SARS-CoV-2 Biological Agent Reference Sheet and Laboratory Guidance

Published: April 30, 2020
Last reviewed: March 23, 2026
Next scheduled review: March 2027, or sooner if CDC, NIH, FSAP, EPA, OSHA, New York State, or Cornell IBC requirements change.

This guidance is maintained by Cornell EHS Biosafety and Biosecurity. It is reviewed periodically and may be revised as federal guidance, medical countermeasures, institutional risk tolerance, or proposed research activities change.

All laboratories proposing work with infectious SARS-CoV-2, SARS-CoV-2 clinical or environmental samples, materials suspected of containing SARS-CoV-2, or recombinant or synthetic nucleic acid work involving SARS-CoV-2 sequences, infectious clones, replicons, pseudoviruses, reverse genetics systems, or chimeric constructs must contact Cornell Biosafety and obtain Cornell IBC approval through an MUA before starting work. Risk group, biosafety level, animal biosafety level, PPE, engineering controls, medical surveillance, and operational requirements are determined by Cornell Biosafety and the Cornell IBC through a site-specific and activity-specific risk assessment.

Work with PCR products and molecular cloning materials may be lower risk when they cannot generate infectious virus; however, residual nucleic acid on researchers, equipment, or in shared research space can confound surveillance or diagnostic results. Please see the guidance for labs performing these procedures.

Laboratories receiving infectious SARS-CoV-2 materials, materials known or reasonably expected to contain SARS-CoV-2, or nucleic acids capable of producing infectious forms of SARS-CoV-2 from outside the United States must determine whether a CDC import permit is required before shipment. Nucleic acids that cannot produce infectious forms of an infectious biological agent may be excluded from CDC import permitting when accompanied by the required importer certification statement.

SARS-CoV-2 itself is not a select agent. However, SARS-CoV/SARS-CoV-2 chimeric viruses resulting from deliberate manipulation of SARS-CoV-2 to incorporate nucleic acids coding for SARS-CoV virulence factors, or vice versa, are HHS select agents and restricted experiments. Proposed work to create, possess, use, or transfer these chimeric viruses must be submitted to the Federal Select Agent Program for review and approval before work begins.

Summary

Agent Type	Risk Group	Biosafety Level	Animal Housing Biosafety Level
Virus	RG2 starting point under the NIH Guidelines for research subject to the NIH Guidelines; final institutional determination is based on Cornell IBC/EHS risk assessment.	Containment is assigned by activity-specific risk assessment. BSL-2 may be appropriate for some approved activities, but BSL-2 Enhanced, BSL-3, or additional controls may be required for infectious virus, propagation, high-titer or large-volume work, genetic manipulation, animal work, or procedures with elevated aerosol or exposure potential.	ABSL containment is assigned by animal- and activity-specific risk assessment. ABSL-2 may be appropriate for some approved animal work, but ABSL-3 or additional controls may be required based on species, route, dose, shedding, procedures, and facility conditions.

Federal guidance note: CDC's current SARS-CoV-2 laboratory biosafety page is directed primarily to clinical laboratory and support staff handling or processing SARS-CoV-2 specimens, cultures, and environmental samples. It recommends BSL-2 facilities, practices, and procedures as a minimum for diagnostic research, anatomic pathology, environmental testing, and virus propagation, and ABSL-2 as a minimum for animal models. This is not a blanket institutional authorization for all SARS-CoV-2 research at BSL-2. Research protocols, including recombinant or synthetic nucleic acid work, infectious clone or rescue work, high-titer or large-volume work, animal inoculation, or activities with elevated aerosol or exposure potential, must be reviewed under the NIH Guidelines and Cornell's IBC risk assessment process; Cornell may require BSL-2 Enhanced, BSL-3, ABSL-3, or other additional controls.

Agent Characteristics

Description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA virus in the Coronaviridae family. It was first reported in association with pneumonia cases of unknown etiology in Wuhan, China in late 2019. Related coronaviruses that cause human disease include 229E, NL63, OC43, and HKU1, which usually cause mild to moderate respiratory illness, and SARS-CoV and MERS-CoV, which can cause severe disease.

Host Range: Humans and multiple susceptible animal species, including species used in research or known to be naturally infected. Final animal containment requirements are determined by species, route of exposure, viral strain or variant, dose, shedding, procedures, and facility controls.

Host Shedding:

Respiratory fluids, droplets, and aerosol particles
Saliva and oral/nasal secretions
Feces and other specimens, depending on infection status, specimen type, and host species
Direct contact with infected hosts or contaminated materials

Routes of Exposure to Humans: SARS-CoV-2 exposure can occur through inhalation of virus-containing droplets and aerosol particles, deposition of respiratory particles onto mucous membranes of the eyes, nose, or mouth, and contact with contaminated hands, materials, or surfaces followed by contact with mucous membranes. In laboratories, risk is driven by the material handled, viral concentration, infectious status, procedure type, aerosol or splash potential, sharps use, animal work, and effectiveness of primary containment.

Aerosol/inhalation
Droplet or splash exposure to mucous membranes
Direct contact
Contaminated items or surfaces followed by mucous membrane contact
Sharps or percutaneous exposure, when sharps are used

Infectious Dose: The infectious dose for humans is not precisely established. Laboratories should assume that exposure to infectious virus may present a meaningful risk and select containment and work practices through a site-specific and activity-specific risk assessment.

Incubation Period: Symptoms may appear 2-14 days after exposure.

Health Hazards

Signs and Symptoms: People with COVID-19 may have a wide range of symptoms, from mild illness to severe disease. Symptoms may change with new variants and may vary by vaccination status. Possible symptoms include:

Fever or chills
Cough
Shortness of breath or difficulty breathing
Sore throat
Congestion or runny nose
New loss of taste or smell
Fatigue
Muscle or body aches
Headache
Nausea or vomiting
Diarrhea

Immunizations: COVID-19 vaccines are available. Personnel should follow current CDC vaccine recommendations and any Cornell occupational health requirements applicable to their work.

Treatment / Medical Countermeasures: Antiviral treatment may be available for persons with mild to moderate COVID-19 who are at higher risk for severe disease. Options include nirmatrelvir-ritonavir (Paxlovid), remdesivir (Veklury), and molnupiravir (Lagevrio), when clinically appropriate. Treatment decisions are made by a licensed medical provider and are most effective when started early after symptom onset.

Personnel with medical conditions or other factors that may increase risk for severe COVID-19 should consult an appropriate healthcare provider or Occupational Medicine before performing work with a potential SARS-CoV-2 exposure risk. Work restrictions, accommodations, or additional medical surveillance may be required based on the approved MUA and occupational health assessment.

Agent Viability

Survival Outside Host	Disinfection	Inactivation
SARS-CoV-2 viability outside the host depends on surface or material type, temperature, relative humidity, organic load, and other environmental conditions. Laboratories should not rely on time alone as a decontamination method unless specifically justified and approved.	Use an EPA-registered disinfectant with a label claim for SARS-CoV-2, including products on EPA List N. Follow the manufacturer's label for dilution, surface compatibility, wet contact time, safe handling, and disposal.	All inactivation methods used to reduce containment requirements must be included in the approved MUA and written SOPs. Inactivation methods must be verified or otherwise accepted by Cornell Biosafety and the Cornell IBC before inactivated materials are handled under reduced containment.

Laboratory Hazards

Procedures with high likelihood of generating aerosols or droplets, including pipetting, centrifuging, grinding, blending, shaking, mixing, sonicating, vortexing, opening containers of infectious material, intranasal inoculation of animals, and harvesting infected tissues from animals or eggs
Handling viable virus, high-titer materials, large volumes, or concentrated virus preparations
Genetic modification, rescue, reverse genetics, infectious clone, or replicon work
Splash- or droplet-producing activities, including liquid culture handling and mechanical pipetting
Equipment contamination and cross-contamination of shared instruments or work areas
Sharps use, percutaneous injury, exposed skin, or uncovered wounds

Laboratory-Acquired Infections: Laboratory-associated SARS-CoV-2 infections have been reported at other institutions. Because community transmission can complicate attribution, this page does not maintain a fixed case count; proposed work must instead be evaluated by activity, containment, personnel, and facility risk factors.

Laboratory Handling Guidance

Risk assessment of lab activities is required before work begins, including nucleic acid extractions, work with clinical or environmental specimens, recombinant or synthetic nucleic acid work, and any work with infectious virus. All covered work must have an approved Memorandum of Understanding and Agreement with the IBC.

Containment Category	BSL-2 Baseline Activities	BSL-2 Enhanced Activities	BSL-3 or Additional Containment When Required
Materials and Activities	Automated instruments and analyzers when risks are controlled and the activity is approved in the MUA Staining and microscopic analysis of fixed smears after fixation/inactivation conditions are approved Pathologic examination and processing of formalin-fixed or otherwise approved inactivated tissues Molecular analysis of extracted nucleic acid preparations that cannot generate infectious virus Final packaging of specimens for transport by trained personnel Use of inactivated specimens after the inactivation method has been accepted or verified as required by the approved MUA	Centrifugation, vortexing, pipetting, or aliquoting of viable clinical or environmental specimens collected from known or strongly suspected infected sources for research purposes Preparation of chemical- or heat-fixed specimens for microscopic analysis before inactivation is complete or verified Nucleic acid extraction of potentially infectious specimens Preparation of inactivated specimens for laboratory assessments when primary material may contain infectious virus Activities requiring enhanced PPE, restricted access, dedicated equipment, or additional administrative controls under the approved risk assessment	Activities with infectious virus, virus propagation, high-titer or large-volume material, or procedures with elevated aerosol or exposure potential when Cornell Biosafety and the Cornell IBC determine that BSL-3 or additional containment is required Generation, rescue, or manipulation of infectious clones, recombinant/synthetic SARS-CoV-2, or SARS-CoV-2 systems capable of producing infectious virus when risk assessment requires BSL-3 or additional containment Inactivation of materials with high viral load when required by risk assessment, including endotracheal aspirates, lung tissue, bronchoalveolar lavage, or other high-risk specimens Use of live SARS-CoV-2 in animal models when ABSL-3 or additional containment is required by risk assessment Functional assays with infectious virus, including plaque assays, neutralization assays using live virus, virus capture/binding assays involving infectious material, or other procedures designated by the MUA Any SARS-CoV/SARS-CoV-2 chimeric virus work that is regulated as a select agent or restricted experiment, after all required institutional and federal approvals are in place

Personnel must not report to the laboratory when they have symptoms consistent with COVID-19 or another transmissible respiratory illness unless cleared under the applicable institutional process. Any symptom monitoring, testing, work restrictions, or medical surveillance requirements will be specified in the approved MUA, occupational health assessment, or incident response instructions.

Inactivation

All laboratories working with inactivated SARS-CoV-2 materials must describe the inactivation method in the MUA and in written SOPs. Inactivation methods used to reduce containment requirements must be verified by the laboratory or otherwise accepted by Cornell Biosafety and the Cornell IBC before work with the inactivated material proceeds under reduced containment. Verification data must be made available to EHS Biosafety and the Cornell IBC Chairs upon request.

Samples for RNA extraction are often collected in lysis or storage buffers designed to inactivate proteins and preserve RNA. These buffers may contain detergents or chaotropic agents that can inactivate enveloped viruses when used according to manufacturer instructions, but the effectiveness of a method depends on the sample matrix, volume, ratio of sample to reagent, contact time, temperature, organic load, and downstream handling. Laboratories must follow the approved SOP and may be required to verify the method when using conditions outside the accepted method.

Trizol and certain commercial extraction buffers have been evaluated for inactivation of SARS-CoV-2 or related coronaviruses under specified conditions. Use of these methods must follow the manufacturer's instructions and the approved MUA. Any deviation from accepted conditions, including changes in sample type, volume, reagent ratio, or contact time, may require additional verification.

Heat inactivation and chemical fixation may be acceptable for specific sample types and procedures when approved by the IBC. Heat, formalin, paraformaldehyde, alcohol-based fixation, and paraffin embedding methods must be evaluated based on sample thickness, viral load, matrix, temperature, exposure time, and downstream use. Manufacturer or published protocols do not replace the requirement to include the method in the approved MUA and SOPs.

All inactivation methods used must be included in the submitted MUA and written standard operating procedures (SOPs).

Personnel must demonstrate proficiency in carrying out the procedure successfully and as written; this proficiency should be documented by the designated principal investigator.
- If the laboratory wishes to use a method other than an accepted or approved method, the method must be verified before use under reduced containment.
Any inactivation procedure that requires opening the sample container or has the potential for aerosol or splash generation must take place inside a certified biosafety cabinet or other approved primary containment device.
Before any change to an inactivation method, a new or updated SOP must be submitted to EHS Biosafety for risk assessment and IBC review, as applicable.

Training

For BSL-2 and BSL-2 Enhanced Work

EHS Laboratory Safety Training
BSL-2 Training
Lab-specific protocol training, including specimen handling, spill response, waste handling, and inactivation procedures
Shipping training for personnel who package or ship regulated materials

For BSL-3 or ABSL-3 Work

BSL-3 or ABSL-3 training and documented demonstration of proficiency
Facility-specific entry, exit, PPE, emergency, medical surveillance, and incident response training

Lab Engineering Controls

For BSL-2 and Enhanced BSL-2

Certified Class II Biosafety Cabinet (BSC) or other approved primary containment device for aerosol- or droplet-generating procedures
Centrifuge safety cups, sealed rotors, or sealed carriers; load and unload samples inside a BSC when required by risk assessment
Screw-cap tubes or other secure primary containers in place of snap-cap tubes when feasible
Aerosol-resistant pipette tips
Dedicated equipment or decontamination procedures to prevent cross-contamination of shared work areas

For more information about engineering controls in a BSL-3 lab, review the BSL-3 Program Manual.

Personal Protective Equipment

BSL-2 Lab, where aerosol-generating activities can be contained within a BSC or other approved primary containment device

Gloves; double gloves may be required or recommended based on activity
Front-close or solid-front lab coat, as determined by risk assessment
Eye protection when splash, spray, or mucous membrane exposure is possible

BSL-2 Enhanced Conditions

Double gloves. Note: When coming out of a biosafety cabinet, outer gloves are disposed of in biohazard trash within the cabinet.
Closed-front or solid-front lab coat or disposable gown
Face shield or goggles when splash or mucous membrane exposure is possible
Respiratory protection, such as an N95 or higher-level respirator, when aerosol-generating activities cannot be fully contained within a BSC or other primary containment device, during spill cleanup, or when required by risk assessment. Personnel wearing a respirator for these purposes must be enrolled in the respiratory protection program.

In a BSL-3 Lab

Powered Air-Purifying Respirator (PAPR) or other approved respiratory protection, as specified by the facility and MUA
Disposable solid-front gown or facility-specific protective clothing
Lab-specific scrubs or other facility-required clothing
Additional PPE as required by the BSL-3 Program Manual, facility SOPs, and approved MUA

Waste Management: Regulated Medical Waste (RMW), with additional chemical or hazardous waste requirements when disinfectants, fixatives, or extraction reagents create mixed waste concerns.

Shipping Guidance: Suspected or confirmed SARS-CoV-2 positive specimens, cultures, or isolates must be packed and shipped as UN 3373 Biological Substance, Category B unless another classification is required. Personnel must be trained according to their function-specific shipping responsibilities. Review EHS Biological Substances Shipping before shipment.

Animal Vivarium Guidance

Animal Housing Biosafety Level: ABSL containment is assigned by Cornell IBC, CARE, and EHS Biosafety risk assessment. ABSL-2 may be appropriate for some approved animal work, but ABSL-3 or additional controls may be required based on the animal species, strain or variant, dose, route, shedding, procedures, personnel exposure potential, and facility design.

Animal Biosecurity: Experimental animals are housed separately and managed according to the approved animal protocol, MUA, facility SOPs, and CARE requirements.

Perform Inoculations: in a Biosafety Cabinet (BSC) or other approved primary containment device, unless otherwise approved through risk assessment.

Change Cages: in a Biosafety Cabinet (BSC) or other approved containment equipment, unless otherwise approved through risk assessment.

Exposure and Spill Procedures

Mucous Membranes: Flush eyes, mouth, or nose for 15 minutes at an eyewash station. See: Responding to Biological Exposures.

Other Exposures: Wash with soap and water for 15 minutes for open wounds, broken skin, or potentially contaminated skin, or wash a minimum of 20 seconds for areas with intact skin when no exposure to broken skin occurred.

Small Spills: Notify others working in the laboratory. Don appropriate PPE. Allow aerosols to settle if needed and safe to do so. Cover the spill with absorbent material, work from the perimeter toward the center, and remove visible organic material. Apply an approved disinfectant effective against SARS-CoV-2 and allow the required wet contact time listed on the disinfectant label or in the approved SOP. Discard contaminated materials as regulated medical waste. See: Responding to a Biological Spill.

Large Spills: Request assistance from the EHS Spill Team by calling CUPD dispatch. Call 911 from a campus phone or 607-255-1111 from a mobile phone.

Incident Reporting: Immediately report the incident to the supervisor and complete the EHS online injury/illness report as soon as possible. Report significant problems, violations, exposures, or research-related illnesses involving recombinant or synthetic nucleic acid molecules according to Cornell IBC and NIH Guidelines reporting requirements.

Medical Follow-Up:

For students, seek medical attention at Cornell Health or a local primary care provider. Call Cornell Health at 607-255-5155 (24-hour phone consultation line) or local urgent care.
For faculty and staff, seek medical evaluation with a local primary care provider, urgent care, or the medical provider identified in the approved occupational health plan. Cornell Health does not see employees for post-exposure care.
Emergencies: Call 911 from a campus phone or 607-255-1111 from a mobile phone.

Primary External References

This page is informed by current federal guidance and regulations, including the following sources. Cornell Biosafety and the Cornell IBC may require additional controls based on institutional risk assessment.

Revision History

Date	Type of Change	Summary	Primary Basis
March 2026	Substantive guidance update	Updated SARS-CoV-2 risk group and containment framing. SARS-CoV-2 is treated as an RG2 starting point under current NIH guidance, but containment remains activity-specific and may require BSL-2 Enhanced, BSL-3, ABSL-3, or other additional controls based on Cornell Biosafety and IBC risk assessment.	NIH OSP biosafety considerations; NIH Guidelines; Cornell IBC risk assessment process

More Information

The following resources are provided for additional background. Cornell Biosafety and the Cornell IBC make final determinations of biosafety level, animal biosafety level, PPE, engineering controls, medical surveillance, and other requirements through protocol-specific risk assessment.

Current Federal and Institutional Guidance Sources

Current CDC, EPA, and Professional Resources

Selected Technical Literature

Chin AWH, Chu JTS, Perera MRA, Hui KPY, Yen H-L, Chan MCW, et al. Stability of SARS-CoV-2 in different environmental conditions. The Lancet Microbe. 2020.
Riddell S, Goldie S, Hill A, Eagles D, Drew TW. The effect of temperature on persistence of SARS-CoV-2 on common surfaces. Virology Journal. 2020;17:145. doi:10.1186/s12985-020-01418-7
Pastorino B, Touret F, Gilles M, Luciani L, de Lamballerie X, Charrel RN. Evaluation of Chemical Protocols for Inactivating SARS-CoV-2 Infectious Samples. Viruses. 2020;12(6):624. doi:10.3390/v12060624
Pastorino B, Touret F, Gilles M, de Lamballerie X, Charrel RN. Heat Inactivation of Different Types of SARS-CoV-2 Samples: What Protocols for Biosafety, Molecular Detection and Serological Diagnostics? Viruses. 2020;12(7):735.
Patterson EI, Prince T, Anderson ER, Casas-Sanchez A, Smith SL, Cansado-Utrilla C, et al. Methods of Inactivation of SARS-CoV-2 for Downstream Biological Assays. Journal of Infectious Diseases. 2020;222:1462-1467. doi:10.1093/infdis/jiaa507
Welch SR, Davies KA, Buczkowski H, Hettiarachchi N, Green N, Arnold U, et al. Analysis of Inactivation of SARS-CoV-2 by Specimen Transport Media, Nucleic Acid Extraction Reagents, Detergents, and Fixatives. Journal of Clinical Microbiology. 2020.
Darnell MER, Subbarao K, Feinstone SM, Taylor DR. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV. Journal of Virological Methods. 2004;121:85-91. doi:10.1016/j.jviromet.2004.06.006
Kumar M, Mazur S, Ork BL, Postnikova E, Hensley LE, Jahrling PB, et al. Inactivation and safety testing of Middle East Respiratory Syndrome Coronavirus. Journal of Virological Methods. 2015. doi:10.1016/j.jviromet.2015.07.002