Frequently Asked Questions about Biosafety and COVID-19

Updated June 5, 2020

Specimen Handling

All laboratories should perform a site-specific and activity-specific risk assessment to identify and mitigate risks and determine if enhanced biosafety precautions are warranted based on situational needs, such as high testing volumes, and the likelihood to generate infectious droplets and aerosols. Risk assessments and mitigation measures are dependent on the procedures performed, identification of the hazards involved in the process and/or procedures, the competency level of the personnel who perform the procedures, the laboratory equipment and facility, and the resources available.

The risk assessment should identify all potential scenarios of a particular activity that could produce a negative outcome. The risk assessment should prioritize those potential negative outcomes, or risks, based on an evaluation of the likelihood and consequences of each of those identified risks. The risk assessment should determine the most appropriate control measures, and how the system will measure the effectiveness of those control measures.

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For procedures with a high likelihood to generate aerosols or droplets, use either a certified Class II Type A1 or A2 BSC or additional precautions to provide a barrier between the specimen and personnel. Examples of these additional precautions include personal protective equipment (PPE), such as a surgical mask or face shield, or other physical barriers, like a splash shield; centrifuge safety cups; and sealed centrifuge rotors to reduce the risk of exposure to laboratory personnel.

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For viral testing of specimens conducted outside of a traditional clinical laboratory, such as rapid respiratory testing, use Standard Precautions to provide a barrier between the specimen and personnel during specimen manipulation.

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If laboratory personnel have direct contact with suspected or confirmed COVID-19 patients, they should follow recommended PPE for health care providers while in the presence of these patients.

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Routine viral testing of patient specimens, such as the following activities, can be handled in a BSL-2 laboratory using Standard Precautions:
• 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
• Electron microscopic studies with glutaraldehyde-fixed grids

For additional information, refer to the following:

Decontaminate work surfaces and equipment with appropriate disinfectants. Use EPA-registered hospital disinfectants with label claims to be effective against SARS-CoV-2external icon. Follow manufacturer’s recommendations for use, such as dilution, contact time, and safe handling.

Store specimens at 2-8oC for up to 72 hours after collection. If a delay occurs in extraction, store specimens at -70oC or lower. Store extracted nucleic acid samples at -70oC or lower.

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Handle laboratory waste from testing suspected or confirmed COVID-19 patient specimens as all other biohazardous waste in the laboratory. Currently, there is no evidence to suggest that this laboratory waste needs additional packaging or disinfection procedures.

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Personnel should adhere to standard procedures associated with other respiratory pathogens, such as seasonal influenza and other human coronaviruses, when they transport specimens within a facility. Personnel should perform site- and activity-specific risk assessments to determine if enhanced biosafety precautions are warranted based on situational needs.

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Standard Precautions are based on the principle that all blood, body fluids, secretions, nonintact skin, mucous membranes, and excretions (except sweat) may contain transmissible infectious agents. Standard Precautions include hand hygiene and the use of personal protective equipment (PPE) such as laboratory coats or gowns, gloves, and eye protection.

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Aerosols and droplets containing particles that are <100 μm in diameter are not visible to the naked eye. Laboratory workers may not be aware that such particles can be generated during many laboratory procedures and that these particles could be inhaled or could cross-contaminate work surfaces, materials, and equipment.

Infectious aerosols are small liquid or solid particles suspended in the air that contain infectious agents. They can disperse throughout the laboratory and remain infective over time and distance. These particles are of a size that may be inhaled into the lower respiratory tract (<5 μm in diameter). Examples of organisms transmitted by aerosols include spores of Aspergillus spp., Mycobacterium tuberculosis, rubeola virus (measles), and varicella-zoster virus (chickenpox).

Droplets traditionally are defined as larger infectious particles (>5 μm in diameter) that rapidly fall out of the air, contaminating gloves, the immediate work area, and the mucous membranes of the persons performing the procedure.

Examples of infectious agents that are transmitted via the droplet route include Bordetella pertussis, influenza viruses, adenovirus, Mycoplasma pneumoniae, SARS-associated coronavirus (SARS-CoV), group A streptococcus, and Neisseria meningitidis.

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Many routine laboratory procedures can potentially generate aerosols and droplets that are often undetectable. The following laboratory procedures have been associated with the generation of infectious aerosols and droplets: centrifugation, pipetting, vortexing, mixing, shaking, sonicating, removing caps, decanting liquids, preparing smears, flaming slides, aliquoting and loading specimens, loading syringes, manipulating needles, syringes or sharps, aspirating and transferring blood and body fluids, subculturing blood culture bottles, spilling specimens, and cleaning up spills.

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It depends on the type of specimen being transported:

  • CDC recommends that respiratory specimens from patients with suspected or confirmed COVID-19 should not be transported through pneumatic tubes. At this time, this recommendation only applies to suspected or confirmed COVID-19 respiratory specimens. Examples of respiratory specimens include nasopharyngeal (NP) and oropharyngeal (OP) swabs, nasal mid-turbinate (NMT) swabs, tracheal and lower respiratory tract aspirates, bronchoalveolar lavage (BAL) specimens, and sputum.
  • Based on currently available data, other types of specimens, such as blood, urine, and feces, are still acceptable to transport through pneumatic tubes.

Facilities should ensure that all personnel who transport specimens via pneumatic tubes are trained in safe handling practices, specimen management, and spill decontamination procedures.

Each facility should also evaluate its risks and determine the most appropriate biosafety measures and practices to implement.

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Testing sites that operate a POC diagnostic instrument must have a current Clinical Laboratory Improvement Amendments of 1988 (CLIA) certificate. During the COVID-19 public health emergency, the Centers for Medicare & Medicaid Services (CMS) will permit a laboratory to extend its existing Certificate of Waiver to operate a temporary COVID-19 testing site in an off-site location (e.g., long-term care or correctional facilities). The temporary COVID-19 testing site is only permitted to perform waived tests, consistent with the laboratory’s existing CLIA certificate, and must be under the direction of the existing laboratory director.

Laboratories should consider the following when using POC instruments for COVID-19 diagnostic purposes:

  • Use the instrument in a location that has a current CLIA certificate.
  • Perform a site-specific and activity-specific risk assessment to identify and mitigate safety risks.
  • Train staff on the proper use of the instrument and ways to minimize their risk of exposure.
  • Follow Standard Precautions when handling clinical specimens, including hand hygiene and the use of PPE, such as laboratory coats or gowns, gloves, and eye protection. If needed, additional precautions can be used, such as a surgical mask or face shield, or other physical barriers, such as a splash shield to work behind.
  • When using patient swabs, minimize contamination of the swab stick and wrapper by widely opening the wrapper before placing the swab back into the wrapper.
  • Change gloves after adding patient specimens to the instrument.
  • Decontaminate the instrument after each run by using an EPA-approved disinfectant for SARS-CoV-2 and following the manufacturer’s recommendations for use, including dilution, contact time, and safe handling.

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Specimen Packing and Shipping

For transporting patient specimens, cultures or isolates, personnel must be trained in the proper safety, packing, and shipping regulations for Division 6.2, UN 3373 Biological Substance, Category B in accordance with the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulations (DGR)external icon. Personnel should be trained in a manner that corresponds to their function-specific responsibilities.

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Pack and ship suspected or confirmed SARS-CoV-2 patient specimens, cultures or isolates as UN 3373 Biological Substance, Category B, in accordance with the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulations (DGR)external icon:

  1. A leakproof primary container.
  2. A leakproof, watertight secondary packaging with absorbent material.
  3. A rigid outer packaging to protect the specimens during shipment.

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Specimens should be shipped at 2-8oC with ice packs. If the specimen is frozen, ship overnight on dry ice. The primary receptacle and the secondary packaging should maintain their integrity at the temperature of the refrigerant used as well as the temperatures and the pressures which could result if refrigeration were lost. Packages containing dry ice should be designed and constructed so as to prevent the buildup of pressure and to allow the release of gas that could rupture the packaging.

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A: Ensure the outer package has been properly marked and labeled with the following:

  1. Hazard labeled with UN Identification Number already on label – UN 3373
  2. Biological Substance, Category B
  3. Shipper’s name, address, and phone number
  4. Receiver’s name, address, and phone number
  5. Name and phone number of a responsible person is optional if it is on the airway bill

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Ensure the outer package has been properly marked and labeled with the following:

  1. Hazard labeled with UN Identification Number already on label – UN 3373
  2. Biological Substance, Category B
  3. Hazard Labeled with UN Identification Number- UN 1845
  4. Dry Ice along with the net weight (kg) of the dry ice
  5. Shipper’s name and address
  6. Receiver’s name and address
  7. Name and phone number of a responsible person.

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The overpack should be marked in accordance with the packing instructions required for the outer package:

  1. Hazard labeled with UN Identification Number already on the label – UN 3373
  2. Biological Substance, Category B
  3. Shipper’s name, address, and phone number
  4. Receiver’s name, address, and phone number
  5. Package Orientation Label
  6. Marked with the word “Overpack”
  7. Name and phone number of a responsible person is optional if it is on the airway bill

For additional information, refer to the following:
• IATA Dangerous Goods Regulations Packaging Instruction 650pdf iconexternal iconpdf iconexternal icon
• Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)

A shipper’s declaration is not required for UN 3373 Biological Substances, Category B shipped samples. If an Air Waybill is used, the “Nature and Quantity of Goods” box should show “UN 3373 Biological Substance, Category B” along with the number of packages. If specimens are shipped on dry ice, include UN 1845, Dry Ice, 9, along with the net weight of the dry ice. See IATA PI 650 for additional information.

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Decontaminate work surfaces and equipment with appropriate disinfectants. Use EPA-registered hospital disinfectants with label claims to be effective against SARS-CoV-2external icon. Follow manufacturer’s recommendations for use, such as dilution, contact time, and safe handling.

For additional information, refer to the following:

Anatomic Pathology

Manual processing of fresh unfixed specimens, including frozen sections, should be conducted in a manner that provides a barrier between the specimen and personnel during specimen manipulation. In addition, protect the mucous membranes of the eyes, nose, and mouth during procedures that are likely to generate splashes, sprays, droplets, and aerosols. Examples of these barriers include:

  • Performing tissue dissection in a certified Class II A1 or A2 biological safety cabinet (BSC) if available
  • Working behind a splash shield
  • Using combinations of PPE, such as:
    • surgical mask with attached eye shield
    • surgical mask and goggles
    • mask and a face shield that fully cover the front and sides of the face
    • double gloves or mesh cut-resistant gloves
    • surgical scrubs, shoe covers, full gown, plastic apron, and hair covering
    • N95 respirators or powered air-purifying respirators (PAPRs) (the use of respiratory protection requires fit testing and appropriate training)

All laboratories should perform a site- and activity-specific risk assessment and follow Standard Precautionspdf icon  when handling specimen containers and paper requisitions that could have been contaminated by tissue and fluid specimens. This risk assessment may suggest use of some of these mitigation strategies:

  • Use face shields and/or work behind a splash guard whenever possible.
  • Store human specimens in closed containers that can be decontaminated before moving them to a secure area.

Place specimen containers in closed and clearly labeled plastic bins until pick-up and disposal according to your institutional waste management policies.

Avoid frozen sectioning from confirmed COVID-19 patients whenever possible. Talk with the relevant clinical and surgical teams about the clinical necessity and benefit of frozen sectioning and consider appropriate alternatives for suspected and confirmed COVID-19 cases. When frozen sectioning is unavoidable, the following are recommended, if possible:

  • Receive specimens in an area apart from administrative staff
  • Consider using a cryostat that has a downdraft and other safety features.
  • Use cryostats in a closed room that has inward directional (negative) airflow vented directly to the outside or recirculated through a HEPA filter to avoid contaminating the rest of the surgical pathology suite.
  • Provide grossing rooms with inward directional air flow.
  • Reduce the number of operators to a minimum.
  • Wear appropriate PPE, including but not limited to:
    • Fluid-resistant disposable double gloves and gown,
    • Fluid-resistant disposable apron,
    • Eye protection (face shield or goggles), and
    • N95 respirator or fluid-resistant surgical mask.
  • Do not use freezing sprays; they are not recommended by the manufacturers of cryostat instrumentation.
  • Wear cut-resistant, stainless steel mesh gloves during disassembly, cleaning, and disinfection of microtome knives.
  • Collect accumulated instrument shavings and discard them as biohazardous waste.
  • Follow local standard decontamination procedures of the cryostat and other surfaces. Ultraviolet lights are not a substitute for terminal cleaning of the instrument.

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Human tissues submitted for permanent pathologic examination typically undergo several processing steps with chemicals that have been shown to inactivate coronaviruses:

  • Studies with SARS-CoV-1 and MERS-CoV have shown that virus inactivation for these coronaviruses occurs in a time-dependent fashion with both formalin fixation and temperatures of 56°C or above.
  • Alcohol at 70% concentration or higher has been shown to inactivate the virus and tissue processing typically includes a series of alcohol dehydration steps that use 70% to 100% alcohol prior to paraffin embedding.
  • In addition, the final step of applying a glass or plastic coverslip to the slide provides an additional barrier between the personnel and the tissue.

For additional information, refer to the following:

Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoVexternal icon

Inactivation and safety testing of Middle East Respiratory Syndrome Coronavirusexternal icon

 Practical Guide to Specimen Handling in Surgical Pathologypdf iconexternal icon

Coronavirus disinfection in histopathologyexternal icon

NSH-COVID-19: Novel Coronavirus Resourcesexternal icon

No. Grossing stations pull formalin fumes away from the person who is doing the dissecting. In general, grossing stations are not as effective as biosafety cabinets at protecting the user from exposure to biological agents.

For additional resources related to biological safety cabinets, refer to: