Working with SARS-CoV-2

The Institutional Biosafety Committee (IBC) has final determination on the biosafety level based on a risk assessment of the proposed work with SARs-CoV-2 and COVID-19 materials.

SARS-CoV-2 is a human betacoronavirus and the causative agent of the respiratory disease COVID-19. It is a positive-sense single-stranded RNA virus (+ssRNA) with a lipid envelope, a nucleocapsid that covers the RNA, and a “halo” of spike proteins, which assist with cellular entry and give viruses in this family the characteristic crown-like shape. Center for Disease Control & Prevention (CDC) and National Institute of Health (NIH) categorizes this virus as a Risk Group-2 (RG-2) pathogen. Under Cal-OSHA regulations it is also categorized as an aerosol transmissible disease. 

Biosafety Levels set the standard for the appropriate facility, engineering controls, administrative controls, work practices, and personal protective equipment to manage the hazards and risks inherent in life science research. The following Biosafety Levels, materials, or procedures serve as a framework to aid researchers in performing a risk assessment to determine the acceptable biosafety level for SARS-CoV-2 virus and COVID-19 patient samples.

Conducting Research with COVID-1 Samples or SARS-CoV-2 virus is general guidance on what type of work may be conducted at what biosafety level.

BSL-1

The following activities are suitable for BSL-1

• Fixed specimens or samples
• Inactivated samples including inactivated virus lysate
• Staining and microscopic analysis of fixed smears
• Molecular analysis of extracted nucleic acid preparations rendered non-viable
• Using automated instruments and analyzers (if aerosol containment is a feature) FACS – fixed samples
• Performing electron microscopic studies with glutaraldehyde- fixed grids
• Work with synthetically generated SARS-CoV-2 nucleic acids which lack a means of cellular entry.

BSL-2

The following activities are suitable for BSL-2 (BSL-2 facilities with BSL-2 work practices):

• Examination of bacterial cultures grown from known or suspected COVID-19 samples
• Aliquoting and/or diluting patient or environmental specimens
• Performing diagnostic tests that do not involve propagation of viral agents in vitro or in vivo
• Nucleic acid extraction procedures involving potentially infected specimens (human or animal).
• Precipitation or membrane filtration
• Preparation and chemical- or heat-fixing of smears for microscopic analysis
• Work with SARS-CoV-2 recombinant nucleic acids in host-vector systems (e.g. in viral vectors or prokaryotic models).
• Work with samples that generate aerosols must be handled within the biosafety cabinet.
• Handling of animal models within a biosafety cabinet (ABSL-2)
• Housing post infection (ABSL-2)

BSL-2+ work [BSL-2 Facility and BSL-3 Work Practices]

Work which may require BSL-2 facilities with BSL-3 work practices includes but is not limited to, processing of certain clinical samples from COVID-19 patients and work with the virus.

Work with SARS-CoV-2 virus requires the SARS-CoV-2 (BSL-2+) HCP.  

The following activities are suitable for BSL-2+ (BSL-2 facilities with BSL-3 work practices),

• Respiratory samples and secretions
• Work with virus including virus isolation in cell culture and initial characterization of viral agents recovered in cultures of SARS-CoV-2 specimens
• High Speed Cell Sorting or FACS with viable virus
• Inoculation of animal models using live virus (ABSL-2+)

In addition to BSL-2 practices and containment, when working with SARS-CoV-2 virus the following BSL-3 practices are required: 

1. All work must be performed in a biosafety cabinet and all items are disinfected prior to removal from the biosafety cabinet.  
   • No work on the open bench or in open bay laboratories. Any work on the open bench or in open bays requires detailed procedural description, aerosol mitigation measures, and IBC review and approval.
   • Sealed samples must be wiped with disinfectant upon removing them from the biosafety cabinet for transfer.
   • Waste is managed within a Biosafety cabinet. Disinfect tips with 10% bleach prior to disposal as biohazard waste. Disinfect the exterior of the biohazard waste bag prior to removal from BSC.
   • Exterior gloves are changed after working in the biosafety cabinet. All researchers must wash their hands with soap and water immediately after removing gloves.

2. Sealed safety cups or sealed rotors must be used when centrifuging outside of the biosafety cabinet.  Cups and rotors must be opened within a biosafety cabinet.
3. All sharps must have engineered protection devices.
   • Provide a written response as to why this cannot be accomplished in the BUA for IBC to review and approve. The IBC will review exceptions on a case by case basis.  
4. No glass is to be used.
   • Provide a written response as to why this cannot be accomplished in the BUA for IBC to review and approve. The IBC will review exceptions on a case by case basis.
5. Double gloves must be worn;
   • In cases where double gloving limits dexterity, then a single layer of nitrile gloves can be used. This exception must be approved by the IBC.  
   • When using double gloves, the interior glove must be taped (use lab tape, masking tape, painters’ tape) to the laboratory coat to prevent bare skin exposure.  
6. No eating or drinking is allowed in laboratory areas where this agent is handled.  
7. Regular and strenuous surface disinfection is required.  
8. Vaccination against SARS-CoV-2 is strongly advised. All those handling SARS-CoV-2 virus are required to complete a vaccine attestation. By reviewing and acknowledging the SARS-CoV-2 BSL-2+ Hazard Control Plan, you are confirming your understanding that vaccination against SARS-CoV-2 is strongly advised.
9. SARS-CoV-2is a regulated agent under the United States Government (USG) policy for Dual Use Research of Concern and Pathogens of Enhanced Pandemic Potential (DURC-PePP) as Category 2. Work with this agent may require review by the UC San Diego Institutional Review Entity (IRE). For questions or assistance about DURC-PePP materials and requirements, please visit Dual Use Research of Concern (DURC) or email DURC-IRE@ucsd.edu.

BSL-3

Experiments and agents are assigned Biosafety Level 3 if considered high risk for the individual, community, or environment. Researchers can request re-evaluation of the Biosafety Level as additional information is known. The IBC will evaluate these requests on a case-by-case basis.

The following is appropriate for BSL-3:

• Emerging variants of SARS-CoV-2 virus not yet characterized that will be cultured or grown out. Patient samples should continue to be handled at BSL-2 unless determined by the IBC to require BSL-3.
• Chimeric viruses
• Experiments or agents determined by the IBC on a case-by-case basis