Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)
Summary of Recent Changes
- This guidance is intended for clinical laboratory and support staff who handle or process specimens associated with COVID-19. Guidance for Point-Of-Care Testing can be found here.
- All laboratories should perform a site-specific and activity-specific risk assessment and follow Standard Precautions when handling clinical specimens. See Biological Risk Assessment: General Considerations for Laboratories
- Refer to List Nexternal icon on the Environmental Protection Agency (EPA) website for EPA-registered disinfectants that have qualified under EPA’s emerging viral pathogens program for use against SARS-CoV-2.
- Cultures of SARS-CoV-2 should be handled in a Biosafety Level 3 (BSL-3) laboratory using BSL-3 practices, and inoculation of animals with infectious wild-type SARS-CoV-2 should be conducted in an Animal Biosafety Level 3 (ABSL-3) facility using ABSL-3 practices and respiratory protection.
- Suspected and confirmed SARS-CoV-2 positive clinical specimens, cultures, or isolates should be packed and shipped as UN 3373 Biological Substance, Category B.
All clinical specimens may contain potentially infectious materials. Precautions should be taken when handling specimens suspected or confirmed to be positive for SARS-CoV-2, the virus that causes COVID-19. Timely communication between clinical and laboratory staff is essential to minimize the potential risk of handling specimens from patients with possible SARS-CoV-2 infection. These specimens should be labeled accordingly, and the receiving laboratory should be alerted to ensure proper specimen handling. General and specific biosafety guidelines for handling SARS-CoV-2 specimens are provided below. For additional information on handling SARS-CoV-2 specimens, refer to the Laboratory Frequently Asked Questions.
All laboratories should perform a site-specific and activity-specific risk assessment to identify and mitigate risks. Risk assessments and mitigation measures are dependent on:
- The procedures performed
- Identification of the hazards involved in the process and procedures
- The competency level of the personnel who perform the procedures
- The laboratory equipment and facility
- The resources available
Follow Standard Precautions | Section IV when handling clinical specimens, all of which may contain infectious materials. Standard Precautions include hand hygiene and the use of specific personal protective equipment (PPE) determined by the potential for exposure to blood, body fluids, and infectious material. PPE, such as laboratory coats or gowns, gloves, eye protection, or a disposable mask and face shield, can help protect the skin and mucous membranes of the eyes, nose, and mouth.
For more information, see
- Biological Risk Assessment: General Considerations for Laboratories
- Core Infection Prevention and Control Practices for Safe Healthcare Delivery in All Settings
Decontaminate work surfaces and equipment with appropriate disinfectants by using an EPA-approved disinfectant for SARS-CoV-2external icon. Laboratory waste generated during processing and testing should be discarded as biohazardous waste. Waste disposal regulations vary from state to state; therefore, all waste disposal procedures must comply with local, regional, state, national, and international regulations. See EPA regulationsexternal icon and State Universal Waste Programs in the United States | Hazardous Waste | US EPAexternal icon for more information.
For training courses available online, see Biosafety Training | CDC.
Routine diagnostic testing procedures, such as the following activities, can be handled in a BSL-2 laboratory using Standard Precautions:
- Initial processing of specimens
- Using automated instruments and analyzers
- Staining and microscopic analysis of fixed smears
- Examination of bacterial cultures
- Pathologic examination and processing of formalin-fixed or otherwise inactivated tissues
- Molecular analysis of extracted nucleic acid preparations
- Final packaging of specimens for transport to diagnostic laboratories for additional testing (specimens should already be in a sealed, decontaminated primary container)
- Using inactivated specimens, such as specimens in nucleic acid extraction buffer
- Performing electron microscopic studies with glutaraldehyde-fixed grids
- Performing routine antibody or antigen detection tests
The practice of anatomic pathology plays a critical role in determining accurate disease diagnoses by studying organ tissues and fluids. Anatomic pathology includes surgical pathology, histotechnology, cytology, and autopsy.
Risks associated with surgical pathology and some cytology procedures occur during the manipulation of fresh tissue and body fluids from patients who may have an unknown or known infectious disease, such as COVID-19. Risks are increased in the surgical grossing room during manual specimen handling, tissue dissection, and the preparation of frozen sections of tissue using a cryostat. These procedures can result in percutaneous exposures from punctures or cuts, droplet or aerosol exposures from splashes of blood and body fluids, and exposures from surfaces contaminated with the virus.
Clinical laboratory and support staff need to be aware of these risks and provided effective mitigation procedures. See Laboratory Frequently Asked Questions for more information.
For information on autopsies, see Collection and Submission of Postmortem Specimens from Deceased Persons with Known or Suspected COVID-19
Note: Anatomic pathology uses different procedures and workflows than those used in clinical pathology, and therefore the risks and mitigation controls needed to protect personnel may be different. At a minimum, all personnel—whether practicing anatomic or clinical pathology should follow Standard Precautions | Section IV when handling clinical specimens, including hand hygiene and the use of PPE, such as laboratory coats or gowns, gloves, eye protection or a disposable mask and face shield, to help protect the skin and mucous membranes of the eyes, nose, and mouth.
Point-of-Care (POC) tests are intended to supplement laboratory testing or extend testing to communities and populations that cannot readily access laboratory testing. In addition, POC testing helps address emerging outbreaks quickly.
See Guidance for SARS-CoV-2 Point-of-Care and Rapid Testing | CDC for more information.
For self-test kits, see Self-Testing | CDC.
This guidance for environmental testing is intended only for laboratories that perform virus concentration as part of the procedure for wastewater/sewage surveillance testing. This guidance does not include public health or clinical diagnostic laboratories that handle COVID-19 clinical specimens or BSL-3 laboratories that perform culture and isolation of SARS-CoV-2. Site- and activity-specific biosafety risk assessments should be performed to determine if additional biosafety precautions are needed based on situational activities, such as high testing volumes, and the likelihood of generating infectious droplets and aerosols.
Procedures that concentrate viruses, such as precipitation or membrane filtration, can be performed in a BSL-2 laboratory with unidirectional airflow and BSL-3 precautions, including respiratory protection and a designated area for donning and doffing PPE. The donning and doffing spaces should be separated from each other to avoid cross-contamination. Work should be performed in a certified Class II biological safety cabinet (BSC).
Suspected or confirmed SARS-CoV-2 positive specimens, cultures, or isolates must be packed and shipped ppt icon[14 MB, 10 pages] | Download pdf icon[1 MB, 10 pages] as UN 3373 Biological Substance, Category B, in accordance with the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulationsexternal icon and U.S. Department of Transportation’s (DOT) Transporting Infectious Substances Safelypdf iconexternal icon publication. Personnel must be trained to pack and ship according to the regulations and in a manner that corresponds to their function-specific responsibilities.
Procedures with a high likelihood of generating aerosols or droplets should be conducted using either a certified Class II BSC or additional precautions to provide a barrier between the specimen and personnel. Examples of these additional precautions include centrifuge safety cups, sealed centrifuge rotors to reduce the risk of exposure to laboratory personnel, and additional PPE, such as an N95 respirator or disposable mask with a face shield.
Site- and activity-specific biosafety risk assessments should be performed to determine if additional biosafety precautions are warranted based on situational needs, such as high testing volumes.
Virus isolation in cell culture and initial characterization of viral agents recovered in cultures of SARS-CoV-2 should be conducted in a BSL-3 laboratory using BSL-3 practices. To determine appropriate biosafety mitigation measures, laboratories should perform an activity-specific biosafety risk assessment that evaluates laboratory facilities, personnel and training, practices and techniques, safety equipment, and risk mitigation measures. Biosafety professionals, laboratory management, and scientific and safety experts should be involved in the risk assessment process.
Inoculation of animals with infectious wild-type SARS-CoV-2 virus should be conducted in an ABSL-3 laboratory using ABSL-3 practices and respiratory protection.
For more information, see:
Laboratory waste generated during processing and testing should be discarded as biohazard waste. All waste disposal must comply with local, regional, state, national, and international regulations. Note that waste disposal regulations may vary at the state and local level; therefore, see Environmental Protection Agency regulationsexternal icon and State Universal Waste Programs in the United States | Hazardous Waste | US EPAexternal icon for more information.
- APHL Risk Assessment Best Practicespdf iconexternal icon
- Biological Risk Assessment: General Considerations for Laboratories
- Biosafety in Microbiological and Biomedical Laboratories (BMBL), 6th Editionpdf icon
- CDC 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settingspdf icon
- CDC Guidance for Point-Of-Care Testing
- CDC Isolation Precautions
- CDC Laboratory Frequently Asked Questions
- CDC Schematic for packaging, UN 3373 Category Bpdf icon
- CFR 49 PART 173.134 Class 6, Division 6.2external icon
- CFR 49 PART 173.199 Category B Infectious Substancesexternal icon
- CFR 49 PART 173 General Requirements for Shipments and Packaging external icon
- Environmental Protection Agency (EPA) regulationsexternal icon
- EPA List N: Disinfectants for Use Against SARS-CoV-2external icon
- FAQs to Lower Minimum Required Biosafety Containment Level for Research Subject to Guidelines (NIH)external icon
- Guidelines for Safe Work Practices in Human and Animal Medical Diagnostic Laboratoriespdf icon
- Guide to Packaging Category B Diagnostic Samplespdf iconexternal icon
- IATA Packing Instructions 650 for UN 3373external icon
- Click on “Infectious substances,” then the download option packing instructions.
- Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19)
- Laboratory Biosafety Guidance for Research with SARS-CoV-2 and IBC Requirements (NIH)external icon
- Longhorn PrimeStore Molecular Transport Medium Fact Sheet pdf icon
- Preparing and Supporting Laboratories Responding to COVID-19
- Safe Labs | CDC
- Saf-T-Pak Packaging Checklist, see Category Bpdf icon
- SARS-CoV-2 Specimens: Packing and Shipping ppt icon[14 MB, 10 pages] | Download pdf icon[1 MB, 10 pages]
- SARS-CoV-2 (COVID-19) Fact Sheet: Guidance – Proposed Use of Point-of-Care (POC) Testing Platforms for SARS-CoV-2 (COVID-19) pdf icon
- Standard Precautions | Section IV
- State Universal Waste Programs in the United States | Hazardous Waste | US EPAexternal icon
- WHO Laboratory biosafety guidance related to the novel coronavirus (2019-nCoV)-World Health Organizationpdf iconexternal icon
- WHO Laboratory Biosafety Manual, 3rd editionpdf iconexternal icon
Revisions made on September 19, 2020 include:
- New link under Resources to DLS Preparing and Supporting Laboratories Responding to COVID-19 page
Revisions made on August 7, 2020 include:
- Standard Precautions
Revisions made on July 16, 2020 include:
- Added DOT resources to Specimen Packing and Shipping and Resource section
Revisions made on July 13, 2020 to update:
- Language for virus isolation
Revisions made on June 3, 2020 include:
- Added anatomic pathology guidance for COVID-19
- Updated Point-of-Care testing guidance for COVID-19
Revisions made on May 11, 2020 include recommendations for:
- Point-of-Care testing guidance for COVID-19
- Added information on PPE to the “General Guidance” section
- Added Biological Risk Assessment: General Considerations for Laboratories resource to the “General Guidance” section
- Added Core Infection Prevention and Control Practices for Safe Healthcare Delivery resources to the “General Guidance” section
- Added OSHA Bloodborne Pathogens Standard resource to the “General Guidance” section
- Added EPA-approved disinfectant for SARS-CoV-2 resource to the “General Guidance section
- Added Environmental Protection Agency (EPA) regulations and State Universal Waste Programs in the United States | Hazardous Waste | US EPA resources to the “General Guidance” section
- Added information on PPE to the “Anatomic Pathology” section
- Deleted “Decentralized and Point-of-Care Testing” section and provided a link to the updated Guidance for SARS-CoV-2 Point-of-Care and Rapid Testing webpage
- Added information on N95 respirator and disposable mask to “Procedures with a High Likelihood of Generating Droplets or Aerosols” section
- Added language on avoiding cross-contamination to the “Environmental Testing” section
- Add language on Animal Biosafety Level 3 (ABSL-3) practices during inoculation of animals with infectious wild-type SARS-CoV-2 virus to the “Virus Isolation” section
- Added link for state EPA regulations to the “Laboratory Waste Management” section
- Added links to the “Additional Resources” section