From Autoclaving to Zoonoses: How the Biosafety and Biosecurity Community Embraces Improvement

By Rachel-Paige Casey, Biodefense PhD Student


As we near the one-year mark into the COVID-19 pandemic, the world has suffered over 67 million cases and over 1.5 million deaths from the novel coronavirus. In the United States, total cases exceed 15 million and the death toll is climbing toward 300,000. COVID-19 has exposed critical gaps in preparedness, but also global health security in general. Beyond the severe health impacts of SARS-CoV-2, the economic and social impacts from the pandemic have proven nightmarish. As declared by the 2019 Global Health Security Index, which is the first comprehensive assessment of global health security capabilities in 195 countries, no country is adequately prepared for outbreaks, and every country has important deficiencies to address. The 63rd Annual ABSA Biosafety and Biosecurity Virtual Conference addressed several such gaps. 

As microbial challenges develop and diversify, the biosafety and biosecurity community has to continually adapt and evolve to address issues in effective, efficient, and often imaginative ways. Antimicrobial resistance is a hot topic, as the list of resistant microbes continues to grow while the list of effective antimicrobials dwindles. There is a critical need for novel therapeutics to fight various drug-resistant infections. Recently, there has been much effort toward improving best practices in biosafety, tackling zoonotic challenges in the laboratory, and creating a flexible biosafety risk assessment framework for commercial scale cell and gene therapy manufacturing.

The 63rd American Biological Safety Association (ABSA) Annual Biosafety and Biosecurity Virtual Conference convened the global community of biosafety and biosecurity practitioners and experts from November 4 –6, 2020. This conference focused on a broad variety of topics dealing with biosafety, biosecurity, and bioethics with an emphasis on activities and challenges related to COVID-19.

Overview of ABSA Virtual Conference Report

I attended this virtual conference along with my GMU Biodefense Program colleagues Mr. Yong-Bee Lim and Ms. Sally Huang. To provide our readership with a comprehensive report on the ABSA conference, we self-assigned sessions that we would write about. This report provides an overview, details, and comments on the following sessions:

  1. Session III: Pathogen Genomics from Antibiotic Resistance to COVID-19
  2. Session XI: Regulatory Updates
  3. Session XIII: Biosafety Assortment – Emerging Fields of Drug Therapies & Commercial Scale Production Challenges 
  4. Session XVI: High-Containment

Session III: Pathogen Genomics from Antibiotic Resistance to COVID-19

Dave Engelthaler, director of the Pathogen and Microbiome Division at the Translational Genomics Research Institute (TGen), was the invited speaker for this year’s conference, and he presented on pathogen genomics. Improvements in rapid and inexpensive genome sequencing technologies have enabled improved diagnostics and microbial surveillance, which is critical to combating the spread of antimicrobial resistance (AMR). AMR is the characteristic in which microorganisms – viruses, bacteria, and fungi – change over time and in ways that that render antimicrobial medicines futile against them. Dr. Engelthaler shared a few shocking statistics:

  • Methicillin-resistant Staphylococcus aureus (MRSA) causes 80,461 severe infections and 11,285 deaths annually
  • Carbapenem-resistant Enterobacteriaceae causes 9,000 drug-resistant infections and 600 deaths annually
  • Drug-resistant non-typhoidal salmonella causes 100,000 drug-resistant infections and $365,000,000 in medical costs annually

These are merely a few examples of the drug-resistant diseases plaguing the human population. Antibiotic resistance proliferates as a result of selective pressure in which a population of bacteria contains a subset of antibiotic-resistant organisms that survive treatment and are able to cause new infections. Dr. Engelthaler discussed the concepts of pre-resistance, in which a minor component of a population of treated patients presents with drug resistance, and, hopefully, revealing an opportunity to detect resistance early. Quelling the spread of antimicrobial resistance requires not only complex tools for pathogen genomics, but also a One Health approach that appreciates the interconnection between humans, animals, plants, and their shared environment.

Switching gears toward COVID-19, Dr. Engelthaler described the tracking and findings of the novel coronavirus’ genomics. He explained the genomic tracking of SARS-CoV-2 as building a viral family tree, akin to using “ for COVID.” The goal of genomic tracking is to discover where the virus came from and predict where it is going as well as identify and understand its mutations. The spike-protein D614G mutation is suspected of being the mutation that made the pandemic. The D614G mutation was first found in strains that took over Europe, but came from Asia, before hitting the United States. In January, in Arizona, a student at ASU returned home from a visit to Wuhan. This one of the first four cases in the United States; however, the viral lineage died with that case. Interestingly, there was a substantial outbreak from a strain out of Tucson and this specific regional population has this one mutation that has not been found elsewhere. Dr. Engelthaler pointed out that the popular strains of SARS-CoV-2 tend to be highly transmissible, but with low lethality.

Session XI: Regulatory Updates

Dr. Kathryn L. Harris from the National Institutes of Health (NIH) provided a briefing on the latest updates from the Office of Science Policy, including NIH guidelines with COVID-19 research and development and activities of the Novel and Exceptional Technology and Research Advisory Committee (NExTRAC). The NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules was amended in April 2019. The Guidelines set minimum biosafety requirements regarding physical containment and biosafety levels for research with recombinantly or synthetically modified SARS-CoV-2 in whole or portions of the virus. There are four risk groups for human etiologic agents defined by their relative pathogenicity for health human adults, where Risk Group 1 agents are not associated with disease in health adults and Risk Group 4 agents are likely to cause serious or lethal disease for which preventative or therapeutic intervention is not usually available. Under the Guidelines, appropriate biosafety level for conducting research with SARS-CoV-2 depends on the modifications to and manipulation of the agent: recombinantly or synthetically modified SARS-CoV-2 (whole virus) would generally require a minimum of biosafety level 3 containment, whereas experiments using only a fragment of the virus may be able to be safely conducted at a lower level. SARS-CoV-2 clinical trials involving the administration of recombinant or synthetic vaccines that are subject to the NIH Guidelines require review and approval by the Institutional Biosafety Committee (IBC).

NExTRAC focuses on the scientific, safety, and ethical issues associated with emerging biotechnologies, such as gene editing, gene drives, synthetic biology, and neurotechnology. Additionally, NExTRAC serves as a public forum for transparent discourse on challenging issues, a source of advice to the NIH Director, and a resource for the scientific community and general public. The Working Group on Biosafety Guidance and Conditions for Field Release of Gene Drive Modified Organisms provides advice on the diverse applications and species that may be used in gene drive research with different risks as well as the knowledge and conditions should be in place to help ensure that field release research of gene drive-modified organisms could be conducted safely and ethically.  

Dr. Thomas J. Cremer from the Centers for Disease Control and Prevention (CDC) discussed the response of the Import Permit Program (IPP) to the COVID-19 pandemic. The program regulates the importation of infectious biological materials that could cause disease in humans in order to prevent their introduction and spread into the US. In 2012, the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) became a Select Agent and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) requires additional permits for distribution. Given that all coronaviruses have a positive-stranded RNA genome, the complete RNA genome is regulated by the CDC and subsequent distribution requires additional permits. As a novel coronavirus, SARS-CoV-2 is not currently a Select Agent; however, it is subject to an additional permit for subsequent transfers. Isolates or cultures of SARS-CoV-2 and materials known or suspected to contain the virus require a different IPP application than unembalmed human known or reasonably expected to be infected with SARS-CoV-2. In response to the pandemic, inspections by the Division of Select Agents and Toxins were made virtual until September. IPP is working to expedite all requests for SARS-CoV-2 for research and development.

Dr. Aufra C. Araujo, also from the CDC, highlighted the biosafety contributions of the Division of Laboratory Systems (DSL) to the COVID-19 response. As of 26 October, 7,478 CDC personnel are supporting the pandemic response, 131 COVID-19 studies have been published in the Morbidity and Mortality Weekly Report (MMWR), 141 million COVID-19 tests have been conducted in US laboratories, and 34.4 million uses of the Coronavirus Self-Checker have occurred. The DSL’s role in the response includes laboratory biosafety guidance, addressing biosafety inquiries, and supporting development of training and educational materials. Since the start of the pandemic, DLS has received many inquiries regarding data and reporting, situational awareness, sample collection and handling, logistics, testing, and biosafety. As the pandemic persists, and cases surge, the DLS continues to provide laboratory guidance and training.  

Finally, Dr. Daniel Tuten from the CDC described the Federal Select Agent Program (FSAP) Laboratory Examination Tool (LET). The FSAP regulates the possession, use, and transfer of biological select agents and toxins and it is jointly managed by the Division of Select Agents and Toxins (DSAT) at the Centers for Disease Control and Prevention (CDC) and the Agriculture Select Agent Services (AgSAS) under the Animal and Plant Health Inspection Service’s Agriculture Select Agent Services (APHIS) at the US Department of Agriculture (USDA). The primary purpose of the FASP-LET is to aid FSAP-regulated entities to conduct annual, internal inspections. Section 9(a)(6) of the select agent regulations requires a Responsible Official (RO) to certify that an annual inspection is performed for each registered space where select agents and toxins are stored or used in order to assess compliance with the requirements of the select agent regulations. The tool is available online and all data in the system – including deficiencies, comments, and corrective actions – are encrypted. The FSAP-LET is intended to help laboratories comply with the select agent and toxin regulations, but it is not exhaustive and does not address all regulatory requirements, thus, regulated entities are responsible for ensuring they are compliant. In late 2019, the tool was moved to the electronic FSAP information system, which improves efficiency and the exchange of information for collaboration.

Session XIII: Biosafety Assortment – Emerging Fields of Drug Therapies & Commercial Scale Production Challenges 

Dr. Susan E. Vleck from Stanford University covered zoonotic challenges in biosafety, including a case study of a possible laboratory acquired infection (LAI), and how Stanford’s Animal Research Occupational Health and Safety Program has facilitated collaborative improvements between environmental health and safety (EH&S) and the Veterinary Services Center. The Animal Research Occupational Health and Safety Program is a central resource for Stanford researchers and staff who are working with animals, and particularly for those working with hazards overseen by EH&S. The program was created to address animal-related EH&S queries, trainings or assessments, and assist Occupational Health by advising on the medical surveillance program. In biosafety, moving from in vitro to in vivo creates additional issues in which the biological agent must be considered along with its tropism, replication and spread, but also issues such as animal housing and potential shedding of the agent. Dr. Vleck pointed out that zoonoses can occur within a research colony in three situations: (1) infected animals are introduced into the colony; (2) a human transmits a disease to the animals; or (3) research is conducted with agents that can cause zoonoses and the necessary safety protocols are not followed. Such safety failures are especially concerning for laboratories that work with the “big three” zoonotic diseases: Coxiella burnetii in sheep, Herpes B virus in non-human primates, and tuberculosis or MMR in humans. In order to protect personnel and research subjects, Stanford employs a three-pronged approach: (1) animals are tested before arrival, quarantined upon arrival, and then tested again; (2) any staff who has routine contact with animals may undergo medical surveillance; and (3) all personnel are educated on zoonotic risks associated with the big three diseases.

In 2018, a potential exposure was reported, which involved a person working male sheep that had oral and nasal lesions upon arrival. These sheep were suspected to be infected with Orf, a viral sin disease caused by a parapoxvirus, and classified as a Risk Group 2 agent. Transmission can occur should a human come in direct contact with a lesion or fomite, and the individual in question did present with a rash that spread from the upper right extremity to the upper left extremity and torso. Given that this event created a concern over disseminated disease, a collaborative investigation into the case was carried out, and the exposure route was likely a floor drain. As a result of this incident, several practices were updated, to include a more thorough cleaning of rooms and tools, requiring arm covers as part of minimum PPE, establishing formal training on PPE and zoonoses, and designed door and pen signage for when any animal in the colony had lesions or a positive test. This incident also highlighted the need for improved communication between departments; however, the after-action efforts enabled an improved understanding on the roles and responsibilities of each group, and the clear need to communicate.

Kim DiGiandomenico from AstraZeneca presented on an environmental health and biosafety risk assessment framework for commercial scale cell and gene therapy manufacturing, developed by the Biophorum or Cell and Gene Therapy (CGT). Cell and gene therapies aim to treat diseases by altering genes in specific cells and insert those cells back into the body. The Biophorum is a global collaboration comprised of industry leaders and experts throughout the biopharma value chain. The CGT was formed in 2018 as the first environmental health and safety and biosafety (EHS&B) Biophorum. The goals of the CGT are to develop best practices and standards, improve risk controls, increase the speed of learning, and help regulatory agencies in drafting guidance or policies around CGT development and manufacturing. The existing industry risk assessment methodologies lacked guidance related to the CGT-associated risks and commercial scale CGT manufacturing as they were created for monoclonal antibody and biologic production. To fill in this gap, a framework for EHS&B professionals includes a Risk Assessment Template that alerts the reader to the “complexity of commercial scale manufacturing, areas to assess, potential questions to ask and other pertinent parties who may input to the risk assessment.” The resulting safety profile devised by a cross-functional team helps mitigate risks related to product biological contamination, failures or breaches of the system, spills, material and waste flows, and surface cleanability. Ms. DiGiandomenico emphasized that risk assessments are a shared responsibility by multiple disciplines at all levels of an organization and that there does not exist a one-size-fits-all risk assessment scheme, because risk varies based on infrastructure, scale, and personal competencies.

Session XVI: High-Containment

Fahim Manzur from the Plum Island Animal Disease Center in New York detailed the four lessons learned from bringing a new high-containment effluent decontamination system (EDS) online, which resulted in some costly mistakes. Leaks were observed from newly installed stainless steel piping sections placed below storage tanks after several months of testing with clean water, causing microbiologically induced corrosion of the piping. The existing piping was replaced with carbon steel, the diameter was decreased to increase flow rate, and the thermal and liquid decontamination of all storage tanks and piping was conducted. There was a potential Select Agent release event when hose lines suffering mechanical wear failed on multiple cook tanks during the decontamination cycle. To mitigate the issue, piping was rearranged to reduce turbulence on the hoses and floating sleeves were added. A third lesson from the buildup of solids in the system required a rework of the force main (a pressurized pipe that transports sewage flows under pressure) and the installation of a redundant force main. The final lesson revolved around the failure of components in a seawater-based secondary cooling system after 18 months of use, which was repaired by reinstalling all secondary cooling heat exchanger bundles and developing a future plan to implement a different type of system. Each of these lessons cost $13,000 to $560,000 for a total of $1,064,000. Manzur’s example of pricey lessons learned emphasizes the importance of learning from other facilities, conducting root cause analyses to mitigate failures, and understanding the cost of up-front redundancies versus the cost in terms of money, time, and work to operations to handle failures.

Sheryl Major, a Biosafety and High-Containment Officer at the University of California (UC), discussed the management of high-containment facilities for the future. There are several High-Containment Lab Initiatives at UC spanning biosafety level 3 (BSL3) laboratories, COVID-19 research, and governance and structure. A BSL-3 laboratory requires biological safety cabinets, containment equipment, powered air purifying respirators, Tyvek suits, sleeves, and disposable gowns. After several laboratory incidents at the CDC and FDA involving anthrax and smallpox became high publicized, UC decided to evaluate its BSL-3 program with a focus on safety and consistency and established the Biosafety/Biosecurity Task Force. The goals of the Task Force included establishing a system-wide high-containment laboratory oversight committee and groups, designating high-containment laboratory directors, offering training courses, performing site surveys at BSL-3 laboratories, and conducting biohazardous materials inventories. These initiatives successfully led to the development of minimum standardized training requirements, annual budget models for BSL-3 laboratories on campus, decommissioning checklists, annual facility verification recommendations, and a design standard for BSL-3 laboratories.

Andrea Smida, a Biosafety Officer at the University of Saskatchewan in Canada, told the Cinderella story of Blastomyces dermatitidis, a Risk Group 3 fungus, requiring a Containment Level (CL) 3 facility for any in vitro and in vivo work, that is the causal agent of blastomycosis. A local risk assessment of the fungus was conducted in a CL-2 laboratory and small animal facilities at the University of Saskatchewan in Canada for a research group in the College of Pharmacy and Nutrition. The team wanted to conduct an in vitro evaluation of the efficacy of a monoclonal antibody in killing B. dermatitidis and an in vivo evaluation of the efficacy and long-term toxicity of the radioimmunotherapy. In short, the team wanted to find out if this Risk Group 3 fungus could be used in an enhanced CL-2 or CL-2+ facility. A pathogen risk assessment determined B. dermatitidis as a human and animal RG3 organism that can be worked on in a CL-2 facility adhering to CL-3 operational processes. This determination was based on the thermal dimorphic nature of the fungus, which means that the yeast form is not as pathogenic and communicable in comparison to the spore form, and the fact that the yeast form can be easily maintained when the temperature is 37°C or lower. The “happily ever after” of this story is that the B. dermatitidis research was initiated in April 2019 when the samples were supplied to the team. Currently, there is no Blastomyces work being conducted and the fungus is sitting in storage at -80°C; however, future work is planned for early 2021. Future implications of this Cinderella story include a new Public Health Agency of Canada-Canadian Food Inspection Agency biosafety directive for Risk Group 3 fungi at CL-2 laboratories.

Heather Blair, an Associate Biosafety Office at Colorado State University, trains principal investigators, visiting scientists, post-docs, and graduate and undergraduate students on how to work safely in BSL-2 and BSL-3 laboratories. Her first point is about the difference between disinfecting and autoclaving biological liquid for disposal. Disinfection is a process that removes many or all microorganisms, except bacterial spores, on inanimate objects by applying antimicrobial pesticides. Disinfectants include acids, alcohols, aldehydes, alkalis, biguanides, oxidizing agents, halogens (hypochlorite and iodine), phenolics, and quaternary ammoniums. Sterilization is a process that removes or eliminates all forms of microbial life using physical or chemical methods. Sterilization destroys all microorganisms on the surface of an article or in a fluid to prevent disease transmission. Autoclaving is used to sterilize liquids as well as inanimate objects and surfaces. In order to maintain safety and protect samples, Blare recommends spraying a surface that is clean, such as a towel or cloth, instead of the contaminated surface and then wiping down the contaminated area. Proper gloves must be donned when disinfecting and sterilizing to protect staff and samples. Biological safety cabinets (BSCs) require undisrupted airflow and, for staff safety, a researcher would work at least 4 inches from the front air vent in the middle. Additionally, work should be done horizontally such that there is a clean to dirty flow while working in the BSC.

Embracing Improvement  

The biosafety and biosecurity community faces constant challenges from microbial dangers, but also from the maintenance of safe laboratory environments in order for research to continue. Dr. Kathryn L. Harris highlighted the regulatory updates made to address minimum biosafety requirements regarding physical containment and biosafety levels for research with recombinantly or synthetically modified SARS-CoV-2. Dr. Daniel Tuten described the Federal Select Agent Program Laboratory Examination Tool (FSAP-LET), which debuted a new system to increase efficiency by greatly enhancing information exchange with FSAP and collaboration. Kim DiGiandomenico emphasized the importance of risk assessments in order to mitigate risks arising in the laboratory. Fahim Manzur detailed how lessons were learned and improvements were made from a series of failures at a facility with a new high-containment effluent decontamination system. Heather Blare trains researchers and students on how to work safely in BSL-2 and BSL-3 laboratories. These examples show the dedication of laboratory scientists and researchers to improvements in safety and best practices.  

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