Impact of COVID-19 on Manufacturing of Cell and Gene Therapy and Biotech Products, and Overall Clinical Trial Landscape

Novel coronavirus SARS-CoV-2, the causative agent for COVID-19, has disrupted the global clinical trial landscape in just a few short months. This virus is part of a larger family called Coronaviridae, which includes viruses that can infect only animals, cause mild colds or be communicable and pathogenic like the SARS virus of the early 2000’s. COVID-19 is highly transmissible and can progress to life-threatening complications. While the main public health concern at the present is human-to-human spread of infection, there are other issues related to viral spread - for example, potential contamination of biologics that are intended for human use. One question manufacturers are likely to have is whether the virus could infiltrate the medicinal supply, like HIV and hepatitis virus did in the 1980’s. FDA has recognized this possibility and has just released draft guidance to address GMP considerations during the COVID-19 outbreak: “Good Manufacturing Practice Considerations for Responding to COVID-19 Infection in Employees in Drug and Biological Products Manufacturing: Guidance for Industry” (June 2020).¹

FDA has acknowledged that the risk varies between product classes and recommends a risk-based approach considering multiple factors, such as personnel practices, robustness of process controls and testing and clearance by purification. While FDA very sensibly recommends each firm conduct a product-risk assessment, in the estimation of the authors there’s a very low risk of SARS-CoV-2 contamination affecting protein-based biotech products. In this case multiple levels of safety precautions like use of established cell banks, timely in-process material screening and virus filtration are feasible. However, the authors believe theoretical risk of disease transmission through cell-based products that the appears to be higher as some of the routine biopharmaceutical safety precautions are not feasible. FDA acknowledges as such in a footnote in the June 2020 guidance. In this article we will discuss the relative risks and potential mitigation strategies specific to cell and gene therapy, as well as biotech products. It’s important to keep in mind that although SARS-CoV-2 contamination of cell therapy-based products has not been observed, it’s still important to be aware of the theoretical risks of viral contamination until more information about the true risks becomes available.

Impact on Existing Non-COVID Clinical Trials and COVID-Related Activities

The spread of COVID-19 globally has disrupted existing clinical trials for many reasons, as summarized in a recent Nature news article.² At the same time, the pandemic has created a massive mobilization of private and government resources to facilitate development of novel diagnostics, prophylactic vaccines and treatments. Cell and gene therapy manufacturers have participated in all facets of this mobilization. As of May 12, 2020, according to clinicaltrials.gov, there are approximately 70 ongoing trials of cell and gene therapies that are intended to prevent or treat COVID-19. Gene therapy approaches are being applied to develop non-traditional prophylactic vaccines. Cell therapy products, which have anti-inflammatory mechanisms of action that appear well-suited for a COVID-19 therapy, are also being studied.³

Cell and gene therapies comprise a wide variety of products, including: 1) autologous and allogeneic off-the-shelf cellular products; 2) gene modified autologous and allogeneic off-the-shelf cellular products; 3) gene therapy products; 4) tissue engineered products that can include scaffolds or cellular components isolated from HCT/Ps; and 5) other products, such as acellular products manufactured from Human Cells, Tissues, and Cellular and Tissue-Based Products (HCT/Ps).

Background on SARS-CoV-2 (Also Referred to as HCov-19) is the Causative Agent for the Novel Infectious Disease Known as COVID-19

SARS-CoV-2 belongs to a broad family of viruses that are composed of enveloped capsid containing positive sense single-stranded RNA. Transmission occurs primarily through spread of respiratory droplets and indirect contact with contaminated surfaces, on which viral particles can remain for days, depending on the composition of the surface -- e.g., steel, plastic, copper, or cardboard.⁴ There is also concern of GI involvement arising from viral RNA being detectable in stool samples from infected persons. As reports of COVID-19 infection were linked to the Hunan Market in Wuhan China, it has been presumed that the source of this virus is animals. It is difficult to know when the initial transmission from animals to humans occurred. The earliest report linking this disease with the Wuhan market, which had been visited by the first patient to be hospitalized with what was later diagnosed as COVID-19, notes that this patient started exhibiting symptoms as early as December 12, 2019.⁵ The exact mechanisms of transmission of SARS-CoV-2 are very complex, but what is known is that it appears to be transmitted much more easily than flu virus, and infected people who are asymptomatic can still transmit the virus to others.

In the most vulnerable population, elderly and immune compromised patients with pre-existing medical conditions, the viral illness can progress rapidly to life-threatening pulmonary, hematologic, cardiovascular, and renal conditions.

There are no vaccines or approved therapies that are effective in preventing or treating COVID-19 infection. Like other large enveloped viruses, SARS-CoV-2 is sensitive to detergents and alcohol, which can be used as disinfectants.⁶

The Potential Impact of SARS-CoV-2 on Drug Manufacturing

During manufacture of cell and gene therapy products, viral contamination can come from a number of different sources, which include: 1) contaminated HCT/Ps; 2) contaminated supply biological raw materials; 3) manufacturing environment, including infected personnel/operators; and 4) infected clinical site personnel who prepare the final drug product and administer it to patients.

There is at most a low risk of SARS-CoV-2 transmission to biotech products that are commonly amenable to closed-system manufacturing, filtration and viral reduction steps.^7,8 Biopharmaceutical manufacture has several unique features that mitigate against SARSCoV-2 risk. The use of cell lines (CHO, murine myeloma) and protein-free culture conditions make it unlikely that this form of manufacturing will promote SARS-CoV-2 propagation. In addition, based on the timing of MCB and WCB development and production prior to the presumed date of the start of human-to-human transmission (December of 2019), the vast majority are safe from this standpoint.5 Further, bioreactor harvests are routinely screened for adventitious viruses using sensitive assays. This product class can also be subjected to virus retentive filtration during drug substance purification, a key safety step with respect to viruses; as Coronaviruses are a family of large enveloped viruses, they too are likely to be removed. All of these considerations are mentioned in the 2020 FDA guidance as risk factors firms should consider during their process specific CoV-2 risk assessment.

Unlike biotech products, it is virtually impossible in some cases to subject cell and gene therapy drug products to viral inactivation steps, as the process of inactivation has been shown to adversely impact product quality. Similarly, viral filters are effective in filtering out viral particles, but can also remove the actual product; therefore, filtration is generally not feasible in this situation. For these reasons, it’s important to focus on preventing the spread of communicable diseases by off-the-shelf cell therapy products, including allogeneic CAR-T products, through establishing Donor Eligibility (DE) for Human cells, Tissues, and Cellular and Tissue-Based Products (HCT/Ps) that are collected from allogeneic donors. Currently, DE requirements, as per 21 CFR 1271 Subpart C, do not include testing of donors for Coronavirus, but FDA has recently been very proactive in changing the requirements as the public is confronted with new infectious agents. For example, in response to the recent outbreak of Zika Virus, the agency issued several guidance documents in which Zika Virus was added to the list of Relevant Communicable Disease Agents and Diseases (RCDAD) for HCT/Ps and blood derived products. Questions as to whether Coronavirus poses a significant risk of disease transmission when products are derived from allogeneic sources or cultured and manipulated in the presence of human-derived components remain to be answered. However, in view of the complexity of these products, the authors concur that the risk of disease transmission for Coronavirus will need to be evaluated using a risk-based case-by-case approach, as suggested by the 2020 FDA guidance document, depending on the scientific data.

Table 1 summarizes factors that could potentially impact the risk of COVID-19 disease transmission in cell and gene therapy manufacturing, which include:

Supply chain quality: Cell and gene therapy manufacturing can involve a variety of biological materials that are derived from humans and animals. The risk of contamination of the materials sourced from human plasma and blood remain to be clarified, but implementation of voluntary screening and testing of the donor and donor materials for SARS-CoV-2 may be a prudent measure.

Manufacturing process (open versus closed systems): Although there is a current trend toward a shift from the use of open manufacturing platforms to more closed systems, a large number of products for early phase studies are still manufactured in less-closed and/or more open platforms – utilizing in all cases a biological safety cabinet for environmental control which are sometimes located in a non-cGMP environment. This lower level of control introduces an additional risk of product contamination by operators potentially infected with SARS-CoV-2.

Manufacturing operators#: Historically, personnel who are responsible for manufacturing cell and gene therapies, similar to others in this industry, do not typically undergo any thorough infectious disease screening or testing procedures on a frequency beyond the normal population#. It should be noted that the FDA guidance recommends firms follow CDC guidance for COVID-infected employees at manufacturing sites.1

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Manufacturing facility: In the current environment, an increasing number of products are being manufactured in multi-product facilities, which increases the risk associated with cross-contamination. For example, it is possible that the same clean room facility is being used for autologous and allogeneic product manufacturing.

Clinical site environment and operators (collection, product manipulation at clinical site): Another aspect of operator control relates to what happens to cell and gene therapy products at the clinical sites, where some of them undergo further manipulation (thaw and wash and testing) prior to administration in largely non-cGMP environments.

HCT/P, blood donor screening and testing: The quality of biological source material is probably the most important aspect of quality control. The agency has published advisory guidance documents suggesting that donors be screened for COVID-19 infection when these starting biological materials are used for manufacturing of the final drug products.9 However, due to the evolving understanding of the disease transmission and prioritization of testing for public health screening, it is not clear when the agency may formalize their specific recommendations regarding COVID-19 infection of donors.

Producer cells or cell lines: Most cell lines that are used to manufacture viral products (AAV and lentiviral vectors) are derived from human and primate source materials, which in theory could be more permissive to SARS-CoV-2 infection than CHO cells for example. This, in turn, is expected to increase the risk of disease transmission, provided that these lines are exposed to contaminated materials or infected operators.

Viral clearance: Unlike traditional biopharmaceutical products, most cell and gene therapy products cannot undergo viral inactivation steps. This issue may not apply to acellular products, such as exosomes, which are derived from human cell lines, and certain gene therapy products. For example, some small gene therapy vectors in theory could still be filtered with large virus retentive filters, for example that target viruses greater than 50-60 nm. Whether this step has been implemented for these products on a widescale basis is not publicly available. The inability to undergo viral inactivation steps could contribute to a higher risk of disease transmission.

Product filtration: Unlike biotech products, cell therapy products cannot undergo a 0.2 micron sterile filtration step and/or virus retentive filtration, Tangential Flow Filtration (TFF) or TFD methods typically used for biotechnology products.

Batch size: Although the batch size for autologous products is N=1, the batch size of some off -the-shelf products manufactured from HCT/Ps is scaled to potentially treat a large number of patients.

Patient population: The risk of disease transmission should also be viewed in terms of the risk to the intended patient population. Various factors, such as patient age, general health, and immune status, are likely to impact the risk to a given patient populations.

Time for testing: In general, for products which have a long shelf life (e.g., cryopreserved products,) there is sufficient time to conduct testing of the DS/DP in a manner that allows all test results to be available prior to release. However, for fresh products, there is a limited time available between completion of manufacturing and administration to patients, which makes it very difficult to conduct product testing.

Table 2 provides a summary of risks associated with each type of product, with the highest risk of transmission being associated with off -the shelf allogeneic products that are comprised of either tissue engineering products, cell therapies, or gene modified cellular products. This next highest risk is for tier 2 risk products that include autologous products, followed by products that are closer in nature to biotech products, such as gene therapy (AAV) products or exosomes (defined as Tier 3).

Although it is very difficult to know exactly how this novel virus will impact manufacture of products in the cell and gene therapy space, it is safe to say that a risk-based approach to prevent transmission of SARS-CoV-2 is a prudent approach.

Recommendations for Cell and Gene Therapy Products

In view of current uncertainty related to SARS-CoV-2 virus disease transmission, diagnostic and testing, the authors concur that implementation of a case-by-case review of the product’s risk profile, as recommended by the FDA guidance, is warranted to mitigate risk of disease transmission. The authors propose that this goal could be accomplished by instituting a subset, or all, of the recommendations outlined below:

For all allogeneic off -the-shelf products that belong to the highest risk category, the following is recommended:

1. Voluntary testing of the final drug product using sensitive validated tests for SARS-CoV-2
2. Voluntary screening of donors for tissue HCTPs recovered after January 1, 2020*+9
3. Voluntary testing of human-derived materials manufactured from tissue collected after January 1, 2020
4. Voluntary screening and/or testing of all operators who come into contact with the product. Comply with recent FDA guidance on COVID-19 impacted facility personnel.
5. Implement rigorous application of CGMP including considerations for product segregation, cleaning and environmental controls, line clearance and change over during manufacturing and product manipulation at the clinical site.

Impact on Biotech Products

The risk profile for SARS-CoV-2 contamination of biopharmaceuticals as discussed above is very low. SARS-CoV-2 is unlikely to get introduced in the first place, given the pre-existence of cell banks and extent of closed processing from start to finish during manufacturing. The most conceivable portal of entry to open parts of the process would be from asymptomatic operators, perhaps during pre-culture open manipulations. However, extensive gowning, use of LAF hoods and other aseptic procedure precautions strongly mitigate against this risk. It should be noted that the FDA guidance recommends firms to follow CDC guidance for COVID-infected employees at manufacturing sites.¹

Propagation of SARS-CoV-2 in a commercial CHO cell bioreactor culture is at most a low risk. Based on a literature review, three of four cases of attempts to grow Coronaviruses in CHO failed;10-13 the only successful case was a different Coronavirus and only in serum containing media. Thus, propagation of Cov-2 in protein-free CHO cell bioreactor cultures is very unlikely, but not impossible. In contrast, routine harvest testing by the routine indicator cell co-cultivation screen is highly likely to detect contaminating SARS-CoV-2; this new virus as well as the related CoV-1 virus that caused the SARS outbreak in the last decade forms CPE in Vero cells very rapidly.¹³

In contrast to some of cell and gene therapy products, process clearance of Coronaviruses during biotechnology manufacture is likely to be very robust. Clearance evaluation of smaller and more hardy viruses like parvoviruses is an industry standard practice, as outlined in the regulatory guidance ICH Q5A.14 A typical bioprocess can remove nine to ten+ log10 of hardy and small viruses like Parvovirus, and several log10 more of larger enveloped viruses like murine retrovirus. Coronaviruses are ss (+) strand RNA viruses that are enveloped and relatively large (100-160 nm, depending on the type). The large size of Coronaviruses all but assures complete clearance by both small and large virus retentive filters that are standard in bioprocessing. Many biotech manufacturing schemes also include detergent inactivation steps, which would likely dissolve their membranes.

These procedures are mandated by the International Conference on Harmonization14 already and almost completely assure the safety of biotech products with respect to Coronavirus. They also address the main recommendations of the June 2020 FDA guidance for assessing the overall Cov-2 risk of bioprocesses:

• The potential for the production cell line to replicate SARS-CoV-2
• Whether current cell bank and harvest testing for viruses would detect SAR-CoV-2
• The effectiveness of viral clearance and inactivation steps for SARS-CoV-2
• Controls are in place for procedures taking place in open systems (e.g., buffer and media preparation areas)

In the authors’ estimation, CoV-2 is unlikely to get introduced in the first place, and propagation of in CHO cell bioreactor cultures is unlikely but not impossible. Routine harvest testing that is in place is highly likely to detect contamination by CoV-2. If present, Coronavirus would be completely removed from the product stream by virus filtration and probably by other steps.

Overall Conclusions

In conclusion, we fully support the recommendations in the June

2020 FDA guidance for industry covering GMP considerations in the Coronavirus era.

• Although the risk posed by the Cov-2 virus is minimal in terms of getting into or remaining in biopharmaceutical products.
• The nature of the supply chain poses a relatively higher risk of disease transmission as human donor material collection is involved. This needs to be balanced against the fact that, although the impact of COVID-19 on clinical trial operation has been significant, the pandemic has generated a sense of urgency and new opportunities for the development of therapies supported by private and public governmental agencies, particularly in the field of cell and gene therapy.
• Prudent flexibility is key. As an example, if a sponsor is currently developing an allogeneic cellular product, the theoretical risks discussed do not necessarily warrant a change in the development plan, Rather, gaining a thorough understanding of the potential risks should allow the sponsor to determine whether or not implementation of additional mitigation procedures may be prudent.

In summary, it’s clear that cell and gene therapy as well as biotechnology product field should stay the course but with some adjustments and enhancements to viral safety approaches.

References

*The draft guidance published April 1, 2020 states: “At this time, FDA does not recommend that establishments use laboratory tests to screen asymptomatic HCT/P donors. Based on available information, it appears that SARS-CoV-2 has only been detected in blood samples of a small percentage of severely ill patients. The HCT/P establishment’s responsible person must evaluate a prospective donor and determine eligibility (21 CFR 1271.50). Based on the limited information available at this time, establishments may wish to consider, whether, in the 28 days prior to HCT/P recovery, the donor

• cared for, lived with, or otherwise had close contact with individuals diagnosed with or suspected of having COVID-19 infection; or
• been diagnosed with or suspected of having COVID-19 infection.

For HCT/Ps regulated as biological products under Section 351 of the Public Health Service Act, FDA is continually assessing available scientific evidence, and evaluating benefits and risks, to determine whether SARS-CoV-2 testing is warranted on certain types of HCT/Ps used in the manufacture of a biological product and/or warranted for the final product.

FDA will continue to monitor the situation and will issue updates as information becomes available”.

+ Donor testing is not recommended at this time since as outlined in regulation donor testing must be performed using FDA licensed, cleared or approved test kit and testing must be conducted by a CLIA certified lab or lab meeting equivalent requirements as determined by the Center for Medicare and Medicaid Services and for the timing of specimen collection for testing, manufacturers must collect the donor specimen for testing at the time of recovery of cells or tissue from the donor or up to 7 days before and after recovery except for leukocyte rich cells whereby manufacturers may collect donor specimens 30 days before recovery (21 CFR 1271 .80).

# “Any person shown at any time (either by medical examination or supervisory observation) to have an apparent illness or open lesions that may adversely affect the safety or quality of drug products shall be excluded from direct contact with components, drug product containers, closures, in-process materials, and drug products until the condition is corrected or determined by competent medical personnel not to jeopardize the safety or quality of drug products. All personnel shall be instructed to report to supervisory personnel any health conditions that may have an adverse effect on drug products” (21 CFR 211.28 (d)).

References

1. FDA. 2020. Good Manufacturing Practice Considerations for Responding to COVID-19 Infection in Employees in Drug and Biological Products Manufacturing. US Food and Drug Administration, Silver Spring Maryland
2. https://www.nature.com/articles/d41586-020-00889-6
3. https://www.linkedin.com/feed/update/urn:li:activity:6670885699127951360
4. https://www.nih.gov/news-events/news-releases/new-coronavirus-stable-hourssurfaces
5. https://science.sciencemag.org/content/367/6485/1412.full
6. https://www.cdc.gov/coronavirus/2019-ncov/community/organizations/cleaningdisinfection.html
7. https://regulatory-access.parexel.com/covid-19/virus-filtration-a-key-manufacturingstep-keeping-medicines-safe-including-from-emerging-viruses-like-covid-19-4
8. https://regulatory-access.parexel.com/covid-19/regulatory-blog-bioprocessing-andbiologics-risk-from-coronavirus-4
9. https://www.fda.gov/vaccines-blood-biologics/safety-availability-biologics/2020-safety-and-availability-communications
10. Francis MJ. 2003. Propagation of bovine coronavirus in chinese hamster ovary cells. United States Patent 6514502: Schering-Plough Veterinary Corporation.
11. Berting, A., Farcet, M., Kriel, T. 2010. Virus Susceptibility of Chinese Hamster Ovary (CHO) Cells and Detection of Viral Contaminations by Adventitious Agent Testing Biotechnol. Bioeng. 106:598
12. Wiebe, ME, Becker, F, Lazar R, May L, Casto B, Semense M, Fautz C, Garnick R, Miller C, Masover G, Bergmann D, Lubiniecki AS. A multifaceted approach to assure that recombinant tPA is free of adventitious virus. In: Advances in animal cell biology and technology for bioprocesses. Speir RE, editor. London: Butterworths: 1989, 68-71.
13. Mossel, E., Huang, C., Narayanan, K., Makino, S., Tesh, R., Peters, C. . 2005 Exogenous ACE2 Expression Allows Refractory Cell Lines To Support Severe Acute Respiratory Syndrome Coronavirus Replication. J. Virology 79(6): 3846-3850
14. ICH. 1998. Q5A (R1) Quality of Biotechnological Products: Viral Safety Evaluation of Biotechnology Products Derived from Cell Lines of Human or Animal Origin. International Conference on Harmonization, Geneva Switzerland