Biocontainment: An Introduction To Control Levels & Practical Design Concepts

In part 1 of our article on biocontainment, we discussed the history of biocontainment as an outgrowth of medical research, especially the effort to develop vaccines for various worldwide diseases. We provided some definition of the biosafety levels (BSLs) established by the Centers for Disease Control and Prevention (CDC) based on risk considerations. We also discussed the regulatory regime for biological agents and, specifically, for designing a facility for an FDA or EU regulated product within the confines of the safety practices dictated by the CDC and design requirements of the NIH.
Our discussion continues with the physical application of GMP design practices as influenced by the CDC and NIH regulations. The first part of our design discussion covers various processes and their applicable BSL levels, to understand the risk levels and what types of processes must be contained. Finally, we will provide some practical (and required) design and building concepts that must be integrated into the GMP process to satisfy the FDA and EU, while taking into account requirements from the NIH and CDC.
Containment Controls By Level
For biosafety level 1, the practices and barriers are in line with GMP expectations for commercial manufacturing. Biosafety cabinets are not required at this level. State or other local codes will not typically allow discharge of live genetically engineered organisms.
Typically, a commercial GMP facility will meet the requirements of BSL-1, and single-use systems are amenable to these processes.
An example of a BSL-1 process is a gene therapy process using a recombinant adeno-associated virus. Because the starting bank and final product are infectious, the whole process is BSL-1. Due to the low requirements for BSL-1, GMP requirements will govern the manipulations used in this process. The low safety concern and low throughput make this process a good opportunity for using a waste management company to decontaminate all the waste materials off-site, thus reducing the facility’s footprint.
Biosafety level 2 requires primary barriers and begins to control flows in and out of spaces. Any open process that might generate an aerosol or splashing must be performed in biosafety cabinets or other physical containment apparatus. The facility needs the following:

  • liquid disinfect traps on vacuum lines
  • a method of decontaminating waste
  • handwashing sink and an eyewash station
  • removal of protective clothing/lab coat on leaving the BSL-2 area
  • airflow into the suite is recommended, providing a negative pressure

The vast majority of vaccine processes and therapies that use blood or primary cells fall into this category. While the regulations don’t require air locks or directional airflow, typically these features are added for GMP cross-contamination reasons, as most processes have steps where the bulk substance is no longer infectious. Viral screening and inactivation can be used to reduce the portion of the process that is BSL-2. These facilities typically have dedicated bio-waste drains and inactivation systems. In some cases, cell therapy facilities have been able to use certified medical waste haulers (which incinerate the waste) because the bulk of the contaminated waste is solid material.
In general, the industry has adapted single-use systems with a risk assessment based on thorough supplier vetting and pre-use integrity checks. Minor changes in tubing set construction (e.g., going with molded fittings over zip-tied barb fittings) have reduced the risk of leaks to an acceptable level.
An example of a BSL-2 process is the production of a seasonal influenza vaccine from the virus cell bank through virus attenuation. These facilities typically segregate the virus seed train from the cell culture seed train. The virus seed train can be done in single-use systems. The only limit to utilization of single-use systems would be for incubation of cell culture volumes above the typical single-use bioreactor sizes (2000L) and the associated harvest centrifugation of those large volumes.
Biosafety level 3 continues to build on BSL-2 and drives toward an entirely closed process. All manipulations must happen in a biological safety cabinet (BSC) or other physical containment. The facility needs HEPA filtration on vacuum lines, a method of decontaminating all waste leaving the area, a handwashing sink, and an eyewash station. A protective layer of clothing is to be donned before entering and removed on leaving the BSL-3 area. An airlock is required with airflow into the suite. There must be a way for personnel to verify airflow direction at the area entrance. The air can be recirculated, but only to the BSL-3 area, and all exhaust from the space must be HEPA filtered. Equipment that may produce infectious aerosols must be contained in primary barrier devices that exhaust air through HEPA filtration or other equivalent technology before being discharged into the laboratory area. Air exhausts must be situated away from air intakes. HEPAs need gas-tight isolation with decontamination ports and/or bag in/bag out capacity. Facility design should account for decontamination of large equipment that may have to leave the space. Showers for personnel leaving the space are an optional facility feature in the Biosafety in Microbiological and Biomedical Laboratories (BMBL), but may be required by other authorities. The BSL-3 space should be recertified annually.
There are few BSL-3 processes, and those typically have dedicated single-product facilities. The increased containment adds significant cost and drives the facility layout. The requirement to decontaminate all materials leaving the area results in large decontamination autoclaves at the BSL boundary. Frequently, the suites are designed to be isolated and fumigated. The complexity of dealing with showers and a handwashing sink in/adjacent to a classified space is a challenge brought about by applying laboratory standards to GMP facilities, but the risk of environmental monitoring counts can be reduced by using trap primers that feed disinfectant.
In general, the industry has been reluctant to embrace broad spectrum adoption of single use for BSL-3. One exception has been depth filtration. A single-use filter system can be pushed into an autoclave for decontamination, whereas steaming traditional stainless-steel housings is a challenge due to the bubble point pressure of the loaded filters.
An example of a BSL-3 process is development of a SARS coronavirus vaccine from the wild type virus, from viral bank through attenuation. The virus seed train could start in single-use systems, but would transition to stainless-steel systems once the volume exceeds what one person can easily handle (~20L 2D bag). Seals that contact the virus are typically flushed with clean steam or hot water for injection (WFI). Disc stack centrifuges are the hermetically sealed type or contain additional controls to mitigate aerosols. The bio-waste system is designed to be decontaminated by steam. Additional care should be taken in selecting instruments and electrical enclosures as the additional routine disinfections can take a toll on these installations and hamper any preventative maintenance activity.
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