Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories.

Introduction: Pathogen leak from a high-containment laboratory seriously threatens human safety, animal welfare, and environmental security. Transportation of pathogens from a higher (BSL4 or BSL3) to a lower (BSL2) containment laboratory for downstream experimentation requires complete pathogen inactivation. Validation of pathogen inactivation is necessary to ensure safety during transportation. This study established a validation strategy for virus inactivation. Methods: SARS-CoV-2 wild type, delta, and omicron variants underwent heat treatment at 95°C for 10 minutes using either a hot water bath or a thermocycler. To validate the inactivation process, heat-treated viruses, and untreated control samples were incubated with A549-hACE2 and Vero E6-TMPRSS2-T2A-ACE2 cells. The cells were monitored for up to 72 hours for any cytopathic effects, visually and under a microscope, and for virus genome replication via RT-qPCR. The quality of post-treated samples was assessed for suitability in downstream molecular testing applications. Results: Heat treatment at 95°C for 10 minutes effectively inactivated SARS-CoV-2 variants. The absence of cytopathic effects, coupled with the inability of virus genome replication, validated the efficacy of the inactivation process. Furthermore, the heat-treated samples proved to be qualified for COVID-19 antigen testing, RT-qPCR, and whole-genome sequencing. Discussion: By ensuring the safety of sample transportation for downstream experimentation, this validation approach enhances biosecurity measures. Considerations for potential limitations, comparisons with existing inactivation methods, and broader implications of the findings are discussed.

Cytometry in High-Containment Laboratories.

The emergence of new pathogens continues to fuel the need for advanced high-containment laboratories across the globe. Here we explore challenges and opportunities for integration of cytometry, a central technology for cell analysis, within high-containment laboratories. We review current applications in infectious disease, vaccine research, and biosafety. Considerations specific to cytometry within high-containment laboratories, such as biosafety requirements, and sample containment strategies are also addressed. We further tour the landscape of emerging technologies, including combination of cytometry with other omics, the application of automation, and artificial intelligence. Finally, we propose a framework to fast track the immersion of advanced technologies into the high-containment research setting to improve global preparedness for new emerging diseases.

Cyberbiosecurity in high-containment laboratories.

High-containment laboratories (HCLs) conduct critical research on infectious diseases, provide diagnostic services, and produce vaccines for the world's most dangerous pathogens, often called high-consequence pathogens (HCPs). The modernization of HCLs has led to an increasingly cyber-connected laboratory infrastructure. The unique cyberphysical elements of these laboratories and the critical data they generate pose cybersecurity concerns specific to these laboratories. Cyberbiosecurity, the discipline devoted to the study of cybersecurity risks in conjunction with biological risks, is a relatively new field for which few approaches have been developed to identify, assess, and mitigate cyber risks in biological research and diagnostic environments. This study provides a novel approach for cybersecurity risk assessment and identification of risk mitigation measures by applying an asset-impact analysis to the unique environment of HCLs. First, we identified the common cyber and cyberphysical systems in HCLs, summarizing the typical cyber-workflow. We then analyzed the potential adverse outcomes arising from a compromise of these cyber and cyberphysical systems, broadly categorizing potential consequences as relevant to scientific advancement, public health, worker safety, security, and the financial wellbeing of these laboratories. Finally, we discussed potential risk mitigation strategies, leaning heavily on the cybersecurity materials produced by the Center for Internet Security (CIS), including the CIS Controls®, that can serve as a guide for HCL operators to begin the process of implementing risk mitigation measures to reduce their cyberbiorisk and considering the integration of cyber risk management into existing biorisk management practices. This paper provides a discussion to raise awareness among laboratory decision-makers of these critical risks to safety and security within HCLs. Furthermore, this paper can serve as a guide for evaluating cyberbiorisks specific to a laboratory by identifying cyber-connected assets and the impacts associated with a compromise of those assets.

Decontamination of High-Containment Laboratories for Demolition: A Risk-Based Approach.

Introduction: Decontamination of redundant laboratories, contained plant space, and support buildings used to handle high consequence animal pathogens (North America BSL-3Ag, UK SAPO4) was required before demolition to mitigate the risk that infectious material was released into the environment. Methods: Given the age of the buildings and their construction, bespoke qualitative risk-based methods were developed by biorisk personnel, in consultation with specialist contractors where applicable. This approach was to give assurance that suitable decontamination was achievable, sometimes through multilayered approaches to disinfection. Time was considered as a contributing factor in decontamination. Different means of achieving decontamination were employed, and waste management was considered as part of the overall process ensuring a "cradle to grave" approach. Summary: This article describes the challenges and solutions, faced by a UK facility licensed to work on high hazard pathogens, including foot-and-mouth disease virus and African swine fever virus. The risk-based approach (and methods described herein) may also be applicable to routine decontamination of younger buildings, that is, during renovations or temporary derestriction.

The Impact of Air Inflow and Interfering Factors on the Performance of Microbiological Safety Cabinets.

Introduction: The operator protection factor (OPF) of four biological safety cabinets (BSCs) has been measured under standard and suboptimal conditions. Methods: The OPF for one BSC1, two BSC2, and an acid-fast bacilli staining station (AFBSS) was measured using the potassium iodide method for in situ testing of BSCs (CEN12469) over a range of inflow velocities under standard conditions and with common interfering factors (fans, opening doors, and walk pasts). Results: The BSC1 and the AFBSS gave a high level of protection under standard test conditions at all airflows (down to 0.3 and 0.38 m/s, respectively). During interfering processes, the BSC1 and AFBSS gave a high level of protection (OPF >105) at the specified inward airflow. At lower airflows, there was a predictable deterioration in performance. There was a significant difference in performance between the two BSC2s tested, with one model passing all tests under all interfering conditions at all airflows. The second BSC2 failed the standard test at the lowest airflow and provided poor levels of protection (OPF <105) in all tests carried out with interfering processes. Conclusion: Although BSC2s are capable of giving a high level of performance, this is design dependent and the BSC1 and AFBSS give a more predictable level of performance due to their simpler design. In environments where BSC certification is not possible, they may provide more robust and sustainable primary containment.

Preclinical coronavirus studies and pathology: Challenges of the high-containment laboratory.

The COVID-19 pandemic has highlighted the critical role that animal models play in elucidating the pathogenesis of emerging diseases and rapidly analyzing potential medical countermeasures. Relevant pathologic outcomes are paramount in evaluating preclinical models and therapeutic outcomes and require careful advance planning. While there are numerous guidelines for attaining high-quality pathology specimens in routine animal studies, preclinical studies using coronaviruses are often conducted under biosafety level-3 (BSL3) conditions, which pose unique challenges and technical limitations. In such settings, rather than foregoing pathologic outcomes because of the inherent constraints of high-containment laboratory protocols, modifications can be made to conventional best practices of specimen collection. Particularly for those unfamiliar with working in a high-containment laboratory, the authors describe the logistics of conducting such work, focusing on animal experiments in BSL3 conditions. To promote scientific rigor and reproducibility and maximize the value of animal use, the authors provide specific points to be considered before, during, and following a high-containment animal study. The authors provide procedural modifications for attaining good quality pathologic assessment of the mouse lung, central nervous system, and blood specimens under high-containment conditions while being conscientious to maximize animal use for other concurrent assays.

High-Containment Agriculture Animal Research: An AAALAC International Perspective.

Institutions that conduct high-containment agricultural research involving domestic livestock represent a specialized category of programs that are accredited by AAALAC International. The accreditation process includes a comprehensive assessment of the overall program of animal care and use. However, the complex design of these facilities and the unique care required for animals in this type of environment often mean that additional attention will be directed at areas regarded as higher risk when the programs are evaluated. Specific issues that may stimulate additional discussion and interest include animal housing practices, environmental conditions inside the facility, maintenance of procedure and support areas, methods for obtaining and safely transporting healthy research animals, strategies to minimize animal pain and distress, unusual protocol review challenges, and institutional policies relevant to personnel training and safety. These issues are further discussed to inform institutions of potential concerns that should be reviewed and assessed during internal preparations for accreditation visits by AAALAC site visit teams.

Challenges and Solutions With Agricultural Animal High Containment Waste Disposal.

Waste disposal in Agricultural Animal High Containment Animal Biosafety Level 3Ag and Animal Biosafety Level 4Ag (ABSL-3Ag and ABSL-4Ag) research facilities necessitates significantly more attention to detail in operations than that required in lower-containment-level laboratories. The unique features and requirements of agricultural-related research involve additional equipment and systems to safely transfer decontaminated waste out of the facility. The waste stream coming from ABSL-3Ag and ABSL-4Ag facilities, or high containment agricultural research waste, consists of many forms and differs from most research facility waste in that it is produced from research with livestock or other species loose housed, with the animal room serving as primary containment. This is in contrast to small laboratory animals being housed in primary containment caging. Waste handling equipment in agricultural research facilities may include autoclaves, effluent decontamination systems, incinerators, high-temperature renderers, alkaline tissue digester systems, high-efficiency particulate air filtration of exhaust and supply air, gas decontamination systems, and laundry facilities. This article focuses primarily on the disposal of waste from ABSL-3Ag livestock facilities, including procedures and lessons learned over 10 years of facility operation.

Significance of High-Containment Biological Laboratories Performing Work During the COVID-19 Pandemic: Biosafety Level-3 and -4 Labs.

High containment biological laboratories (HCBL) are required for work on Risk Group 3 and 4 agents across the spectrum of basic, applied, and translational research. These laboratories include biosafety level (BSL)-3, BSL-4, animal BSL (ABSL)-3, BSL-3-Ag (agriculture livestock), and ABSL-4 laboratories. While SARS-CoV-2 is classified as a Risk Group 3 biological agent, routine diagnostic can be handled at BSL-2. Scenarios involving virus culture, potential exposure to aerosols, divergent high transmissible variants, and zoonosis from laboratory animals require higher BSL-3 measures. Establishing HCBLs especially those at BSL-4 is costly and needs continual investments of resources and funding to sustain labor, equipment, infrastructure, certifications, and operational needs. There are now over 50 BSL-4 laboratories and numerous BSL-3 laboratories worldwide. Besides technical and funding challenges, there are biosecurity and dual-use risks, and local community issues to contend with in order to sustain operations. Here, we describe case histories for distinct HCBLs: representative national centers for diagnostic and reference, nonprofit organizations. Case histories describe capabilities and assess activities during COVID-19 and include capacities, gaps, successes, and summary of lessons learned for future practice.

Biosafety Level 4 Laboratory User Training Program, China.

Experienced, qualified personnel certified to work in high-level biocontainment laboratories contribute to the safe operation of these facilities. China began a training program for laboratory users after establishing its first Biosafety Level 4 laboratory, the Wuhan National Biosafety Laboratory (Level 4) of the Chinese Academy of Sciences. We provide an overview of the content of this training program, which can serve as a reference for developing national norms for high-containment laboratory training.

Opinion: Airtightness for Decontamination by Fumigation of High-Containment Laboratories.

Introduction: While the European legislation states that laboratories of high-containment must be sealable for fumigation, they do not prescribe a minimal value for airtightness. Starting from a previous study in which we measured the airtightness in 4 BSL-3 laboratories with blower-door tests, we discuss the connection between airtightness and a successful decontamination by fumigation. Methods: Biological indicators (BIs) consisting of spores of Geobacillus stearothermophilus on metal disks were laid out in laboratories of different levels of airtightness before performing a fumigation with aerosolized hydrogen peroxide using an automated device, according to the manufacturer's instructions. Results: Incubation of all BI disks placed in the facility with the highest level of airtightness showed complete inactivation of spores. However, in the facility with a lower level of airtightness, not all spores were inactivated. Discussion: Air leaks might be a factor in the outcome of the decontamination of a room by fumigation, as seen in the laboratory with a lower level of airtightness, but other factors associated with the fumigation process might also be critical for a successful decontamination. Conclusion: We argue that a validation of the decontamination procedure, before first use or after important renovations of a laboratory of high-containment, is a more effective endpoint than reaching a predefined level of airtightness.

Smart Card Decontamination in a High-Containment Laboratory.

Validated procedures for decontamination of laboratory surfaces and equipment are essential to biosafety and biorisk programs at high-containment laboratories. Each high-containment laboratory contains a unique combination of surfaces, procedures, and biological agents that require decontamination methods tailored to specific facility practices. The Plum Island Animal Disease Center (PIADC) is a high-containment laboratory operating multiple biosafety level (BSL)-3, ABSL-3, and BSL-3 Ag spaces. The PIADC facility requires the use of federally issued smart cards, called personal identity verification (PIV) cards, to access information technology (IT) networks both outside and within the high-containment laboratory. Because PIV cards may require transit from the BSL-3 to office spaces, a validated procedure for disinfecting PIV card surfaces prior to removal from the laboratory is critical to ensure biosafety and biosecurity. Two high-risk select agents used in the PIADC high-containment laboratory are foot-and-mouth disease virus (FMDV) and swine vesicular disease virus (SVDV). We evaluated disinfection of PIV cards intentionally spotted with FMDV and SVDV using a modified quantitative carrier test and the liquid chemical disinfectant Virkon® S. Our experimental design modeled a worst-case scenario of PIV card contamination and disinfection by combining high concentrations of virus dried with an organic soil load and use of aged Virkon® S prepared in hard water. Results showed that FMDV and SVDV dried on PIV card surfaces were completely inactivated after immersion for 30 and 60 seconds, respectively, in a 5-day-old solution of 1% Virkon® S. Therefore, this study provided internal validation of PIADC biosafety protocols by demonstrating the efficacy of Virkon® S to inactivate viruses on contaminated smart cards at short contact times.

High-Containment Pathogen Preparation in the Intensive Care Unit.

The recent Ebola virus disease outbreak highlighted the need to build national and worldwide capacity to provide care for patients with highly infectious diseases. Specialized biocontainment units were successful in treating several critically ill patients with Ebola virus disease both in the United States and Europe. Several key principles underlie the care of critically ill patients in a high-containment environment. Environmental factors, staffing, equipment, training, laboratory testing, procedures, and waste management each present unique challenges. A multidisciplinary approach is key to developing effective systems and protocols to maintain the safety of patients, staff, and communities.

Validating the Inactivation Effectiveness of Chemicals on Ebola Virus.

While viruses such as Ebola virus must be handled in high-containment laboratories, there remains the need to process virus-infected samples for downstream research testing. This processing often includes removal to lower containment areas and therefore requires assurance of complete viral inactivation within the sample before removal from high-containment. Here we describe methods for the removal of chemical reagents used in inactivation procedures, allowing for validation of the effectiveness of various inactivation protocols.

A rapid Orthopoxvirus purification protocol suitable for high-containment laboratories.

Virus purification in a high-containment setting provides unique challenges due to barrier precautions and operational safety approaches that are not necessary in lower biosafety level (BSL) 2 environments. The need for high risk group pathogen diagnostic assay development, anti-viral research, pathogenesis and vaccine efficacy research necessitates work in BSL-3 and BSL-4 labs with infectious agents. When this work is performed in accordance with BSL-4 practices, modifications are often required in standard protocols. Classical virus purification techniques are difficult to execute in a BSL-3 or BSL-4 laboratory because of the work practices used in these environments. Orthopoxviruses are a family of viruses that, in some cases, requires work in a high-containment laboratory and due to size do not lend themselves to simpler purification methods. Current CDC purification techniques of orthopoxviruses uses 1,1,2-trichlorotrifluoroethane, commonly known as Genetron®. Genetron® is a chlorofluorocarbon (CFC) that has been shown to be detrimental to the ozone and has been phased out and the limited amount of product makes it no longer a feasible option for poxvirus purification purposes. Here we demonstrate a new Orthopoxvirus purification method that is suitable for high-containment laboratories and produces virus that is not only comparable to previous purification methods, but improves on purity and yield.

Enabling Rapid Response to the 2014-2016 Ebola Epidemic: The Experience and the Results of the National Institute for Infectious Diseases Lazzaro Spallanzani.

The unprecedented epidemic of Ebola virus disease (EVD) in West Africa highlighted the need for stronger systems for disease surveillance, response, and prevention worldwide. Tackling an epidemic event today requires a broader view, not only limited to medical management of the patients, but which also includes heroic efforts by clinicians and public health personnel.Since its foundation in 1936, INMI has been devoted to the prevention, diagnosis and care for infectious diseases. In 2009, INMI became a WHO collaborative center for clinical care, diagnosis, response and training on Highly Infectious Diseases. This paper is aimed to present the activities and the challenging issues encountered by INMI during the 2014-2015 EVD outbreak in terms of preparedness and response to the epidemiological, clinical, diagnostic and research controversial aspects of EVD, both in Italy and in the field.