Viral contamination in biologic manufacture and implications for emerging therapies.

Recombinant protein therapeutics, vaccines, and plasma products have a long record of safety. However, the use of cell culture to produce recombinant proteins is still susceptible to contamination with viruses. These contaminations cost millions of dollars to recover from, can lead to patients not receiving therapies, and are very rare, which makes learning from past events difficult. A consortium of biotech companies, together with the Massachusetts Institute of Technology, has convened to collect data on these events. This industry-wide study provides insights into the most common viral contaminants, the source of those contaminants, the cell lines affected, corrective actions, as well as the impact of such events. These results have implications for the safe and effective production of not just current products, but also emerging cell and gene therapies which have shown much therapeutic promise.

AAVrh10 Vector Corrects Disease Pathology in MPS IIIA Mice and Achieves Widespread Distribution of SGSH in Large Animal Brains.

Patients with mucopolysaccharidosis type IIIA (MPS IIIA) lack the lysosomal enzyme sulfamidase (SGSH), which is responsible for the degradation of heparan sulfate (HS). Build-up of undegraded HS results in severe progressive neurodegeneration for which there is currently no treatment. The ability of the vector adeno-associated virus (AAV)rh.10-CAG-SGSH (LYS-SAF302) to correct disease pathology was evaluated in a mouse model for MPS IIIA. LYS-SAF302 was administered to 5-week-old MPS IIIA mice at three different doses (8.6E+08, 4.1E+10, and 9.0E+10 vector genomes [vg]/animal) injected into the caudate putamen/striatum and thalamus. LYS-SAF302 was able to dose-dependently correct or significantly reduce HS storage, secondary accumulation of GM2 and GM3 gangliosides, ubiquitin-reactive axonal spheroid lesions, lysosomal expansion, and neuroinflammation at 12 weeks and 25 weeks post-dosing. To study SGSH distribution in the brain of large animals, LYS-SAF302 was injected into the subcortical white matter of dogs (1.0E+12 or 2.0E+12 vg/animal) and cynomolgus monkeys (7.2E+11 vg/animal). Increases of SGSH enzyme activity of at least 20% above endogenous levels were detected in 78% (dogs 4 weeks after injection) and 97% (monkeys 6 weeks after injection) of the total brain volume. Taken together, these data validate intraparenchymal AAV administration as a promising method to achieve widespread enzyme distribution and correction of disease pathology in MPS IIIA.

Vesivirus 2117: Cell line infectivity range and effectiveness of amplification of a potential adventitious agent in cell culture used for biological production.

Vesivirus 2117 (VV-2117) has been recently described as a contaminant of cell culture operations in several biologics manufacturing facilities. VV-2117 has been poorly studied and little information exists about its biology, pathogenicity and infectivity range in cell culture settings. In this study we evaluated the potential in vitro viral infectivity of VV-2117 using a range of established mammalian cell lines from various species, the effectiveness of virus amplification in CHO-K1 cells at differing infection levels, and the relative sensitivity of two test methods (cytopathic effect [CPE] and polymerase chain reaction [PCR]) to detect infection and viral amplification. Of eight cell culture systems studied, two originating from hamster (CHO-K1 and BHK-21) and one from canine (MDCK) were positive for CPE and also showed a marked increase of viral RNA in a reverse transcriptase quantitative PCR (RT-qPCR) test. CHO-K1 cell cultures inoculated at 10, 1 and 0.1 genome copies per cell (gc/cell) showed both CPE and amplification of VV-2117 RNA, indicating that infection had occurred in these cultures. CHO-K1 cultures inoculated at 0.01, 0.001, 0.0001 and 0.00001 gc per cell showed neither CPE nor VV-2117, indicating that infection had not occurred. Therefore, the minimum dose necessary for infection of CHO-K1 cells was approximately 0.1 genome copies per cell. At any infection level where VV-2117 amplification was observed by RT-qPCR, the cultures also showed CPE. There was no low-level infection that could be detected by RT-qPCR without developing signs of CPE. However, the RT-qPCR assay appeared more sensitive in that it detected VV-2117 infection earlier than the onset of observable CPE.

Detection of adventitious agents using next-generation sequencing.

Next-generation sequencing has been evaluated at Genzyme as a means of identifying bioreactor contaminants due to its capability for detection of known and novel microbial species. In this approach, data obtained from next-generation sequencing is used to interrogate databases containing genomic sequences and identities of potential adventitious agents. We describe here the use of this approach to help identify the causative agent of a bioreactor contamination. We also present the results of spiking experiments to establish the limits of detection for DNA viruses, RNA viruses, and bacteria, in a background of Chinese hamster ovary cells, a cell line used for production of many human therapeutics. Using Illumina sequencing-based detection, all of the viruses included in this study were detected at less than 1 copy per cell, and bacteria were detected at 0.001 copy per cell. Thus, next-generation sequencing-based detection of adventitious agents is a valuable approach that can fill a critical unmet need in the detection of known and novel microorganisms in biopharmaceutical manufacturing. LAY ABSTRACT: Because biological products are manufactured in cells, the living environment must be kept sterile. Any introduction of microorganisms into the culture vessel may affect the growth and other biological properties of the cells or contaminate the product. It is therefore important to monitor the culture for such contaminants, but many methods can only detect a specific microorganism. In this study, we show that next-generation sequencing-based detection is a sensitive and complementary approach that can potentially detect a wide range of organisms.

Inactivation of caliciviruses.

The Caliciviridae family of viruses contains clinically important human and animal pathogens, as well as vesivirus 2117, a known contaminant of biopharmaceutical manufacturing processes employing Chinese hamster cells. An extensive literature exists for inactivation of various animal caliciviruses, especially feline calicivirus and murine norovirus. The caliciviruses are susceptible to wet heat inactivation at temperatures in excess of 60 °C with contact times of 30 min or greater, to UV-C inactivation at fluence ≥30 mJ/cm2, to high pressure processing >200 MPa for >5 min at 4 °C, and to certain photodynamic inactivation approaches. The enteric caliciviruses (e.g.; noroviruses) display resistance to inactivation by low pH, while the non-enteric species (e.g.; feline calicivirus) are much more susceptible. The caliciviruses are inactivated by a variety of chemicals, including alcohols, oxidizing agents, aldehydes, and ß-propiolactone. As with inactivation of viruses in general, inactivation of caliciviruses by the various approaches may be matrix-, temperature-, and/or contact time-dependent. The susceptibilities of the caliciviruses to the various physical and chemical inactivation approaches are generally similar to those displayed by other small, non-enveloped viruses, with the exception that the parvoviruses and circoviruses may require higher temperatures for inactivation, while these families appear to be more susceptible to UV-C inactivation than are the caliciviruses.

Identification and quantitation of Vesivirus 2117 particles in bioreactor fluids from infected Chinese hamster ovary cell cultures.

The prevention of adventitious agent contamination is a top priority throughout the entire biopharmaceutical production process. For example, although viral contamination of cell banks or cell cultures is rare, it can result in serious consequences (e.g., shutdown and decontamination of manufacturing facilities). To ensure virus free production, numerous in vivo and in vitro adventitious agent assays and biophysical characterizations such as electron microscopy are conducted on cell banks, raw materials, process materials, and drug substances throughout the manufacturing process. Molecular assays such as PCR and other nucleotide-based techniques are also routinely used for screening and identification of any viral agents. However, modern techniques in protein identification of complex protein mixtures have not yet been effectively integrated throughout the industry into current viral testing strategies. Here, we report the identification and quantitation of Vesivirus 2117 particles in bioreactor fluid from infected Chinese hamster ovary cell cultures by global protein sequencing using mass spectrometry in combination with multi-dimensional liquid-chromatography. Following mass spectrometric data acquisition and rigorous data analysis, six virus specific peptides were identified. These peptides were fragments of two structural proteins, capsid protein pre-cursor (four unique peptides) and small structural protein (two unique peptides), from the same species: Vesivirus 2117. Using stable heavy isotope-labeled peptides as internal standards, we also determined the absolute concentration of Vesivirus particles in the bioreactor fluid and the ratio of two capsid proteins (VP1:VP2) in the particles as approximately 9:1. The positive identification of Vesivirus 2117 was subsequently confirmed by RT-PCR.

Polyomavirus inactivation - a review.

Polyomavirus inactivation has been studied since the 1950s when it became apparent that certain polio vaccines were contaminated with SV40. Relatively high temperatures (≥70 °C) are required to effect thermal inactivation of the polyomaviruses. The chemical inactivants that are effective (ß-propiolactone, ethanol, sodium hydroxide, and formaldehyde) are those that have displayed efficacy for other small, non-enveloped viruses, such as the circoviruses. Low pH inactivation can be effective, especially at pH at or below 3 and at higher temperatures. Polyomaviruses are more resistant to UV-C irradiation than are other small non-enveloped viruses such as the parvoviruses and caliciviruses. The efficacy of photodynamic inactivation of polyomaviruses is very much dye-dependent, with toluidine blue, acridine orange, and methylene blue dyes being effective photosensitizers. Ionizing radiation can be effective, depending on the conditions employed and the inactivation matrix. Inactivation of the oncogenic properties of the polyomaviruses may require higher doses of inactivant than those required to inactivate infectivity. While the polyomaviruses are considered to be highly resistant to inactivation, the degree of resistance is dependent upon the specific approach under consideration. For certain approaches, such as UV-C and gamma-irradiation, the polyomaviruses appear to be more resistant than other small non-enveloped viruses.

Gamma irradiation of animal sera for inactivation of viruses and mollicutes--a review.

Animal-derived materials such as animal sera represent a low, but finite, risk for introduction of an adventitious agent (virus or mollicute) into a biological bulk harvest during upstream manufacturing processes involving mammalian cell substrates. Viral and mollicute (Mycoplasma sp. and Acholeplasma sp.) contamination events have been relatively rare, but many of those that have been reported have been attributed to use of infected animal sera in growth media during cell expansion. The risk of introduction of viruses and mollicutes may be mitigated by elimination of the use of animal sera and implementation instead of chemically defined or serum- and animal-derived material-free cell culture media. When use of animal sera is unavoidable, however, mitigation of the risk of introducing an adventitious contaminant may involve treatment of the sera to inactivate potential contaminants. Gamma irradiation is one of the most widely employed methods for viral and mollicute inactivation in animal sera. In this article, we review the inactivation results reported for viral and mollicute inactivation in frozen serum. Studies performed to assess the impact of gamma irradiation on serum quality and performance are also discussed. The available data indicate that inactivation of mollicutes in serum is essentially complete at the gamma radiation doses normally employed (25-40 kGy), while the efficacy and kinetics for viral inactivation in serum by gamma irradiation appear to be dependent in part upon the size of the target virus.