Biosafety and biosecurity for pathogens and toxins news: Q2, July 2022 issue

On this page

• Risk group and containment level requirements for single stranded, positive sense RNA (+ssRNA)
• Human Pathogens and Toxins Act and Regulations review
• RegFacts: #DYK: Conducting controlled activities
• Cybersecurity awareness: Rate of cyber attacks increasing
• Centrifuge cup safety
• Animal incidents
• Biosecurity Plans webinar

Risk group and containment level requirements for single stranded, positive sense RNA (+ssRNA)

The Centre for Biosecurity (CB) recently completed a risk assessment on single-stranded positive sense RNA (+ssRNA). +SsRNA viruses have genomes that function like messenger RNA (mRNA) and can be directly translated after entering a host cell. Examples of +ssRNA viruses include West Nile virus, Enterovirus C (Poliovirus), and Eastern equine encephalitis virus.

Intact full-length viral +ssRNA can cause infection by serving as the template for the synthesis of viral RNAs. This results in replication of the parental virus. However, the infectivity of purified or chemically synthesized +ssRNA is much lower than that of the parental virus, because exogenous RNA is unstable and not readily taken up by cells. Under favourable conditions, efficient transfection can occur.

Risk Group (RG) and Containment Level (CL) requirements for +ssRNA

Under favourable conditions for cellular uptake of full length viral +ssRNA (for example, transfection protocols, in vivo injection), the infectivity of +ssRNA may be similar to that of the source parental intact virus.

• The RG of the full length viral +ssRNA is classified the same as the RG of the parental virus.
• Activities with the full length viral +ssRNA should be performed at the same CL as the parental virus.

Under unfavourable conditions for cellular uptake of full length viral +ssRNA (for example, laboratory analyses, PCR, viral heat inactivation) the infectivity of +ssRNA is very low. However, it does remain potentially infectious.

• Full length viral +ssRNA from regulated viruses (RG2, 3, or 4) is classified as human and animal RG2
• Activities can be safely performed at CL1, as determined by a local risk assessment.

Fragmented or chemically or radiologically altered full length viral +ssRNA aren't considered infectious. They are classified as RG1 and can be safely handled at CL1.

Diagnostic laboratory activities with material containing +ssRNA may be exempt from licensing under Section 27(1) of the Human Pathogens and Toxins Regulations (HPTR). The importation of +ssRNA however, is regulated under the Health of Animals Act and Regulations and a permit to import may be required.

You can find information on full length viral +ssRNA in:

• Section 4.3.9 of the Canadian Biosafety Handbook
• the ePATHogen database which is a comprehensive listing of all biological agents, RGs, and CLs, including +ssRNA
• the SARS-CoV-2 Biosafety Advisory, which contains requirements and recommendations for working with SARS-CoV-2 +ssRNA.

For questions or concerns, please contact the Biosafety Risk Assessment team at pathogens.pathogenes@phac-aspc.gc.ca.

Human Pathogens and Toxins Act and Regulations review

The Human Pathogens and Toxins Act (HPTA) and associated regulations (HPTR) came into full effect on December 1, 2015. Their purpose was to protect public health and safety from risks posed by human pathogens and toxins.

The Public Health Agency (PHAC) committed to a legislative review every 5 years, which serves as the Human Pathogens and Toxins Act and Regulations (HPTA/R) life-cycle review. This was delayed due to the COVID-19 pandemic. Now, 7 years later, we mark a new phase of reviewing and addressing biosafety and biosecurity risks in Canada.

PHAC's Office of Audit and Evaluation (OAE) lead an evaluation which focused primarily on issues of effectiveness and efficiency, specifically on activities related to the implementation of the HPTA/R from 2015-2016 to 2020-2021. The comprehensive evaluation included evidence about:

• performance data
• white papers on specific topics
• findings from an online questionnaire administered to:
  • external stakeholders (April to May 2019)
  • other government departments (May to June 2021)
  • key informants from CB (January 2020 to September 2021)

The evaluation found that the HPTA/R Program has shown early signs of success and that regulated organizations:

• have the information they need to understand and comply with legislative and regulatory requirements
• comply with legal and regulatory requirements and improve biosafety and biosecurity in their facilities
• identify and proactively address risk to improve institutional biosafety and biosecurity

The evaluation also identified the following areas for further examination:

• security clearance requirements, specifically expanding the criteria for those who should have a security clearance
• licensing, including clearly defining roles and responsibilities between Biological Safety Officers (BSO) and Licence Holders (LH)
• the use of virtual inspections

The OAE developed a Management Action Response Plan (MRAP), which identified actions to address their recommendations, including to:

• complete a statutory and regulatory review of the HPTA/R
• identify potential amendments to respond to the recommendations by spring 2023

The commitment to review the HPTA/R also presents an opportunity for CB to consider legislative and regulatory changes to support implementation of the government's:

• Biomanufacturing and Life Sciences Strategy and
• Research security agenda

In response to the COVID-19 pandemic, the domestic life sciences and biomanufacturing sector expanded rapidly, drawing attention to vulnerabilities in Canada's biosafety and biosecurity program.

We will publish the final HPTA/R evaluation report including MRAP this summer on PHAC's evaluation reports page.

RegFacts: #DYK: Conducting controlled activities

Did you know that under section 5 of the HPTR, a person conducting controlled activities authorized by a Pathogen and Toxin Licence must notify the LH and the BSO in writing when they intend to increase:

• the virulence or pathogenicity of a human pathogen
• the communicability of a human pathogen
• the resistance of a human pathogen to preventive or therapeutic treatments
• the toxicity of a toxin

This is especially important when conducting gain of function research, in which an organism is genetically altered to enhance the pathogenicity, transmissibility, or host range. Such modifications of a pathogen or toxin may or may not result in a change to the RG category defined in section 3 of the HPTA.

These measures help to promote biosafety and biosecurity with respect to human pathogens and toxins.

Cybersecurity awareness: Rate of cyber attacks increasing

In April 2022, the Communications Security Establishment (CSE) and its international partners released a joint cyber security advisory on Russian state-sponsored and criminal cyber threats to critical infrastructure.

CSE and its partners recommend the following mitigation measures.

• Create, maintain, and exercise (for example tabletop, functional, or full-scale exercises) a cyber incident response and continuity of operations plan.
• Maintain offline (physically disconnected from network connections) backups of data.
• Ensure all backup data is encrypted, immutable (cannot be changed or deleted), and covers the entire organization's data infrastructure.
• Identify a resilience plan that addresses how to operate if you lose access to, or control of, the IT assets within your system.

You can find more information on this joint advisory from Cybersecurity and Infrastructure Security Agency (CISA).

Take action

CSE and its partners encourage you to take these easy steps to protect your system. You can also implement mitigation measures for routinely exploited vulnerabilities.

If you wish to test your IT systems for vulnerabilities, Public Safety Canada offers free review and analysis tools. You can include their assessments in your facility's Biosecurity Risk Assessment and Biosecurity Plan.

If a private company assesses your IT system, make sure they have the appropriate security clearance to access information about your security access control methods.

If you have a question about your systems, the Canadian Centre for Cyber Security (CCCS) is your first point of contact. They are the national authority for cybersecurity in Canada.

Centrifuge cup safety

Since 2016, CB has received reports of 1 suspected laboratory acquired infection and 6 exposure incidents related to the use of centrifuges.

The causes of these incidents were:

• opening a centrifuge without additional safety measures, following a tube breakage
• centrifugation of pathogens in a centrifuge without a sealed safety cups/rotor
• unloading sealed safety cups/rotor outside of a biosafety cabinet
• conducting maintenance of a centrifuge that was not decontaminated

To minimise the risk of incidents related to the use of centrifuges, CB reminds you to:

• use sealed safety cups/rotors for the centrifugation of pathogens for which the main route of transmission is by aerosols (RG2 pathogens) or of any pathogen that is RG3 and higher
• unload sealed safety cups/rotors in a biosafety cabinet
• when the use of sealed safety cups/rotor is not possible, allow sufficient time for aerosols to settle before opening the centrifuge
• routinely verify the integrity of the centrifuge as per the manufacturer's specifications (for example, visually inspect the containers and O-rings regularly, and grease O-rings as required)
• decontaminate centrifuges prior to maintenance
• for spills in refrigerated centrifuges, allow the rotor, chamber, and centrifuge cups to come to room temperature before applying disinfectant

Chapter 12-1 of the CBH provides more details on the use of centrifuges.

Animal incidents

In vivo work with pathogens and toxins involving live animals presents a unique safety challenge for laboratory workers. The added complexity of managing an animal's behaviour, particularly when ill or stressed, poses an increased risk of injury to the health and safety of those who work with, and care for, laboratory animals.

Between January 1, 2016 and December 31, 2021, CB received 25 mandatory reports (24 exposures and 1 suspected laboratory acquired infection) for which animal work was the main occurrence type during exposure.

Rodents were involved in most of the incidents (18):

• mouse (14 incidents)
• hamster (2)
• rat (1)
• unspecified rodent (1)

Other animals involved included:

• fish (2 incidents)
• rabbit (1)
• bat (1)
• non-human primate (1)
• not specified (2)

Primary routes of exposure were:

• animal bites (14 incidents)
• animal scratches (3)
• contact with an infected animal's feces (2)

Lab animals indirectly caused 5 other incidents during handling (for example, kicking needle, moving during an injection).

Root causes varied, but the most frequent were:

• standard operating procedure (SOPs) issues such as instances where the SOP is insufficient or is applied incorrectly (12)
• human error such as violations, cutting a corner, a mistake or slip (9)
• equipment issues such as the use of inappropriate or faulty equipment (8)
• the need for additional training (7)

Further insight into the corrective actions of these reports indicated that injury could have been avoided by using puncture resistant gloves. Staff should try to find an appropriate balance between safety and manoeuvrability while minimizing the risk of injury to their colleagues and lab animals.

Complete risk mitigation of animal-related incidents is difficult due to the unpredictable nature and behaviours of living creatures.

Maintaining SOPs and providing ongoing training to all staff (both new and experienced) may prevent further injury. Several reports indicated that exposure resulted from an individual cutting corners or deviating from standard protocols. This involved workers with varying levels of experience and education. Performing routine or repetitive actions may lead to diminished vigilance as workers develop their own methods for completing tasks that may deviate from safer measures.

An additional consideration regarding risk mitigation is workload. Adequate staffing levels and manageable hours will facilitate staff to follow proper safety procedures.

Webinar: Biosecurity plans

We delivered the Biosecurity Plans webinar on June 22, 2022. Recordings and transcripts will be available soon in the Public Health Agency of Canada (PHAC) e-Learning Portal.