Keywords

FormalPara Learning Objectives

This chapter should enable readers to understand and discuss:

  • Limitations of diagnostic assays used to detect new or re-emerging pathogens in animals and the environment

    • The importance of testing samples from various sources and monitoring animal infectious diseases

  • Requirements of the response or research program which determine field laboratory criteria

    • Critical elements for the adequacy of a laboratory and clinical research site

    • Determinative factors for the selection of laboratory assays and equipment for research response

  • The need for regulatory management tools, expedited evaluation and approval processes, and diagnostic preparedness during an emergency outbreak in low-resource settings

  • Challenges to specimen collection, transport, and storage

  • The role of effective laboratory biosafety and biosecurity for preventing and controlling infection

  • The critical roles of data management and effective documentation for delivering accurate patient test results, epidemiological investigation, and supporting accurate interpretation and implementation of findings from clinical studies

  • Key advances in laboratory, point-of-care, and imaging diagnostic tools; applications of innovative diagnostics in outbreaks; and why multiple, versatile diagnostic technologies are important for research response

  • How the lack of diagnostic capacity contributed to ongoing transmission of the Ebola virus from a small village in Guinea to the cities of West Africa

  • Obstacles that may hinder the rapid deployment of laboratories to outbreak emergencies

1 Introduction

Clinical and research laboratories are indispensable elements of clinical studies to assess candidate medical countermeasures (MCMs), whether for long-duration trials or for trials meant to rapidly establish the safety and efficacy of MCMs in an infectious disease emergency. Over the last two decades, there has been increasing recognition that clinical trials can be central to meeting the goals of emergency response, that is, to (a) save lives and avert suffering, (b) accelerate the end of the outbreak, and (c) develop measures to prevent and mitigate future outbreaks (► Introduction 1 and Chap. 3). Not surprisingly, calls to rapidly deploy laboratory assets in response to infectious disease outbreaks or other public health emergencies have markedly increased in the last decade and continue to rise. Historically, diagnostic assays used to detect a new or re-emerging disease have been limited by a lack of commercial availability. When available, often they are highly complex, requiring specialized equipment and multiple steps, and are designed for use in CLIA-certified laboratories.Footnote 1 Deployment and scale-up of highly or even moderately complex assays are limited by available infrastructure, including trained personnel, making their use in low-resource settings challenging.

The size and infrastructure requirements for traditional clinical and research equipment and the logistical challenges associated with transporting and operating such equipment have also contributed to limiting the laboratory’s role during outbreaks and the ability to support response research, particularly in low-resource and remote environments (► Chaps. 37 and 38). As a result, the footprint of the deployed laboratory has often been small, and the range of assays performed restricted. Technological advances have led to the development of smaller, more rapid, and more robust equipment designed to use commercially available assays that can be performed at or near the point of patient care. This equipment is designed for lower complexity assays and requires minimal operation and data processing training. The availability of assays to detect high-consequence but low-frequency pathogens and emerging diseases has increased, including assays for use near or at the point of care. These newer-generation assays often have improved sensitivity and specificity. Advances in genomic sequencing have slashed the time and cost of sequencing novel pathogens, facilitating the rapid development of candidate diagnostic assays and vaccines (► Chaps. 11 and 12). As these newer technologies and assays have made it to the field, the role of the laboratory has been reimagined, setting a new standard for what is possible, even in the most remote settings.

2 Who, What, Where, When, and Why

Multiple outbreak-associated factors, along with the requirements of the response or research program, define the requirements of the field laboratory. The requirements, combined with local capacities and available infrastructure, will shape the capability and capacity of the field laboratory. Often, these are described as the “Who? What? Where? When? Why?” of the laboratory response (◘ Fig. 1). Command and control in a dynamic, high-stress environment are critical. The laboratory response must be nested within the larger outbreak response efforts, requiring coordination with local and national authorities, partner agencies, and healthcare providers. Partnership requires defining who will be responsible for the infrastructure, supply, set-up, and operation of the laboratory response. Partners should coordinate to prevent duplication of effort or waste of limited resources and ensure that efforts are meeting host country needs. “Who” also includes the research participants and their communities. It is essential to recognize that the laboratory is one component of a larger response effort and must be integrated into the response framework as a whole. Many aspects of the logistical arrangements needed for a research program in a low-resource environment are described in Book Part VII.

Fig. 1
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Key outbreak-associated factors for field laboratories in low-resource environments. (Authors)

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The what includes the availability of assays suited to the etiological agent of the outbreak, the sample types to be tested, and the requirements for qualitative or quantitative results, which will determine equipment and assay choices. The availability, feasibility, complexity, and cost will narrow or refine selections. In some cases, especially with a novel pathogen, no assay may be available, requiring the rapid development and validation of diagnostic assays before a laboratory can be fully deployed or engaged. The agent/pathogen will drive biosafety and biosecurity needs, including personal protective equipment (PPE), inactivation and decontamination methods, and infrastructure requirements. Depending on the cause of the outbreak, vaccines, pre- and post-exposure prophylaxis, and reliable therapeutics may or may not be available. As patient care becomes a larger part of the response, the need for the laboratory to provide routine clinical laboratory results (e.g., clinical chemistry testing and complete blood cell counts) that impact treatment should be incorporated into design and deployments. To avoid downstream complications, a pathway for reporting patient results while protecting patient confidentiality (to whom, when, and how) must be delineated and strictly adhered to.

Where, when, and why are the greatest drivers of laboratory size and scope. Initial considerations when planning a response include the current size and geographical scope of the crisis and its projected trajectory. These will be overlaid with the distribution of treatment facilities, transport networks for moving samples and materials rapidly (roads, water, and air routes), and the availability of existing laboratories within the region. Several important factors must be considered when selecting a specific site for the laboratory (see ► Sect. 3.1). Dialogue with and input from local communities and community leaders is essential prior to laboratory deployments (► Chap. 18).

Time is critical in emergency response management. In the laboratory, processing time, assay run time, results reporting, and re-supply times must all be planned for. Long wait times for lab results can delay access to treatment, increase the risk of transmission or exposure in quarantine facilities, and discourage patients or potential trial participants. Prolonged transport time or insufficient capacity may degrade sample quality, make results less reliable, and hinder interpretation. Geographically dispersed outbreaks may require the mobilization of multiple laboratories to minimize these variables.

The terms of reference for the laboratory must be clearly defined and prioritized at the onset of operational planning. Early engagement of the laboratory in the design of a clinical trial will help ensure the success of the protocol and the laboratory. Laboratory testing is often essential for determining suitability for enrollment of participants and reliably observing primary and secondary study endpoints. Upon finalization of the operational requirements or study design, the laboratory can identify suitable assays that will meet the needs of the study, procure necessary equipment and supplies, develop data documentation and reporting streams (► Chap. 35), and ensure adequate capacity to support study enrollment or response efforts. Once the laboratory is established, additional service requests are likely to arise in the course of an outbreak or research study. Building or strengthening local capacity to enhance response and promote local resilience is an ethical requirement, often a political necessity, and a practical priority for laboratory staff and operations. Local staff bring cultural and geographical knowledge, have ties with local communities, and provide continuity in cases where expatriate employees rotate in and out—the usual practice where there are hardship conditions or during prolonged response efforts (► Chap. 42). Early engagement of the laboratory during the planning of response efforts and research protocol development is required regardless of the resource level of the study location to prevent delays and minimize potential failures of the studies.

3 Field Laboratories

“Field” or “mobile” laboratories are terms often used interchangeably to describe a temporary structure or facility to collect, process, analyze, and report results on samples received from outbreak patients. As mentioned in the previous section, the size and scope of the laboratory will vary depending on many factors, and emergency deployment is not restricted to low-resource environments. Mobile laboratories have been used for decades in various capacities, including routine surveillance, outbreak response, and research activities (Racine and Kobinger 2019). Over time, the contents and capabilities of mobile labs have evolved to meet the specific needs of outbreak situations. Mobile laboratories for disease diagnostics typically include diagnostic instruments and equipment necessary for detecting and characterizing infectious agents, which must be matched appropriately with the mobile laboratory design. Mobile laboratories have demonstrated their efficacy in disease diagnostics through successful evaluations with simulated specimens (training) and during outbreaks (Roh et al. 2022; Xing et al. 2021). These labs offer the advantage of rapid and flexible deployment to disease transmission hotspots and austere locations, often in resource-constrained settings. Many labs have been expanded to include clinical assay support to guide case management and support response research, including clinical studies. The laboratory design can be as simple as a specimen tent and a lab in a suitcase to vehicles in a range of sizes designed to provide or deliver laboratory space, such as hardened laboratory containers that can remain functional as a laboratory well beyond a typical outbreak response (◘ Fig. 2). Regardless of the size, shape, or location of the laboratory, the same quality and safety standards should always be implemented.

Fig. 2
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Various configurations of mobile and deliverable laboratory systems. (Credit: Tina May/MRIGlobal)

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3.1 Where? Site Location

The following three critical elements must be considered during the site selection process for a laboratory.

  • Safety

    • Personal safety

    • Biosafety

    • Biosecurity

  • Outbreak response requirements

    • Surveillance and epidemiology

      • Diagnostics

      • Pathogen identification and characterization

    • Patient treatment needs

    • Clinical research data collection and analysis

  • Data quality and integrity

The laboratory should be placed where the public health response can be addressed while balancing the needs and safety of the staff. The lab must be close enough to diagnosis and treatment centers to allow samples to be transported, received, and assayed promptly, in a way that does not compromise the testing results. Where roads are unpaved or security is poor, this may mean that laboratories need to be co-located with medical care facilities (◘ Fig. 4). In situations where the outbreak that has spread over a wide geographical area there may be a need for multiple laboratories. As the outbreak evolves, the location, size, and number of laboratories may need to be adjusted. A site location matrix (◘ Fig. 3) is a useful tool for comparing the advantages and disadvantages of candidate sites.

Fig. 3
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A comparison matrix is a useful tool for selecting a clinical site. (Authors)

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The laboratory site must allow for the work to be conducted without compromising biosafety or data integrity. “Biosafety” refers to procedures intended to protect against infection from or release of harmful biological agents, including the ability to effectively respond to a potential laboratory exposure or accident. Ideally, the laboratory is established as early as possible in an outbreak to perform diagnostics (including in some cases assisting with pathogen identification and characterization) and to support early medical response by local health systems or nongovernmental organizations (NGOs) (e.g., Médecins Sans Frontières [MSF] or Doctors Without Borders). Depending on the response activities and requirements, as well as the trajectory of the outbreak, the laboratory capacity may need to be expanded and/or specialized labs established.

Available infrastructure may need to be renovated, or supplemented, to meet the needs of the facility. When permanent buildings are unavailable or unsuitable, tents, labs installed in vehicles or shipping containers, or temporary structures can be considered. If there are sufficient resources, construction of a new facility may also be viable. If an existing structure is repurposed or a new structure constructed, its use after the emergency should be considered: Can the structure be sustained as a medical or research laboratory? Will it have to be decontaminated? What will decontamination entail? Decisions on the location of the laboratory, construction, and disposition of the space at the end of the outbreak must be made in partnership with local officials and other partners.

The following multiple factors contribute to the suitability of a given location to host a laboratory (► Chaps. 32 and 40).

  • Physical security (► Chap. 41)

  • Accessibility of the site

  • Logistics, including resupply chains for reagents and equipment (► Chap. 37)

  • Availability of electronic communications (► Chap. 34)

  • Availability, reliability, and source of electricity (► Chap. 39)

  • Availability of clean water

  • Adequate lighting and environmental control (► Chap. 38)

  • Food and lodging for staff

  • Treatment and/or evacuation of staff in case of accident, illness, or infection

  • Waste disposal (solid and liquid)

The intended and projected workloads of the laboratory are another important variable. Is the space sufficient to address surges in workloads? Secondary sites should be identified and prepared to accommodate work surges if the primary site is insufficient. Are there political (including regional stability) and/or social factors that might impact or drive site selection? (► Chap. 16 and In Practice 16.1). Community engagement or good participatory practice (GPP) is essential for an ongoing, respectful dialogue with the surrounding community to address possible suspicions and misapprehensions, encourage trial recruitment, and mitigate “not in my backyard” sentiments. Every situation is unique, and in an emergency time for selecting laboratory sites is often limited. There may be no perfect site, but a matrix-based approach to identifying candidate laboratory sites may minimize challenges.

3.2 Assay and Equipment Selection

Multiple factors will drive the selection of assays and equipment, including the pathogen and clinical course of disease in patients. The first question for the laboratory is “What are you trying to measure or test for?” or more broadly, “What question are you trying to answer?” The responses combined with the required timeframe will help narrow the selection of available assays or identify where a new assay needs to be developed. Other factors will include the expected number of samples and the turnaround time desired or required. The skill of the laboratory staff must be considered. Can available staff safely and accurately perform complex assays or is there sufficient time to build personnel capacity? Is the available facility suitable for running complex assays? What is the availability of reagents and assays? Biosafety and safe handling of samples cannot be overlooked. Ideally handling of high-hazard samples should be minimized and inactivation should be performed whenever feasible.

During the coronavirus disease 2019 (COVID-19) pandemic and 2014–2016 West Africa Ebola outbreak, laboratories faced substantial challenges with shortages of reagents and disposable supplies. As travel and transport to and from the region was curtailed, shipment of supplies became even more difficult, requiring some laboratories to establish alternate means to transport supplies (i.e., staff hand-carrying large quantities of supplies) or develop capabilities to run multiple different assays for the same agent depending on availability. The need to pivot between assays complicated laboratory operations and required increased training to master additional testing protocols and devise strategies to bridge between different assays. Other factors also influence assay selection, including but not limited to the cost per assay, sample requirements (type and volume of samples), the equipment’s power requirements, and the data’s intended use. As cartridge and multiplex assays, which provide quantitative or semi-quantitative measurement of multiple analytes, have become more commonplace, multiplex assays are often favored as they provide more information from one test procedure. However, these assays are often more expensive and may be unaffordable or unsustainable for many countries. The use of the data will also influence the assays selected. Clinical care, clinical research, diagnostic, and surveillance needs differ. For clinical studies, what is being tested must match the protocol. Moreover, trial participants’ informed consent must include the purpose of testing and analysis. Using human biological samples for purposes participants have not consented to is unethical (though it has not always been considered so) (Garrison 2013).

For more information on the importation of study products, please refer to ► Chap. 38. For transport and storage considerations, see ► Chap. 39.

3.3 Regulatory and Legal Concerns

Managing regulatory and legal requirements during an outbreak is a complex and exacting task, and even more so in low-resource settings. Generic terms like “low-resource settings” or “developing countries” should be accompanied by a deeper understanding of the local context to avoid assumptions and tailor regulatory compliance measures accordingly (van Zyl et al. 2021). Robust regulatory oversight is crucial. In a bilateral partnership, it requires understanding and meeting local, national, and international requirements. Stringent regulatory authorities will not accept evidence from noncompliant trials as evidence for authorization or licensing, but they have shown flexibility in adjusting formal requirements during public health emergencies (► Chap. 6).

As the size of the emergency grows, resources will be strained; low-resource settings where healthcare systems may already face capacity and accessibility constraints are especially vulnerable (Siow et al. 2020). In some environments, gaps may exist in regulatory guidance and responsible regulators may have limited capacity for oversight and guidance. Often the engagement of external experts is beneficial in these situations to augment local resources and help enhance long-term capacity (► Chap. 33, In Practice 33.2, and 33.3). For clinical studies with human participants, it is essential that the proposed study be reviewed and approved by all appropriate research ethics committees (also known as institutional review boards). A data and safety monitoring plan and board to implement it are also essential (► Chap. 23).

3.3.1 Regulatory Management Tools for Emergencies

Governments employed various regulatory management adjustments during the COVID-19 pandemic and other recent public health emergencies. Methods including rapid regulatory impact assessments, consultations with stakeholders, and international partnerships helped ensure robust, substantive regulatory oversight during the pandemic while easing administrative burdens (OECD 2020). Complying with regulatory and legal requirements in low-resource settings during outbreaks requires a multifaceted approach. Governments and regulatory bodies should leverage regulatory management tools and establish expedited evaluation processes to ensure timely access to critical medical interventions while maintaining appropriate oversight (OECD 2020; van Zyl et al. 2021). Working in partnership with ethical review committees and regulators with greater response capacity can help countries with fewer resources perform their own due diligence more readily, for example, by reviewing collected evidence rather than gathering and compiling it de novo (► In Practice 33.3). It is also essential to consider the unique challenges and context of each low-resource setting to develop tailored and effective regulatory strategies (Siow et al. 2020; van Zyl et al. 2021).

Global disparities in healthcare tend to be especially acute in low-resource environments (van Zyl et al. 2021) (► Chap. 5). The effort to address disparities is complicated by inadequate investment in healthcare infrastructure, shortages of trained personnel, and other scarce resources. In some areas, there may be profound distrust or even fear of the healthcare system that has become entrenched through the history of that country or the experiences of some members of the population (Siow et al. 2020). Recognition of disparities and active engagement with the community is essential to ensure widespread access to healthcare for those in need and create or bolster the willingness of community members to report disease, receive treatment, and participate in clinical studies (► Chap. 18 and In Practice 18.1). Social mobilization and outreach are essential to ensure that the laboratory, treatment, and research centers are accepted by the community. Failure to engage the community can increase security risks to treatment and research sites, discourage study recruitment, hinder efforts to contain the emergency and lessen the effectiveness of participant follow-up—all of which could impact the rigor and generalizability of results. For example, failure to recruit study participants representative of the population affected by an outbreak may limit the applicability of study findings and potentially compromise the study results. The engagement of sociologists and anthropologists and the development of robust social mobilization teams are essential to ensure that messages and engagements are understandable, culturally appropriate, and effective (► Chap. 26).

3.3.2 Expedited Evaluation and Approval Processes

During public health emergencies, such as an Ebola outbreak, expedited evaluation and approval processes for diagnostic assays, medical products, and interventions are essential (van Zyl et al. 2021) in order to facilitate prompt access to safe, effective MCMs to mitigate suffering and the loss of life. For many emerging disease threats, there are limited interventions, or interventions such as candidate vaccines are still under development. Use of these early-stage products may be of great benefit but often they have not gone through clinical trials in humans to assess their safety and potential efficacy. Ideally an accelerated clinical trial is designed and implemented to determine as rapidly and definitively as possible whether the candidate product is safe and provides benefit. Advanced development of protocols that could be rapidly adapted to specific situations can help reduce the amount of time to initiate response research and respond to emergencies as effectively as possible. Preplacement of these protocols and engagement of regulatory groups in reviewing these protocols should be encouraged. As their research capacity develops, countries at risk should take ownership of the preparation and implementation of these protocols (► Chap. 8). In an emergency, such products may also be distributed under an expanded access program such as the World Health Organization (WHO) program for monitored emergency use of unregistered and experimental interventions (MEURI). Such programs cannot, however, generally provide the scientifically well-founded results required to demonstrate safety and efficacy to regulators, and in some cases could discourage enrollment in high-quality clinical trials by offering potential participants certain access to an experimental intervention rather than the uncertainty of a randomized controlled trial (WHO 2018).

3.3.3 Diagnostic Preparedness

Pathogens identified as having pandemic potential under the WHO R&D Blueprint, those causing priority diseases designated by the Coalition for Epidemic Preparedness Innovations (CEPI), and the virus families included in the NIAID-sponsored priority pathogen approach require diagnostic preparedness and may all be candidates for advanced development of diagnostics (Cassetti et al. 2022; CEPI 2023; Sigfrid et al. 2020; WHO 2023a) (► Chaps. 11 and 12). Identified pathogens with pandemic potential include, for example, Nipah virus, Ebola virus, Lassa virus, Crimean-Congo hemorrhagic fever virus; potential new species in virus families known to infect humans; and the specter of Disease X, an unknown and unanticipated new human infection. Diagnostic preparedness for these priority pathogens presents the following specific challenges:

  • Lack of rapid diagnostic tests. Developing accurate and rapid diagnostic tests for newly emerging pathogens can be technically challenging and time-consuming. The identification of specific antigens or genetic markers/sequences (of the pathogen) requires extensive research and validation.

  • Limited access to diagnostic tools. Low-resource settings often face limited access to advanced diagnostic technologies, such as PCR or sequencing platforms. The availability and affordability of these tools can be a significant constraint.

  • Diagnostic infrastructure. Establishing and maintaining an efficient diagnostic infrastructure, including laboratories equipped with adequate biosafety and biosecurity measures, trained personnel, and quality assurance systems, is crucial but challenging in resource-limited settings.

Infectious disease emergencies present the following additional challenges to diagnostic preparedness.

  • Rapid response. Timely response is critical during outbreaks, but developing, producing, and deploying diagnostic tests quickly enough to keep pace with a rapidly evolving situation is a demanding project. Work is underway to facilitate accelerated development (► Chap. 11).

  • Diagnostic capacity. Low-resource settings often have limited diagnostic capacity, including inadequate laboratory facilities, shortages of trained personnel, insufficient supply chains for reagents and consumables, and lack of operational equipment to perform complex analysis.

  • Sample collection and transportation. Proper collection, handling, and transportation of samples from suspected cases to diagnostic facilities can be logistically challenging, particularly in remote areas with limited infrastructure and transportation networks. Improper collection, shipping, or processing can lessen the value of the operation (► Chap. 39).

  • Sensitivity and specificity. Ensuring the sensitivity and specificity of diagnostic tests is essential for accurate identification of cases during outbreaks. However, achieving both high sensitivity and specificity can be demanding, requiring extensive validation and quality control measures.

  • Integration and coordination. Coordinating diagnostic efforts among different stakeholders, including healthcare providers, laboratories, public health agencies, and international organizations, is crucial but can be complex, particularly in emergencies when there are not yet accepted standards for identification or diagnosis. Difficulties are compounded in resource-limited settings.

  • Data documentation, management, and reporting. Clear documentation of data is essential to allow correct identification of samples and to reliably link laboratory, epidemiological, and clinical data. Effective data management and reporting systems are necessary for real-time surveillance, monitoring, and decision-making. Poor data documentation and reporting compromise outbreak mitigation efforts and clinical studies. Setting up robust systems and ensuring their functionality can be challenging, especially in low-resource settings with limited digital infrastructure. Systems should not be overly complex, but developed to meet situational needs with available resources. As long as there is Internet connectivity, even if it is sporadic, demanding analytical work can be done in well-equipped data centers elsewhere (► Chap. 35).

3.4 Specimen Collection, Transport, and Storage

Specimen collection, transport, and storage during outbreaks can be daunting (Tripathi et al. 2020). Appropriate packaging of the samples is necessary to protect the safety of the laboratory staff and transportation teams and to ensure the sample can be analyzed (◘ Fig. 4). Accurate, standardized labeling, documentation, and reporting are crucial for epidemiological monitoring and control, and to ensure samples can be properly identified and results reported. Long-distance transport can be complicated by the availability of transport vehicles, personnel, and supplies. Air transport pilots may decline any cargo if they perceive it as a risk to themselves, crew, or others. Moreover, aviation regulations may vary by location and must be considered when attempting to transport samples or materials. During the 2014–2016 West Africa Ebola outbreak, it was difficult for researchers outside the region to obtain samples of the virus and patient sera, largely because the few air transport assets operating in the region were extremely reluctant to transport the sample, no matter how well packaged (Steenhuysen 2014) (◘ Fig. 5).

Fig. 4
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A UN peacekeeping patrol in the Democratic Republic of the Congo during the rainy season. (Credit: MONUSCO Photos)

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Fig. 5
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Packaging an infectious disease sample for transport. (Credit: Bonnie Dighero-Kemp and the overseas support team Integrated Research Facility, Frederick MD)

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Staff with training in packaging and transport—not only the how but the why—is essential for any clinical research operation, but the task becomes harder where transportation and infrastructure are limited. Well-trained staff can pivot and adjust as needed. Training is also needed for sample collection, to ensure samples are packed with clear and adequate documentation, in packaging that will protect the sample, staff, and community, and are transported safely, efficiently, and in compliance with all regulations. All training should be documented. Importantly, refresher training should be done periodically or when breaks in procedures are identified. Transport of samples requires coordination and should only be done with the agreement and permission of the host country and in close coordination with biosafety professionals.

3.5 Obstacles to Proper Sample Packaging and Transport

  • Unreliable electrical power (Cornish et al. 2021)

  • Inadequate inventory management systems for samples and records

  • Failure to develop and implement a system for unique identifiers to link diagnostic, clinical, and epidemiological records

  • Lack of adequate supplies and materials for collection, documentation, packaging, and shipping

  • Insufficient training for packaging and transport

  • Logistical challenges (i.e., roads, vehicles, fuel, etc.)

  • Lack of willing and able personnel to package and transport materials

4 Implementing Effective Laboratory Biosafety and Biosecurity

The Ebola outbreaks and COVID-19 pandemic have highlighted the critical role of effective infection prevention and control (IPC) and the need for biosecurity and biosafety plans. Given the potential number and diverse characteristics of pathogens and wide geographical area at risk, there is no one-size-fits-all solution. Every country, especially ones with life-threatening endemic diseases, must have executable national and facility-based biosecurity plans that can be implemented within their capabilities.

Although the concept of biosecurity originated within the context of biological weapons prohibition, it has expanded to all sectors of the life sciences and is generally used as an encompassing term meant to protect humans, animals, and plants from biological threats (Renault et al. 2021). The U.S. Department of Health and Human Services defines biosecurity as protecting biological agents from theft, loss, or misuse (HHS 2015). International organizations such as WHO and the Food and Agriculture Organization (FAO) of the United Nations have a much broader definition of biosecurity, “a strategic and integrated approach to analyzing and managing relevant risks to human, animal and plant life and health and associated risks for the environment” (FAO 2023; WHO 2020). The overall approach must include the buy-in and support of the local populace and national government, adapted to realistic expectations of each country’s current capabilities and targeted, executable solutions to identified gaps in capabilities. Major obstacles to developing and implementing biosecurity plans include lack of local community and governmental engagement and support, limited national and local infrastructure, inadequate funding, difficulty procuring material and supplies, and shortages of trained professionals.

Transparency and culturally appropriate strategies are necessary. Any perceived secrecy or untoward intentions will derail efforts and create an environment of suspicion and hostility. Without the investment of the local and national government the development and sustainment of a biocontainment or secure research facility will not succeed. The human factor is the most important and sometimes difficult to capture. Inexperienced staff, local instability, and bad actors are all variables that must be considered and addressed.

The state of local and nationwide infrastructure needs to be considered in the feasibility and scope of biosecurity blueprints. The ability of security teams to respond to a site may be hampered by weather, available working vehicles, and infrastructure. Payment of staff is also essential. As resources are stretched, are staff receiving appropriate compensation?

Continuity of electrical power has been previously addressed for storing samples and reagents, but consistent power is also necessary to ensure workers can operate safely. As biosecurity plans are put into place, the impact of a power loss must be considered. The power source, vulnerability, and quality will directly impact the safety and security of the laboratory. As laboratories become increasingly complex, back-up systems, preferably more than one, should be set up to ensure the safety of the personnel in the area, the community, and the security of the samples. These failsafe approaches may include additional generators, solar-powered battery systems, uninterrupted power sources, other engineering features, and training (► Chap. 39).

In the past, the WHO, philanthropic organizations, and other nations have invested in strengthening the biosecurity of less-resourced countries with varying success. The long-term success of any program depends on sustainability over time. Realistic expectations of the local and national budget allocations and partner contributions toward these programs will determine the feasibility of both near- and long-term sustainability. Many countries, due to competing priorities and low gross domestic product (GDP), cannot sustain the cost of running a biological containment facility or simply do not consider it to be a high priority for funding. When budgets are insufficient, cost cuts may include hiring less capable staff or reducing vetting of staff, reducing or halting equipment maintenance, and insufficient PPE and other supplies. Low or intermittent pay will lead to rapid staff turnover and potential nefarious actions by insiders. As biotechnology expands the potential for what can be done in a lab, and as investments continue to be made in secure laboratory infrastructure around the globe, the long-term sustainability of facilities is a prominent concern.

5 Documentation, Data Quality, and Data Management

Effective data management and maintaining data integrity are critical for clinical diagnostics to provide accurate results for the patient, to track the epidemiological evolution of an incident or outbreak, and to allow accurate interpretation and implementation of findings from clinical studies. Any shortfalls in data management and integrity can impact the quality and reliability of diagnostic information, which in turn affects decision-making response efforts and clinical trials results. Data management does not require complex commercial systems. Simple computer software and handwritten records are suitable if the data is legible and well documented—and if the records can be safely maintained. On the other hand, there are dedicated electronic clinical trial data capture and management systems that can be used free of charge and will provide the safety of multiple copies of trial data. However, these systems require careful coordination with the research project information technology team as well as considerable training for users, especially those with minimal computer skills (► Chaps. 34 and 35). It is essential that laboratory, epidemiological, and clinical data are well linked through common or unique identifiers, particularly in larger outbreaks and multisite research efforts.

One essential for a clinical trial is high data quality, data integrity, and security of patient data (Basit et al. 2021). Collecting accurate, reliable data during an outbreak can be hindered by various obstacles (Eck 2018). Therefore, strategies to ensure data quality, such as standardized data collection protocols and rigorous validation, become crucial. Staff should be trained in data collection, documentation, and storage. Training staff in Good Clinical Practice (GCP) (ICH 2016) and standardized data management is also useful. It is essential that data be stored safely, and that backups of data and study notebooks be maintained.

Data analysis and management play a functional role that can extend well beyond the patient-level analysis of clinical diagnostics (O’Hare et al. 2022). Analyzing data from paper and electronic health records (EHRs) can help identify dominant themes and patterns, providing valuable insights into the diagnosis and management of diseases like Ebola virus disease in its post-acute patient sequelae. There is often a need to confirm the diagnosis in patients that have long-term impacts from disease but may have very low serum levels of the virus. Robust data analysis techniques, including machine learning and data mining, can enhance diagnostic capabilities, both in the post-acute phase and in the earliest stages of infection.

Storage and management of data pose specific challenges in emergency and remote clinical diagnostic settings (Eck 2018). All too often, paper or basic spreadsheets are the only available option; these are functional but tend to require more labor for transfer to a purpose-made data storage system. The centralized or compartmentalized nature of paper records (or electronic ones in some cases) may hinder access, limiting clinicians and outbreak response teams from effectively utilizing information to improve patient care while dedicated MCMs remain in the future, for example. In areas with Internet, cellular, or satellite services, cloud-based solutions are increasingly utilized, but must be selected and configured to ensure data integrity and privacy protection. Data integrity is paramount in clinical trials, and ensuring accurate data collection, validation, and preservation are critical aspects of maintaining data integrity. Protecting the personal information of trial participants is an ethical norm and a strict legal requirement in most jurisdictions.

The implementation of next-generation sequencing (NGS) in clinical diagnostic settings offers vast opportunities for comprehensive genetic analysis (Eck 2018). However, it also presents challenges in data storage and management due to the large volume of data generated. Efficient data storage solutions and management strategies are necessary to handle the data influx and ensure its accessibility and security during an outbreak. Transmission of the data may be very slow in areas with limited communication capabilities (► Chap. 37).

Documentation of test control data and equipment validation is sometimes overlooked. Failure to include controls or perform routine equipment calibrations may compromise the integrity of the data. Frequently, quality assurance data such as control runs, maintenance logs, or validation materials are not archived, or archived separately and difficult to access and review. Fast-moving emergency response situations often require the use of whatever equipment is on hand or quickly procurable, and quality documentation for these instruments may be missing or limited. However, laboratories can actively address such concerns through the implementation of control samples, running calibration materials, the use of independent proficiency panels to assess performance, and clear, accessible documentation of these efforts. As an alternative to independent proficiency panels, if more than one laboratory with sufficient bandwidth is available, laboratories may exchange samples for comparison of results. When no other options are available, labs can repeat procedures with a small portion of previously tested samples and incorporate additional performance controls. Documentation of training and competency of all staff should be part of the data quality assurance package. Regardless of the strategies implemented, it is essential that laboratories not just produce results, but implement quality assurance practices to ensure overall data quality and integrity.

In summary, during an outbreak and in response research, any lapse in data quality management and integrity in clinical diagnostics can raise questions that significantly impact decision-making, response efforts, clinical studies, and post-outbreak or post-MCM-licensure data analyses. Ensuring high data quality, employing robust data analysis techniques, addressing storage and management challenges, and prioritizing data integrity is paramount. Adapting to changing conditions and handling large volumes of data are essential aspects of clinical data management during an outbreak. By addressing these challenges, healthcare systems can enhance their diagnostic capabilities and more effectively respond to public health emergencies (◘ Fig. 6).

Fig. 6
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Many recent innovations have made clinical laboratories, including mobile labs and labs set up urgently in emergencies, more capable than ever. Further advances can be expected. (Authors)

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6 Case Study

As the Ebola virus spread from the rural areas of Guinea, Liberia, and Sierra Leone to population-dense urban settings (Conakry, Monrovia, and Freetown), the need to establish diagnostic capabilities reached a crisis point. In 2014, there was no or very limited diagnostic capacity to detect Ebola virus in West Africa. It was not until March 2014 that the viral disease that had appeared in Guinea in December 2013 was identified as Ebola, and until mid-April testing of suspect cases required the transport of samples to a mobile response laboratory run by the European Union in Guinea, taking hours and sometimes days.

The request for laboratory support was unique in that the Liberian Ministry of Health not only desired in-country Ebola testing to be established, but wanted that capability transferred to their national reference laboratory. The inclusion of training as a primary mission objective during an active outbreak adds significant work and stress to deploying teams. This stress is compounded when the previous experience and skill level of the staff to be trained is unknown or limited. The site for the laboratory was preselected at the Liberian Institute for Biomedical Research (LIBR), an aging 1970s research facility located approximately 65 miles outside of the capital. An HIV laboratory diagnostic space composed of a single room with a class II biosafety cabinet (BSC) and several small rooms was identified for the team’s use. Electricity was provided by generators which ran several hours a day; power spikes were common. The facility was without running water during the dry season and water leaked through the roof and carried bat guano into the labs during the rainy season.

Due to the unknown availability of supplies in the country, all equipment and supplies were hand-carried by the team coming to the country on commercial flights. Available assays at the time were limited and there were no assays with regulatory approval. Two assays developed by the U.S. Army, EZ-1 and MGB, were selected because the Army had applied for (but not received) emergency use authorization (EUA) with the Food and Drug Administration and could provide the assays (Bettini et al. 2023; Presser et al. 2021). (The EZ1 assay did receive an EUA designation during the outbreak.) The use of two assays allowed cross-checking to increase stringency and reduce the likelihood of false positives. Samples were considered positive only if both targets were detected. If a single target was detected the sample was considered indeterminate, and repeat testing in 48 h was recommended. In addition, a standard ribonuclease P (RNaseP) assay was included to ensure sample quality. As the outbreak continued, other Ebola virus assays were developed and validated for platforms including Biofire® and Cepheid®.

The provided space consisted of four rooms and a hallway with a single-door access from the LIBR main wing hallway (◘ Fig. 7). To ensure the highest available level of biosafety containment, the room with the biosafety cabinet was used to process all specimens from suspected cases. In the absence of engineering controls, attempts to create directional airflow were implemented by disabling air conditioning in the sample processing room, creating a temperature differential with surrounding rooms. To limit cross-contamination issues, the reagent mixture room and sample loading spaces were segregated as seen in ◘ Fig. 7. Small trash buckets and spray bottles were placed on the entry and exit areas of the space to serve as chemical disinfectant spaces (dunk tanks). Since the location lacked a vestibule area to allow for donning and doffing PPE, a curtain was used to establish an area for this function.

Fig. 7
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Layout of PREVAIL laboratory space at the Liberian Institute of Biomedical Research. (Credit: Saraina Adams/USDA)

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Appropriate PPE is based on a risk analysis intertwined with the facility design, planned procedures, and the primary containment equipment present, and focuses on the type(s) of exposures anticipated (splash, spray, touch) and the overall risk to the staff member when exposed to specific agents. PPE must be durable and appropriate for the task of preventing exposure. Powered air-purifying respirators (PAPR) were selected for multiple reasons. PAPRs have the benefit of preventing accidental contamination of mucosal membranes by staff members touching their faces or adjusting PPE; fit testing for N95s in the field was not possible and the use of PAPRs eliminated the risk posed by face shaving, as micro-abrasions create a potential portal of entry for infection.

A variety of commercial disinfectants have been identified as suitable for Ebola virus decontamination. Given the availability, local use, and effectiveness of chlorine bleach as a disinfectant in clinical settings, it was chosen as a primary method for decontaminating surfaces potentially contaminated with Ebola virus. Full-strength bleach, however, is corrosive, a contact irritant, and emits toxic fumes—not ideal in an unventilated space. A diluted bleach solution was used to reduce these hazards while killing the virus (◘ Fig. 8) (PHAC 2023; WHO 2023b). A contact time of 10 min is ideal and fresh preparations were made daily, or when high amounts of organic material (e.g., blood) were mixed with the solution. In some cases, a 5% solution of water and MicroChem Plus® was used with sensitive equipment and metal that could be damaged by bleach.

Fig. 8
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Instructions for using bleach as a disinfect for Ebola virus and other pathogens. (Credit: Saraina Adams/USDA)

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Local staff had limited prior laboratory experience. A major emphasis in training was how to safely handle samples, hazardous waste disposal (liquid and dry waste), proper biological safety cabinet use, and sample flow to prevent molecular assay contamination. Most notable was learning and practicing the principles of PPE—donning and doffing the PPE in a logical and safe manner, and how to test and care for the PAPR and disposable PPE. Staff were also trained in basic laboratory principles and techniques, such as PCR-based assays, molecular assays, reagent preparation, prevention of common contamination issues, and troubleshooting. Most importantly, they learned to interpret assay results and discussed in depth the implications of false positive or false negative results for the clinical setting. A train-the-trainer approach was used to reinforce training and ensure program sustainability.

LIBR was one of several laboratories eventually established in the region. Many of the laboratories reported common challenges. For example, consistent and reliable electricity was a primary issue. Molecular assays require uninterrupted power during the run and frequent power interruptions and surges compromise runs. In addition, variable power resulted in instrument failures and compromised reagents due to temperature fluctuations in freezers without power.

Communication was also a constant concern. Intermittent Internet, Wi-Fi, and cellular signals at the laboratory compounded problems with logistical issues and data reporting. Internet access was often down for days to weeks during the outbreak.

Waste disposal at the site was another hurdle. The plumbing often failed or was unusable. The site had a purpose-built incinerator, but it was collapsing. Fuel for burning was in short supply. Burn barrels or the use of a pit provided usable alternatives. Safe and secure storage of waste was another common issue. Bags of waste should be stored in a secure area with limited access prior to incineration or destruction.

Sample packing, identification, and quality were also problematic. Samples often arrived unpacked or simply inside a glove, posing risks to everyone from the collector to the delivery team to the laboratory workers. Sample labels were difficult to read or missing. Samples arrived frozen and in varying amounts. Educational materials were prepared to train staff in appropriate sample collection type and labeling, and a drop-off point was established to receive and log samples and provide supplies for collection and transport as the teams needed, including data collection sheets once they were developed.

The teams that responded and worked with the national team at LIBR faced a rapidly changing situation. Sample numbers grew from the tens to the hundreds during the outbreak. Staff had to be adaptable and adjust to the challenges in the field. Training and the overall curriculum had to be adapted daily to meet the needs of the teams. The mission was an overall success, in large part due to local and international partnership and the willingness of the teams involved to be nimble and resilient.

7 Summary and Conclusion

Laboratory responses to emergencies face new, unanticipated obstacles in every outbreak. The first of these is often the logistics of transporting staff, reagents, and equipment to where they are needed. Preparedness of staff for deployment is often not just a matter of a passport and plane ticket. Visas, vaccines, and medications, to say nothing of jobs and family left behind, can delay departure.

Other delays are likely because equipment or reagents are not immediately available for rapid deployment. Since specialized laboratory equipment is often procured through special orders, prestaging or early acquisition of these items can significantly reduce the time from first detection of a new or re-emerging pathogen to deployment of lab teams. This in turn requires resources for the storage and continued maintenance of equipment as well as replenishment of supplies as they approach expiration. Depending on the location of the outbreak, there may be additional considerations, including inadequate transport options, import barriers, and customs clearance that hinder the importation of materials and supplies. National or regional instability may also limit the willingness and ability of staff to deploy to conflict areas.

As rapid deployment of laboratories has become more common, new challenges have emerged. The first is the retention or disposition of samples after an emergency. Establishment of biobanks or biorepositories is of growing interest. However, the use of retained samples raises ethical considerations. Can deidentified samples be used? Are samples collected from deceased individuals covered by human subject guidelines? Were the samples collected with informed consent, and what uses did it cover? What can be done and by whom is a growing discussion area and will be heavily driven by local human subject protection review. The cost–benefit of proposed biobanks should be considered. Maintenance of biobanks requires funds for freezers, fuel, personnel for maintaining samples, and software for inventory and biosecurity features to ensure that samples are maintained safely. The long-term retention of samples containing high-consequence pathogens is a growing global biosecurity concern. Another challenge is the blurring of the line between public health response and research and the desire to publish results and information while protecting individuals’ rights and privacy. All too often, a lab is requested to run additional tests, but concerns are raised when it is unclear how the requested tests support the public health response, patient care, or clinical protocol requirements (► Chap. 7).

The end of the response brings other responsibilities, such as disposition of equipment, reagents, and the laboratory. Working with the local teams, decisions must be made whether to decontaminate and decommission or transfer the lab to local control. Equipment must also be managed accordingly. Broken equipment should be thoroughly decontaminated before disposal. All waste should be inactivated before disposal. Samples should be properly stored and transferred to local authorities or disposed of appropriately. Records should be transferred. If samples, equipment, or facilities are retained, trained local staff and adequate resources are essential, with some assurance provided that the lab will be sustainable. The closing or transfer of the laboratory should be well planned and highly coordinated with local officials and partners. As laboratory response capabilities continue to evolve and grow, the expectations for what laboratory teams can do will grow too, sometimes outstripping reality.

Discussion Questions

  1. 1.

    Discuss the who, what, where, when, and why of outbreak-determined factors and requirements of the response or research program, which shape the capability and capacity of the field laboratory.

  2. 2.

    Define field/mobile laboratories.

  3. 3.

    Describe the critical elements and factors that contribute to the suitability of a given location to host a laboratory.

  4. 4.

    Describe the multiple factors that drive the selection of laboratory assays and equipment for research response.

  5. 5.

    Managing regulatory and legal requirements during an emergency outbreak is a complex and exacting task, especially in low-resource settings. Discuss the need for

    1. (a)

      Regulatory management tools

    2. (b)

      Expedited evaluation and approval processes

    3. (c)

      Diagnostic preparedness

  6. 6.

    What common obstacles are there to specimen collection, transport, and storage?

  7. 7.

    What is the role of laboratory biosafety and biosecurity?

  8. 8.

    Why is good data management essential to successful clinical trials?

  9. 9.

    What advances in laboratory, point-of-care, and imaging diagnostic tools have revolutionized healthcare and outbreak response?

  10. 10.

    How have improved diagnostic tools led to better care and outcomes for patients and potentially infected contacts during outbreaks?

  11. 11.

    How did Ebola virus transmission through chains of contact from rural areas to cities in West Africa demonstrate the need for better diagnostic capacity?