Biosafety advisory: SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus 2)

Biosafety Advisory

November 26, 2020*
*original publication date: January 27, 2020

Summary of recent changes

  • Classification of SARS-CoV-2 as a Risk Group 2 animal pathogen.
  • Additional guidance regarding transportation of primary specimens.

On this page

This biosafety advisory is being provided by the Public Health Agency of Canada (PHAC) to support local risk assessments (LRAs) and assist clinical, diagnostic, and research laboratories in implementing proper biosafety procedures to handle samples that may contain SARS-CoV-2 (previously referred to as 2019‑nCoV, the novel coronavirus that originated in the province of Hubei, China).Footnote 1 SARS-CoV-2 is responsible for the outbreak of COVID-19, which began in China in December 2019. This biosafety advisory is based on currently available scientific evidence as of November 20th, 2020, and is subject to review and change as new information becomes available. SARS-CoV-2 is classified as a Risk Group 3 (RG3) human pathogen and as a Risk Group 2 (RG2) animal pathogen. The regulatory oversight of SARS-CoV-2 is under the authority of the PHAC and the Canadian Food Inspection Agency (CFIA). Laboratories receiving specimens from patients under investigation for COVID-19 must be aware that improper handling of these specimens poses a risk of exposure, which could seriously impact the health of personnel and the community, as well as the animal population.

1.0 Background

The first reports of COVID-19 surfaced in the province of Hubei, China in December 2019.Footnote 2 The novel coronavirus SARS-CoV-2 has been identified as the causative agent and its genetic sequence is publicly available to inform the development of diagnostic tests and support vaccine development research.Footnote 3Footnote 4 Commonly reported symptoms of COVID-19 in humans are listed on Coronavirus disease (COVID-19): Symptoms and treatment.Footnote 5 There are multiple cases of COVID-19 resulting from human-to-human transmission and infection can be life-threatening.Footnote 6Footnote 7Footnote 8 The World Health Organization’s (WHO) website provides information on the number of confirmed cases.

Epidemiological studies have linked many COVID-19 cases in the earlier stages of the outbreak in the province of Hubei, China to a large seafood and live animal market, suggesting a possible zoonotic origin of their infection.Footnote 9 Recent studies have reported that animals infected with SARS-CoV-2 (e.g., cats, dogs, minks, lions, tigers) can develop symptoms of COVID-19 (e.g., digestive symptoms, respiratory symptoms) which may result in mortality.Footnote 10Footnote 11Footnote 12 The World Organization for Animal Health (OIE [Office International des Epizooties]), which provides guidance for Veterinary Authorities, indicates that SARS-CoV-2 is an emerging pathogen and that detection in an animal should be reported to the OIE through the national Veterinary Authority, which, for Canada, is the CFIA.Footnote 13 Individuals are asked to immediately notify the CFIA if SARS-CoV-2 is detected in an animal.

2.0 Risk group classification and licensing requirements

SARS-CoV-2 is classified as an RG3 human pathogen and an RG2 animal pathogen. Licensing and permit requirements are based on sample and activity type, and whether or not the material containing SARS-CoV-2 is imported. More specifically:

Controlled activities are defined in Section 7 of the Human Pathogens and Toxins Act (HPTA). They include possessing, handling, using, producing, storing, permitting access, transferring, importing, exporting, releasing, abandoning, or disposing of a pathogen. In this biosafety advisory, controlled activities only refer to controlled activities with whole live SARS-CoV-2 that is not in its natural environment (i.e., not in a primary specimen). For more information on applying for an import permit or a licence, please visit our website or contact the Licensing Program at the PHAC.

3.0 Biosafety recommendations for diagnostic activities

A pathogen (e.g., SARS-CoV-2) in a primary specimen (i.e., in its natural environment) is excluded from the HPTA and is therefore not regulated by the PHAC as long as the pathogen has not been cultivated or intentionally collected or extracted (e.g., concentrated, cultured). Primary specimens will generally contain lower concentrations of pathogens than found in cultures (i.e., propagated pathogens). Examples of primary specimens include respiratory specimens (e.g., sputum), blood, plasma, feces, and tissues that are collected directly from patients. Diagnostic specimens from naturally exposed animals (i.e., not resulting from in vivo studies) are also considered primary specimens.

A person who carries out laboratory analyses or diagnostic testing that does not involve the cultivation or production of SARS-CoV-2 may be exempt from requiring a licence as per Section 27(1) of the HPTR. When quality control samples and proficiency panels are needed to perform these tests (e.g., SARS-CoV-2 controls), a person may still be exempt from the licensing requirement based on the activities performed.Footnote 14 A person who performs laboratory analyses that involves identified primary specimens (i.e., primary specimens confirmed to contain SARS-CoV-2) may also be exempt from the licensing requirement based on the type of activities planned (i.e., if they do not cultivate or produce whole live SARS-CoV-2).

When a person carrying out diagnostic and laboratory activities is exempt from the licensing requirement, it is still recommended that, at minimum, good microbiological laboratory practices be followed in work areas where primary specimens are handled.Footnote 15 All reasonable precautions must be taken to protect the health and safety of the public against the risk posed by the activities, as per Section 6 of the HPTA. Routine practices and universal precautions are also recommended in laboratories where primary specimens that may contain SARS-CoV-2 are handled.Footnote 16

Diagnostic Activities for which Routine practices and Universal precautions are recommended include, but are not limited to, the following examples:

  • clinical chemistry studies, urinalysis, and hematology and serology testing (e.g., analysis with automated platforms);
  • visual examination of inactivated specimens or tissues (e.g., formalin-fixed);
  • visual examination of bacterial and fungal cultures;
  • routine staining and microscopic analysis of heat- or chemically-fixed smears;
  • assays with virus-inactivated specimens;
  • sample preparation for nucleic acid extraction; and
  • preparation of specimens for packaging and distribution to diagnostic laboratories for additional testing.

Where aerosols may be produced during diagnostic activities with primary specimens from patients under investigation for COVID-19, it is recommended that laboratories also implement additional biosafety recommendations. These recommendations are to be incorporated based on the laboratory’s LRA, which takes into consideration the potential for infectious aerosol and droplet production during diagnostic activities and the resulting risk of exposure. As more information on SARS-CoV-2 becomes available, it may be determined that there is a lower risk of exposure when handling certain types of primary specimens.Footnote 17 For example, current research with primary specimens from patients under investigation for COVID-19 indicates viral load in urine poses a low risk of exposure.Footnote 18Footnote 19Footnote 20Footnote 21 Examples of diagnostic activities that may result in the production of aerosols include inoculation of bacterial or fungal culture media, preparation of smears for microscopic analysis, preparation of samples for RT‑PCR, and the preparation of frozen sections (unfixed tissues) with a cryostat.

Additional biosafety recommendations

Where a biological safety cabinet (BSC) or other primary containment device is available, the following biosafety recommendations may be implemented:

  • A lab coat, gloves, and face/eye protection are worn when handling primary specimens.
  • Certified BSCs, or other primary containment device (e.g., a closed system, high efficiency particulate air [HEPA] filtered isolators), are used for procedures that may produce infectious aerosols or droplets and activities involving open vessels of infectious material (i.e., not yet inactivated).
  • Centrifugation of primary specimens is carried out in sealed safety cups, or rotors, that are loaded/unloaded in a BSC or other primary containment device (e.g., a closed system, HEPA filtered isolators).

Where a BSC or other primary containment device is not available, the following biosafety recommendations may be implemented:

  • A lab coat, gloves, and face/eye protection are worn when handling primary specimens.
  • Unless other appropriate risk mitigation measures have been implemented in the facility (based on the LRA), respiratory protection that provides a level of filtration of 95% or greater (e.g., N95) is worn where activities may potentially generate infectious aerosols or droplets.
  • Centrifugation of primary specimens can be carried out in sealed safety cups or rotors.

Where diagnostic activities take place outside a traditional laboratory setting (e.g., point-of-care [POC] molecular testing), risk mitigation measures should be taken to prevent potential exposure to pathogens and spread of contamination. Depending on the environment, measures could include, but are not limited to:Footnote 22

It is recommended to document any training on the biosafety procedures in place, as documentation can help demonstrate that all reasonable precautions have been taken to protect the public against the risks posed by these activities. Individuals may also refer to the Canadian Biosafety Guideline – Containment Level 1: Physical Design and Operational Practices to identify measures that may help mitigate the risks posed by their activities to the public.Footnote 23

Standard operating procedures

Standard operating procedures (SOPs) may be implemented to reduce the risk of exposure where laboratory activities involve instruments or automated systems that may create aerosols or droplets. For example, these procedures might include inactivating infectious material before it is placed in an automated system (e.g., adding the lysis buffer confirmed to inactivate SARS-CoV-2 before samples are placed in an automated system) or opting to use primary containers that are less prone to breakage (e.g., plastic tubes instead of glass tubes).Footnote 24 Laboratories may also consider a waiting period before opening a device to allow sufficient time for potential aerosols or droplets to settle in the event of leaks or breakage of the primary containers (e.g., when using a centrifuge that does not have sealed safety cups or rotors).

Sample preparation protocols involving inactivation of SARS-CoV-2 may be considered to help mitigate the risk associated with downstream processing of infectious material (e.g., render a sample non-infectious by inactivating SARS-CoV-2).Footnote 25 Many heat-inactivation protocols for coronaviruses (e.g., 56‑60°C for 30‑60 minutes) have been described in the literature (e.g., for serum and plasma samples) and many sample preparation protocols that inactivate enveloped viruses appear to also effectively inactivate SARS-CoV-2 (e.g., solution containing Trizol, lysis buffer containing guanidine).Footnote 21Footnote 26Footnote 27 Nevertheless, it is necessary to always validate such procedures to confirm in house the exact conditions, temperature, and duration of incubation necessary to effectively inactivate SARS-CoV-2. While sample preparation protocols may reduce the risk of exposure to infectious materials (i.e., by reducing the viral load of a primary specimen), a primary specimen can only be safely handled as a non-infectious sample if the sample preparation protocol has been validated to effectively inactivate SARS-CoV-2.

As a precautionary measure, disinfection protocols can also be reviewed internally with personnel to ensure that protocols are followed to prevent incidents and injuries. For example, guanidine has the potential to create a dangerous chemical reaction that releases cyanide gas when exposed to bleach. Guanidine is present in certain solutions and transportation media. Standard procedures can be reviewed with personnel to ensure there is no risk of guanidine-rich solutions being exposed to bleach.


Based on the currently available scientific evidence, chemical disinfectants that are effective against enveloped viruses are suitable for decontamination of SARS-CoV-2. Effective disinfectants include sodium hypochlorite (bleach), 70% ethanol, 70% isopropanol (isopropyl alcohol), 0.5% hydrogen peroxide, quaternary ammonium compounds, and phenolic compounds. It is possible other biocidal agents may be less effective (e.g., 0.05‑0.2% benzalkonium chloride, 0.02% chlorhexidine digluconate).Footnote 22 For material containing SARS-CoV-2 to be properly inactivated, chemical disinfectants must be used according to manufacturer’s instructions or under published use conditions that have been demonstrated to inactivate enveloped viruses. The inactivation of infectious material with a chemical disinfectant depends not only on the concentration of the active ingredient, but also temperature, contact time, and the presence of interfering substances (e.g., organic material). A list of examples of commercially available hard-surface disinfectants that may be effective against SARS-CoV-2 is provided by Health Canada.Footnote 28

4.0 Biosafety requirements for in vitro and in vivo activities

SARS-CoV-2 is classified as an RG3 human pathogen and an RG2 animal pathogen. As a result, there are strict containment requirements to reduce the risks of exposure to, and release of, concentrated or propagated material. The following table summarizes the appropriate minimum containment requirements for laboratories where SARS-CoV-2 is handled knowingly (i.e., intentionally). Unless material is excluded from the HPTA, or a person is exempt from requiring a licence under the HPTR, all in vitro and in vivo activities with SARS-CoV-2 are to be performed in accordance with a Pathogen and Toxin Licence issued under the HPTA and in a facility that meets the minimum applicable requirements for containment indicated in Table 1, and specified in the CBS.Footnote 29 In vivo activities include experimentally exposing an animal to SARS-CoV-2 and the subsequent handling of these animals, and specimens obtained from them, in a research setting.

Table 1: Canadian containment level requirements for SARS-CoV-2
Activities with SARS-CoV-2 Minimum Containment Level Required

Non-propagative in vitro activities

Examples of these activities include, but are not limited to:

  • procedures with human or animal primary specimens to intentionally concentrate or isolate SARS-CoV-2 for research purposes (e.g., ultracentrifugation of a sample).


Propagative in vitro activities

Examples of these activities include, but are not limited to:

  • culturing specimens (e.g., propagated virus);
  • preparatory work for in vivo activities; and
  • processing a culture (i.e., propagated or cultivated) known to contain SARS-CoV-2 for packaging and distribution to laboratories.


In vivo work activities

Examples of these activities include, but are not limited to:

  • preparing inoculum;
  • inoculating animals; and
  • collecting specimens from experimentally infected animals.

CL3Footnote 1


Footnote 1

Work in small animal containment zones (SA zones) must meet the applicable requirements in the CL3 column of the CBS and work in large animal containment zones (LA zones) must meet the applicable requirements in the CL3 Ag column of the CBS.

Return to footnote 1 referrer

Many of the requirements in the CBS are risk- and performance-based and, as such, are dependent on an LRA being performed. Based on the risks associated with in vitro and in vivo activities taking place with SARS-CoV-2, additional biosafety measures may also be applicable at CL3. Facilities are to conduct an LRA for the activities to be undertaken with SARS-CoV-2 to determine the appropriate risk mitigation measures (CBS R4.1.8), and update the LRA and mitigation measures as new information becomes available.

Should new information result in a change in risk group classification or the publication of a biosafety directive or biosafety advisory, such information will be reflected in the ePATHogen ‑ Risk Group Database.Footnote 30

5.0 Transportation

The transportation of SARS-CoV-2 specimens is subject to the Transportation of Dangerous Goods Regulations (TDG Regulations), which include the packaging requirements stipulated in the standard CAN/CGSB-43.125. Packaging requirements are based on the classification of material, which are described in the box below.

Classification of material

SARS-CoV-2 cultures are always assigned to UN2814, INFECTIOUS SUBSTANCE, AFFECTING HUMANS, Class 6.2, Category A.

SARS-CoV-2 samples that are in a form other than a culture are assigned to one of the following classifications:

  • UN3373, BIOLOGICAL SUBSTANCE, CATEGORY B, Class 6.2, Category B, in accordance with the conditions set out in paragraphs 1.39(a) to (c) of the TDG Regulations.

Medical or clinical waste related to SARS-CoV-2 are assigned to:

  • UN2814, if they contain Category A infectious substances (i.e., propagated virus);
  • UN3291, if they contain Category B infectious substances or if there are reasonable grounds to believe that they have a low probability of containing SARS-CoV-2.

Dried blood spots, collected by applying a drop of blood onto absorbent material, are out of the scope of the TDG Regulations. Environmental samples (e.g., food, water, wastewater) that do not pose a significant risk of infection are not subject to the requirements for infectious substances of Class 6.2 under the TDG Regulations However, please note that while dried blood spots and environmental samples may not need to meet specific packaging requirements as per the TDG Regulations, they may still need to meet certain packaging requirements to ensure the quality of the sample (e.g., to allow accurate diagnostic results).

Laboratories may benefit, under certain conditions, from a transportation regulatory relief (see Temporary certificate TU 0764 - Test samples for COVID-19) that has been issued by Transport Canada to assist medical professionals with the increased need for transportation of COVID-19 test samples. Please note this is a temporary measure that has been created to help Canada address the current pandemic.

Primary specimens from asymptomatic individuals that are not known to be positive for an infectious disease such as COVID-19 can be shipped as “exempt human specimens” (i.e., as per usual), following the conditions of Exemption 1.42 of the TDG Regulations. Please note that precautionary measures may be required, based on factors such as the known medical history, symptoms, individual circumstances and endemic local conditions. For example, primary specimens from asymptomatic babies with a mother infected with SARS-CoV-2, or undiagnosed but presenting symptoms of COVID-19, could be classified as Category B infectious substances based on the likelihood of contamination.

For more information, visit the Transport Canada Transportation of Dangerous Goods website or the Transport Canada Shipping Infectious Substances bulletin. To obtain further assistance, contact Transport Canada at:

In the event of an emergency involving dangerous goods, call CANUTEC at 1‑888‑CANUTEC (226‑8832), 613‑996‑6666 or *666 on a cellular phone.

6.0 Contact information

Further biosafety information may be obtained:

To notify the CFIA if COVID-19 is detected in an animal, or to receive more information on reportable and immediately notifiable diseases in animals, contact the CFIA at:

7.0 References and resources


Footnote 1

Government of Canada. (2018). Canadian Biosafety Guideline – Local Risk Assessment. Available from

Return to footnote 1 referrer

Footnote 2

ProMED-mail. (2019). Undiagnosed pneumonia - China (HU) RFI.

Return to footnote 2 referrer

Footnote 3

ProMED-mail. (2020d). Undiagnosed pneumonia - China (Hubei) (05): Novel Coronavirus Identified.

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Footnote 4

GenBank. (2020). Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome. Retrieved 06/10, 2020 from

Return to footnote 4 referrer

Footnote 5

Government of Canada. (2020). Coronavirus disease (COVID-19): Symptoms and treatment. Available from

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Footnote 6

World Health Organization. (2020). Novel Coronavirus – Republic of Korea (ex-China). Retrieved 06/10, 2020 from

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Footnote 7

World Health Organization. (2020). Novel Coronavirus (2019-nCoV) situation reports. Retrieved 06/10, 2020 from

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Footnote 8

World Health Organization. (2020). Novel Coronavirus. Retrieved 06/10, 2020 from

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Footnote 9

Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., et al. (2020). Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. The New England Journal of Medicine, 382(13):1199-1207.

Return to footnote 9 referrer

Footnote 10

Hosie, M. J., Epifano, I., Herder, V., Orton, R. J., Stevenson, A., Johnson, N., et al. (2020). Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK. Retrieved 10/28, 2020 from

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Footnote 11

Molenaar, R. J., Vreman, S., Hakze-van der Honing, R. W., Zwart, R., de Rond, J., Weesendorp, E., et al. (2020). Clinical and pathological findings in SARS-CoV-2 disease outbreaks in farmed mink (Neovison vison). Veterinary Pathology, 57(5):653-657.

Return to footnote 11 referrer

Footnote 12

Bartlett, S. L., Diel, D. G., Wang, L., Zec, S., Laverack, M., Martins, M., et al. (2020). SARS-CoV-2 Infection And Longitudinal Fecal Screening In Malayan Tigers (Panthera tigris jacksoni), Amur Tigers (Panthera tigris altaica), And African Lions (Panthera leo krugeri) At The Bronx Zoo, New York, USA. Retrieved 10/28, 2020 from

Return to footnote 12 referrer

Footnote 13

World Organisation for Animal Health. (2020). Questions and Answers on COVID-19. Retrieved 06/09, 2020 from

Return to footnote 13 referrer

Footnote 14

Government of Canada. (2016). Exemptions from the Licensing Requirements of the Human Pathogens and Toxins Act and Human Pathogens and Toxins Regulations. Available from

Return to footnote 14 referrer

Footnote 15

Society for General Microbiology. (2014). Good microbiological laboratory practice. Retrieved 06/10, 2020 from

Return to footnote 15 referrer

Footnote 16

Government of Canada. (2016). Canadian Biosafety Handbook, 2nd edition, 2016. Ottawa, ON, Canada: Government of Canada. Available from

Return to footnote 16 referrer

Footnote 17

World Health Organization. (2020). Laboratory testing for coronavirus disease (COVID-19) in suspected human cases. Retrieved 06/10, 2020 from

Return to footnote 17 referrer

Footnote 18

Wang, W., Xu, Y., Gao, R., Lu, R., Han, K., Wu, G., & Tan, W. (2020). Detection of SARS-CoV-2 in Different Types of Clinical Specimens. Journal of the American Medical Association, 323(18):1843-1844.

Return to footnote 18 referrer

Footnote 19

Young, B. E., Ong, S. W. X., Kalimuddin, S., Low, J. G., Tan, S. Y., Loh, J., et al. (2020). Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore. Journal of the American Medical Association, 323(15):1488-1494.

Return to footnote 19 referrer

Footnote 20

Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., et al. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, 395(10223):497–506.

Return to footnote 20 referrer

Footnote 21

To, K. K., Tsang, O. T., Leung, W. S., Tam, A. R., Wu, T. C., Lung, D. C., et al. (2020). Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. The Lancet Infectious Disease, 20(5):565-574.

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Footnote 22

World Health Organization. (2020). Laboratory biosafety guidance related to coronavirus disease (COVID-19). Retrieved 06/10, 2020 from

Return to footnote 22 referrer

Footnote 23

Government of Canada. (2017). Canadian Biosafety Guideline - Containment Level 1: Physical Design and Operational Practices. Available from

Return to footnote 23 referrer

Footnote 24

Food and Drug Administration. (2020). CDC’s 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel. Retrieved 06/10, 2020 from

Return to footnote 24 referrer

Footnote 25

Pan, Y., Long, L., Zhang, D., Yan, T., Cui, S., Yang, P., et al. (2020) Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads. American Association for Clinical Chemistry, 66(6):794-801.

Return to footnote 25 referrer

Footnote 26

Kampf, G., Voss, A., & Scheithauer, S. (2020). Inactivation of coronaviruses by heat. The Journal of hospital infection, 105(2):348-349.

Return to footnote 26 referrer

Footnote 27

Pastorino, B., Touret, F., Gilles, M., de Lamballerie, X., & Charrel, R. N. (2020). Heat Inactivation of Different Types of SARS-CoV-2 Samples: What Protocols for Biosafety, Molecular Detection and Serological Diagnostics?. Viruses, 12(7):735.

Return to footnote 27 referrer

Footnote 28

Government of Canada. (2020). Hard-surface disinfectants and hand sanitizers (COVID-19): List of disinfectants with evidence for use against COVID-19. Available from

Return to footnote 28 referrer

Footnote 29

Government of Canada. (2015). Canadian Biosafety Standard, 2nd edition, 2015. Ottawa, ON, Canada: Government of Canada. Available from

Return to footnote 29 referrer

Footnote 30

Government of Canada. ePATHogen - Risk Group Database. Available from

Return to footnote 30 referrer

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