pandemic outbreaks like COVID-19, biologics development strategies need to be optimized to speed up the timeline. Since the advent of therapeutic biologics, strategies of transfection and cell line selection have been continuously improved for greater productivity and efficiency. NGS has also been implemented for accelerated cell bank testing. These recent advances enable us to rethink and reshape the chemistry, manufacturing, and controls (CMC) strategy in order to start supplying Good Manufacturing Practices (GMP) materials for clinical trials as soon as possible. We elucidated an accelerated CMC workflow for biologics, including using GMP-compliant pool materials for phase I clinical trials, selecting the final clone with product quality similar to that of phase I materials for late-stage development and commercial production.
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Affiliation(s)
- Zheng Zhang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Ji Chen
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Junghao Wang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Qiao Gao
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Zhujun Ma
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Shurong Xu
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Li Zhang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Jill Cai
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Weichang Zhou
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
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7
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Van Vo G, Bagyinszky E, Park YS, Hulme J, An SSA. SARS-CoV-2 (COVID-19): Beginning to Understand a New Virus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1321:3-19. [PMID: 33656709 DOI: 10.1007/978-3-030-59261-5_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within the last two decades, several members of the Coronaviridae family demonstrated epidemic potential. In late 2019, an unnamed genetic relative, later named SARS-CoV-2 (COVID-19), erupted in the highly populous neighborhoods of Wuhan, China. Unchecked, COVID-19 spread rapidly among interconnected communities and related households before containment measures could be enacted. At present, the mortality rate of COVID-19 infection worldwide is 6.6%. In order to mitigate the number of infections, restrictions or recommendations on the number of people that can gather in a given area have been employed by governments worldwide. For governments to confidently lift these restrictions as well as counter a potential secondary wave of infections, alternative medications and diagnostic strategies against COVID-19 are urgently required. This review has focused on these issues.
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Affiliation(s)
- Giau Van Vo
- Department of Industrial and Environmental Engineering, Graduate School of Environment, Gachon University, Seongnam-si, Gyeonggi-do, South Korea
- Department of Bionanotechnology, Gachon University, Seongnam-si, Gyeonggi-do, South Korea
- School of Medicine, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Eva Bagyinszky
- Department of Industrial and Environmental Engineering, Graduate School of Environment, Gachon University, Seongnam-si, Gyeonggi-do, South Korea
- Department of Bionanotechnology, Gachon University, Seongnam-si, Gyeonggi-do, South Korea
| | - Yoon Soo Park
- Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Gyeonggi-do, South Korea
| | - John Hulme
- Department of Bionanotechnology, Gachon University, Seongnam-si, Gyeonggi-do, South Korea.
| | - Seong Soo A An
- Department of Bionanotechnology, Gachon University, Seongnam-si, Gyeonggi-do, South Korea.
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8
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Bačnik K, Kutnjak D, Jerič Kokelj B, Tuta N, Lončar T, Vogelsang M, Ravnikar M. Metagenomic characterization of parental and production CHO cell lines for detection of adventitious viruses. Biologicals 2020; 69:70-75. [PMID: 33246870 DOI: 10.1016/j.biologicals.2020.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022] Open
Abstract
Viral contamination is a major concern for biological products. Therefore, virus testing of raw materials and cells is essential for the safety of the final product. We used high-throughput sequencing to detect viral-like sequences in selected CHO cell lines. Our aim was to test various approaches of sample preparation, to establish a pipeline for metagenomic analysis and to characterize standard viral metagenome of production and parental CHO cell lines. The comparison of the metagenomics composition of the differently prepared samples showed that among four tested approaches sequencing of ribosomal RNA depleted total RNA is the most promising approach. The metagenomics investigation of one production and three parental CHO cell lines of diverse origin did not indicate the presence of adventitious viral agents in the investigated samples. The study revealed an expected background of virus-like nucleic acids in the samples, which originate from remains of expression vectors, endogenized viral elements and residuals of bacteriophages.
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Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Barbara Jerič Kokelj
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Nika Tuta
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Tan Lončar
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Matjaž Vogelsang
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Mengeš, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska Cesta, 5000, Nova Gorica, Slovenia
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9
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Khan AS, Blümel J, Deforce D, Gruber MF, Jungbäck C, Knezevic I, Mallet L, Mackay D, Matthijnssens J, O'Leary M, Theuns S, Victoria J, Neels P. Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals. Biologicals 2020; 67:94-111. [PMID: 32660862 PMCID: PMC7351673 DOI: 10.1016/j.biologicals.2020.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 11/20/2022] Open
Abstract
The IABS-EU, in association with PROVAXS and Ghent University, hosted the "2nd Conference on Next Generation Sequencing (NGS) for Adventitious Virus Detection in Human and Veterinary Biologics" held on November 13th and 14th 2019, in Ghent, Belgium. The meeting brought together international experts from regulatory agencies, the biotherapeutics and biologics industries, contract research organizations, and academia, with the goal to develop a scientific consensus on the readiness of NGS for detecting adventitious viruses, and on the use of this technology to supplement or replace/substitute the currently used assays. Participants discussed the progress on the standardization and validation of the technical and bioinformatics steps in NGS for characterization and safety evaluation of biologics, including human and animal vaccines. It was concluded that NGS can be used for the detection of a broad range of viruses, including novel viruses, and therefore can complement, supplement or even replace some of the conventional adventitious virus detection assays. Furthermore, the development of reference viral standards, complete and correctly annotated viral databases, and protocols for the validation and follow-up investigations of NGS signals is necessary to enable broader use of NGS. An international collaborative effort, involving regulatory authorities, industry, academia, and other stakeholders is ongoing toward this goal.
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Affiliation(s)
- Arifa S Khan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | | | | | - Marion F Gruber
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Carmen Jungbäck
- International Association for Biological Standardization for Europe, Lyon, France
| | | | | | | | | | - Maureen O'Leary
- P95 Pharmacovigilance and Epidemiology Services, Leuven, Belgium
| | | | | | - Pieter Neels
- International Association for Biological Standardization for Europe, Lyon, France
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Charlebois RL, Sathiamoorthy S, Logvinoff C, Gisonni-Lex L, Mallet L, Ng SHS. Sensitivity and breadth of detection of high-throughput sequencing for adventitious virus detection. NPJ Vaccines 2020; 5:61. [PMID: 32699651 PMCID: PMC7368052 DOI: 10.1038/s41541-020-0207-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing (HTS) is capable of broad virus detection encompassing both known and unknown adventitious viruses in a variety of sample matrices. We describe the development of a general-purpose HTS-based method for the detection of adventitious viruses. Performance was evaluated using 16 viruses equivalent to well-characterized National Institutes of Health (NIH) virus stocks and another six viruses of interest. A viral vaccine crude harvest and a cell substrate matrix were spiked with 22 viruses. Specificity was demonstrated for all 22 viruses at the species level. Our method was capable of detecting and identifying adventitious viruses spiked at 104 genome copies per milliliter in a viral vaccine crude harvest and 0.01 viral genome copies spiked per cell in a cell substrate matrix. Moreover, 9 of the 11 NIH model viruses with published in vivo data were detected by HTS with an equivalent or better sensitivity (in a viral vaccine crude harvest). Our general-purpose HTS method is unbiased and highly sensitive for the detection of adventitious viruses, and has a large breadth of detection, which may obviate the need to perform in vivo testing.
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Affiliation(s)
| | | | | | | | - Laurent Mallet
- Analytical Sciences, Sanofi Pasteur, Marcy L'Étoile, France
| | - Siemon H S Ng
- Analytical Sciences, Sanofi Pasteur, Toronto, ON M2R 3T4 Canada
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11
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Barone PW, Wiebe ME, Leung JC, Hussein ITM, Keumurian FJ, Bouressa J, Brussel A, Chen D, Chong M, Dehghani H, Gerentes L, Gilbert J, Gold D, Kiss R, Kreil TR, Labatut R, Li Y, Müllberg J, Mallet L, Menzel C, Moody M, Monpoeho S, Murphy M, Plavsic M, Roth NJ, Roush D, Ruffing M, Schicho R, Snyder R, Stark D, Zhang C, Wolfrum J, Sinskey AJ, Springs SL. Viral contamination in biologic manufacture and implications for emerging therapies. Nat Biotechnol 2020; 38:563-572. [DOI: 10.1038/s41587-020-0507-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/01/2020] [Indexed: 01/02/2023]
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12
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Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids. mSphere 2019; 4:4/3/e00298-19. [PMID: 31167947 PMCID: PMC6553555 DOI: 10.1128/msphere.00298-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of a transcriptionally active virus. This improvement in the specificity of viral testing increases the acceptability of HTS as a standard test for cells used in manufacturing biologicals and in biotherapies. The use of high-throughput sequencing (HTS) to identify viruses in biologicals differs from current molecular approaches, since its use enables an unbiased approach to detection without the need to design specific primers to preamplify target sequences. Its broad range of detection and analytical sensitivity make it an important tool to ensure that biologicals are free from adventitious viruses. Similar to other molecular methods, however, identification of viral sequences in cells by HTS does not prove viral infection, since this could reflect carryover of inert viral sequences from reagents or other sources or the presence of transcriptionally inactive cellular sequences. Due to the broad range of detection associated with HTS, the above can potentially be perceived as a drawback for the testing of pharmaceutical biological products using this method. In order to avoid the identification of inert viral sequences, we present a methodology based on metabolic RNA labeling and sequencing, which enables the specific identification of newly synthesized viral RNAs in infected cells, resulting in the ability to unambiguously distinguish active infection by DNA or RNA viruses from inert nucleic acids. In the present study, we report the ability to differentiate Vero cells acutely infected by a single-stranded positive-sense RNA virus (tick-borne encephalitis virus) from cells which have been in contact with nonreplicating virus particles. Additionally, we also found a laboratory contamination by the squirrel monkey retrovirus of our Vero cell line, which was derived from an Old World (African green) monkey, a type of contamination which until now has been identified only in cells derived from primates from the New World. IMPORTANCE The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of a transcriptionally active virus. This improvement in the specificity of viral testing increases the acceptability of HTS as a standard test for cells used in manufacturing biologicals and in biotherapies.
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