Last Revised: May 12, 2023

Issued 4/26/20

Revised 5/5/20, 6/1/2020, 7/2/2020


Research involving COVID-19 patient specimens and SARS-CoV-2 virus is subject to enhanced oversight by the Biosafety office. Given that SARS-CoV-2 is a novel respiratory pathogen, additional precautions are necessary to protect staff and the community when working with potentially infectious materials. As dictated by the CDC, a site-specific risk assessment is required for projects utilizing patient specimens. Appropriate biosafety containment (BSL) will be determined by a biosafety officer after review of study population, type of sample, and proposed experimental manipulations.  


CDC Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with COVID-19
In accordance with CDC guidelines, general containment requirements for research projects are described below.
Biosafety Level Type of Experiment
  • Use of inactivated materials (*inactivation per approved SOPs)
  • Molecular analyses of extracted nucleic acids
BSL-2 Enhanced
  • Processing and inactivation of known or suspected patient samples including: urine, saliva, blood, NP swabs, OP swabs, endotracheal (ET) aspirates
  • Isolation and culture of SARS-CoV-2 virus
  • Amplification of SARS-CoV-2 virus
  • Generation of infectious clones 
  • Inactivation of materials with high viral load, including lung tissue and bronchoalveolar lavage (BAL) 

At this time, the following is not permitted outside of the BSL-3 laboratory:

  • Culture of primary cells from COVID-19 patients (due to potential for growing infectious virus). Contact a Biosafety Officer to discuss alternative approaches.

  • Flow cytometry of unfixed patient specimens. 

Additional projects that are not clearly delineated in the above table must be reviewed and appropriate containment will be set by the Biosafety office.
Note: Projects utilizing the UPenn Flow Cytometry and Cell Sorting Facility require prior review and approval by Dr. Jonni Moore. Investigators must present a written justification and description of experiments to Dr. Moore ( to receive approval.
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COVID-19 and BSL-3 Task Force
Reporting to the Institutional Biosafety Committee (IBC), the Task Force will help facilitate COVID-19 research by ensuring researchers are trained to handle patient samples at enhanced BSL-2 or at BSL-3 and conduct research in the BSL-3 laboratories. The task force will review scientific literature and emergent data to ensure appropriate containment is assigned to projects. Ad hoc meetings will be called as needed to facilitate evolving risk assessments.

The Task Force will advise the IBC on:

  • BSL-3 training requirements
  • Justification for BSL-3 research applications (BSL-3 Application Form II)
  • Experience of personnel proposed for new BSL-3 access and training (BSL-3 Application Form IV)
  • Containment requirements for use of patient specimens and novel experimental paradigms


Task Force Membership:

  • Maureen O’Leary, PhD, MBA, CBSP (ABSA), EHRS Executive Director 
  • Dan Kessler, PhD, Associate Professor of Cell and Developmental Biology, IBC Chair
  • Susan Weiss, PhD, Professor of Microbiology
  • Paul Bates, PhD, Professor of Microbiology
  • Sara Cherry, PhD, Professor of Pathology and Laboratory Medicine
  • Stuart Isaacs, MD, Associate Professor of Medicine, Associate Dean for Animal Research
  • Andrew Maksymowych, PhD, RBP (ABSA), Institutional Biosafety Officer, Associate Director Biosafety Programs


Projects requiring task force review can be submitted directly to EHRS Biosafety Team (

Biosafety Level 2 (BSL-2)
Biosafety Level 2 (BSL-2) is appropriate for work with inactivated patient specimens and extracted nucleic acids. Universal precautions are required for all work with human materials. 
  • Laboratory staff must be up to date on all EHRS-required lab safety training

  • Standard PPE is required: Lab coat, gloves, safety glasses

  • Universal masking is required in accordance with PA requirements

Additional information is available in the Penn Biosafety Manual
Biosafety Level 2 (BSL-2) Enhanced
Biosafety Level 2 (BSL-2) enhanced is required for processing of known or suspected COVID-19 patient samples. After samples have been inactivated by an approved SOP, materials may be handled under standard BSL-2 precautions. 
Working at BSL-2 enhanced requires:
  • Additional training, offered on WorkDay (see below).
  • Dedicated facility with certified Class II Biosafety Cabinet and closed door. 
  • Review of all SOPs to ensure necessary containment and appropriate biosafety measures are in place.
  • Contact EHRS Biosafety Team ( for review of your SOPs.
The BSL-2 enhanced guidance document below provides an overview of facility and procedural requirements for this level of biosafety containment. It is a supplement to specific training and SOP review. This document will be updated as new information becomes available.

BSL-2 Enhanced Guidance Document

WorkDay training can be self-assigned by going to the WorkDay protal and searching the course name BSL2 Enhanced Training for Processing COVID19 Patient Specimens- EHRS.

Biosafety Level 3 (BSL-3)
In accordance with the NIH Guidelines, all work requiring BSL-3 containment must be reviewed and approved by the Institutional Biosafety Committee (IBC).  Specialized training is required for all new BSL-3 users at Penn. Extensive prior research experience and demonstrated proficiency in proposed techniques is required. The following are examples of projects requiring BSL-3 containment and IBC approval:
  • Cell culture experiments with SARS-CoV-2 virus, including viral isolation and amplification, drug screens, and neutralization assays
  • Use of infectious virus for testing novel diagnostic platforms
  • Isolation of virus from patient specimens
  • Manipulation and inactivation of patient specimens with high viral titers, including lung tissue and bronchoalveolar lavage (BAL) fluid
Required documents for IBC review and instructions are available under the BSL-3 special containment page on the EHRS website
SARS-CoV-2 Virus Inactivation
Methods of viral inactivation are approved by the Biosafety office and are based on CDC guidance, published literature, and validation data from the UPenn BSL-3 lab. Currently approved methods of viral inactivation are listed in the following document:
Validated Inactivation Methods for SARS-CoV-2 and COVID-19 Positive Samples

Procedures must be followed exactly to ensure complete viral inactivation. 

The UPenn BSL-3 lab is currently evaluating additional methods of viral inactivation. If your downstream assays are not compatible with current approved methods, contact the COVID-19 and BSL-3 task force to request additional guidance. 

Shipping SARS-CoV-2 and COVID-19 Patient Samples
Anyone offering SARS-CoV-2 and COVID-19 patients samples must be trained to pack and ship according to the regulations and in a manner that corresponds to their function-specific responsibilities.
  • Patient specimens from suspected or confirmed cases of COVID-19 should be transported as UN 3373, “Biological Substance, Category B”, when they are transported for diagnostic or investigational purposes.
  • Viral cultures or isolates of SARS-CoV-2 should be transported as Category A, UN2814, “infectious substance, affecting humans”.
  • Pack and ship all specimens and cultures in accordance with the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulation.
  • The OSHA Bloodborne Pathogens Standard applies when handling/shipping human sourced materials.
For additional information about Dangerous Goods or hazardous materials shipping, refer to the Shipping website.