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

Biosafety Advisory

June 30, 2020*
*original publication date: January 27, 2020

Summary of recent changes

  • Additional guidance on biosafety for diagnostic activities.
  • Additional guidance regarding transportation of primary specimens.

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 advisory is based on currently available scientific evidence as of June 30, 2020 and is subject to review and change as new information becomes available. SARS-CoV-2 remains classified as a Risk Group 3 (RG3) human pathogen by the Centre for Biosecurity. 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.

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 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 Canadian Food Inspection Agency (CFIA).Footnote 10 Individuals are asked to immediately notify the CFIA if COVID-19 is detected in an animal. Should new information result in the classification of SARS-CoV-2 as an emerging animal pathogen, this advisory will be updated to include the CFIA’s regulatory perspective. Until such time, the oversight of activities with SARS-CoV-2 remains under the PHAC’s purview.

2.0 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 Human Pathogens and Toxins Act (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.

Diagnostic and clinical activities with primary specimens that do not involve the cultivation, collection, or extraction (i.e., isolation) of SARS-CoV-2 (e.g., clinical chemistry studies, urinalysis, hematology and serology testing, fixation of tissues) may be exempt from requiring a licence as per section 27(1) of the Human Pathogens and Toxins Regulations (HPTR). Quality control samples and proficiency panels needed to perform these tests (e.g., SARS-CoV-2 controls) may also be exempt from the licensing requirement [under section 27(1) of the HPTR].Footnote 11 Laboratories where activities only involve handling identified primary specimens (i.e., specimens confirmed to contain SARS-CoV-2) may also be exempt from the licensing requirement based on the type of activities planned (e.g., genomic studies that do not require the propagation of the live virus).

Where diagnostic and laboratory activities are 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 12 This is in line with HPTA Section 6, which requires laboratories to take all reasonable precautions to protect the health and safety of the public against the risk posed by their activities. Routine practices and universal precautions are also recommended in laboratories where primary specimens that may contain SARS-CoV-2 are handled (see the examples of diagnostic activities below).Footnote 13

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 additional biosafety recommendations are to be incorporated based on the laboratory’s local risk assessment (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 14 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 15Footnote 16Footnote 17Footnote 18 Examples of diagnostic activities that may result in the production of aerosols include inoculation of bacterial or fungal culture media and the preparation of smears for microscopic analysis, samples for an RT-PCR, and 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, 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 is carried out in sealed safety cups, or rotors, when they are available.

Where diagnostic activities take place outside a laboratory space (e.g., point of care (POC) molecular testing), the additional biosafety recommendations may be implemented. Where equipment serving as a primary containment device is not available (e.g., glove box tent acting as a primary containment device), a facility may determine, based on its LRA, that there are sufficient risk mitigation measures in place to prevent exposure incidents and the spread of contamination within the building. Such risk mitigation measures include, but are not limited to:Footnote 19

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, 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 20 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 21 Based on the current literature, 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 21 While heat-inactivation protocols for coronaviruses (e.g., for serum and plasma samples) have been described in the literature (e.g., 56-60°C for 30-60 minutes), there is currently no consensus in the scientific community regarding the exact temperature and the duration of incubation necessary to effectively inactivate SARS-CoV-2.Footnote 21Footnote 22Footnote 23 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.

Disinfectants

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 24 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 25

3.0 Biosafety requirements for in vitro and in vivo activities

SARS-CoV-2 remains classified as a Risk Group 3 (RG3) human pathogen by the Centre for Biosecurity. 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 excluded from the HPTA, or 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 Canadian Biosafety Standard (CBS).Footnote 26 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).
CL3

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.
CL3

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

Table Footnotes

Table 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 27

4.0 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.

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 classification:

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

Primary specimens from asymptomatic individuals that are not known to be positive for an infectious disease such as SARS-CoV-2 can be shipped as “exempt human specimens” (i.e., as per usual), following the conditions of Exemption 1.42 of the TDG Regulations. 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.

5.0 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:

6.0 References and resources

Footnotes

Footnote 1

Government of Canada. (2018). Canadian Biosafety Guideline – Local Risk Assessment. Available from https://www.canada.ca/en/public-health/services/canadian-biosafety-standards-guidelines/guidance/canadian-biosafety-guidelines/document.html

Return to footnote 1 referrer

Footnote 2

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

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Footnote 3

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

Return to footnote 3 referrer

Footnote 4

GenBank. (2020). Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome. Retrieved 06/10, 2020 from https://www.ncbi.nlm.nih.gov/nuccore/MN908947

Return to footnote 4 referrer

Footnote 5

Government of Canada. (2020). Coronavirus disease (COVID-19): Symptoms and treatment. Available from https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/symptoms.html

Return to footnote 5 referrer

Footnote 6

World Health Organization. (2020). Novel Coronavirus – Republic of Korea (ex-China). Retrieved 06/10, 2020 from https://www.who.int/csr/don/21-january-2020-novel-coronavirus-republic-of-korea-ex-china/en/

Return to footnote 6 referrer

Footnote 7

World Health Organization. (2020). Novel Coronavirus (2019-nCoV) situation reports. Retrieved 06/10, 2020 from https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

Return to footnote 7 referrer

Footnote 8

World Health Organization. (2020). Novel Coronavirus. Retrieved 06/10, 2020 from https://www.who.int/westernpacific/emergencies/novel-coronavirus

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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

World Organisation for animal health. (2020). Questions and Answers on 2019-nCoV Acute Respiratory Disease. Retrieved 06/09, 2020 from https://www.oie.int/en/scientific-expertise/specific-information-and-recommendations/questions-and-answers-on-2019novel-coronavirus/

Return to footnote 10 referrer

Footnote 11

Government of Canada. (2016). Exemptions from the Licensing Requirements of the Human Pathogens and Toxins Act and Human Pathogens and Toxins Regulations. Available from https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/human-pathogens-toxins-act/exemptions-licensing-requirements-human-pathogens-toxins-act-human-pathogens-toxins-regulations.html

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Footnote 12

Society for General Microbiology. (2014). Good microbiological laboratory practice. Retrieved 06/10, 2020 from http://www.microbiologyonline.org.uk/teachers/safety-information/good-microbiological-laboratory-practice

Return to footnote 12 referrer

Footnote 13

Government of Canada. (2016). Canadian Biosafety Handbook, 2nd edition, 2016. Ottawa, ON, Canada: Government of Canada. Available from https://www.canada.ca/en/public-health/services/canadian-biosafety-standards-guidelines/handbook-second-edition.html

Return to footnote 13 referrer

Footnote 14

World Health Organization. (2020). Laboratory testing for coronavirus disease (COVID-19) in suspected human cases. Retrieved 06/10, 2020 from https://www.who.int/publications-detail/laboratory-testing-for-2019-novel-coronavirus-in-suspected-human-cases-20200117

Return to footnote 14 referrer

Footnote 15

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 15 referrer

Footnote 16

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 16 referrer

Footnote 17

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 17 referrer

Footnote 18

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. pii: S1473-3099(20)30196-1.

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Footnote 19

World Health Organization. (2020). Laboratory biosafety guidance related to coronavirus disease (COVID-19). Retrieved 06/10, 2020 from https://www.who.int/publications-detail/laboratory-biosafety-guidance-related-to-coronavirus-disease-(covid-19)

Return to footnote 19 referrer

Footnote 20

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 https://www.aphl.org/Materials/FDANoticetoCDC_AutomatedExtraction_03082020.pdf

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Footnote 21

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.

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Footnote 22

Chang, L., Yan, Y., & Wang, L. (2020). Coronavirus Disease 2019: Coronaviruses and Blood Safety. Transfusion Medicine Reviews, pii: S0887-7963(20)30014-6. [Epub ahead of print]

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Footnote 23

Rabenau, H. F., Cinatl, J., Morgenstern, B., Bauer, G., Preiser, W., & Doerr, H. W. (2005). Stability and inactivation of SARS coronavirus. Medical microbiology and immunology, 194(1-2):1-6.

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Footnote 24

World Health Organization. (2020). Laboratory biosafety guidance related to coronavirus disease (COVID-19). Retrieved 06/10, 2020 from https://www.who.int/publications-detail/laboratory-biosafety-guidance-related-to-coronavirus-disease-(covid-19)

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Footnote 25

Government of Canada. (2020). Hard-surface disinfectants and hand sanitizers (COVID-19): List of disinfectants with evidence for use against COVID-19. Available from https://www.canada.ca/en/health-canada/services/drugs-health-products/disinfectants/covid-19/list.html#tbl1

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Footnote 26

Government of Canada. (2015). Canadian Biosafety Standard, 2nd edition, 2015. Ottawa, ON, Canada: Government of Canada. Available from https://www.canada.ca/en/public-health/services/canadian-biosafety-standards-guidelines/second-edition.html

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Footnote 27

Government of Canada. ePATHogen - Risk Group Database. Available from https://health.canada.ca/en/epathogen

Return to footnote 27 referrer

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