09 NATIONAL LABORATORY SYSTEM

Surveillance with a national laboratory system including relevant sectors, particularly human and animal (domestic animals and wildlife) health, and effective modern point-of-care and laboratory-based diagnostics are in place.

IMPACT:

Effective use of a nationwide laboratory system, including relevant sectors, capable of timely, safely and accurately detecting and characterizing pathogens causing epidemic-prone disease, including both known and unknown threats, from all parts of the country. Expanded deployment, utilization and sustainable use of modern, safe, secure, affordable and appropriate diagnostics tests or devices is established.

MONITORING AND EVALUATION:

(1) A nationwide laboratory system that is able to reliably conduct tests for priority diseases using appropriately identified and collected specimens that are transported safely and securely to accredited laboratories from the majority (at least 80%) of subnational levels/districts in the country. (2) Existence of national quality laboratory standards and systems for licensing laboratories.

Benchmark 9.1

Specimen referral and transport system is in place for relevant sectors

Objective To strengthen specimen referral and transport system

01 NO CAPACITY

  1. No system in place for transporting specimens from peripheral/rural/district levels to national laboratories, or only ad hoc transportation is available.

02 LIMITED CAPACITY

  1. Map existing laboratory capacity for priority diseases and establish referral networks for priority pathogens. *
  2. Map any existing general or disease-specific specimen transport networks. *
  3. Draft national guidance for the collection, management, storage and transportation of specimens for priority diseases and disseminate to all levels. *
  4. Establish a service agreement with a courier company (public or private) where gaps exist and cannot be filled by existing transportation and referral systems. The service agreement should include defined safety and quality norms and standards for transportation of priority specimens in the public sector throughout all major subdivisions of the country and with the possibility to expand capacity when required. *
  5. Establish agreements with neighbouring and partner countries to facilitate border crossing with a dangerous specimen for timely and appropriate testing of samples abroad as required. *
  6. Establish mechanisms to ship specimens internationally in a timely manner for diagnosis or confirmation including: Prepare material transfer agreements, Identify courier companies with capacity to ship specimens, Document availability of staff certified to pack and ship infectious materials, Assess all logistic needs for specimen referral and transport systems. *
  7. Involve relevant sectors for specimen referral and transport systems both at national and subnational levels. *
  8. Develop and maintain a regularly updated list of specimen transportation systems operating in relevant sectors. *
  9. Establish a mechanism for utilizing shipping from relevant sectors to transport a broader range of specimens when capacity is limited. *
  10. Develop training packages for health workers on specimen collection (e.g. stool, throat swab, urine, blood, etc.), secured packing and storage before transportation for suspected cases of priority diseases.
  11. Establish a mechanism for transporting animal specimens to animal health laboratories within district or at the subnational and national level or obtain access to national or international reference laboratories for priority zoonotic diseases.
  12. Develop or revise tools, guidance, SOPs on specimen referral and transport for priority zoonotic diseases.

03 DEVELOPED CAPACITY

  1. Expand service agreements with courier services (public or private) for transporting most priority pathogens from subnational to national level (or from all subnational levels to reference laboratories). *
  2. Train staff from courier companies and health facilities on appropriate management of specimens from suspected cases of priority diseases. *
  3. Establish formal agreements with neighbouring and partner countries if they are responsible for testing referred specimens. *
  4. Provide prepositioned outbreak investigation kits (i.e. sample collection and transportation kits) at subnational levels and facilities as applicable. *
  5. Develop a system for data collection, analysis and M&E for specimen referral and transport system, including turnaround time and specimen integrity. *
  6. Train health workers on sample collection, secured packing and storage before transportation for suspected cases of priority diseases.
  7. Develop strategy, tools and procedures in relevant sectors to reinforce the safety and security of specimen referral and transport
  8. Conduct trainings on sample shipment and referral in relevant sectors.

04 DEMONSTRATED CAPACITY

  1. Establish an efficient transport mechanism for all priority disease specimens from all levels. *
  2. Provide prepositioned outbreak investigation kits (i.e. sample collection and transportation kits) at all levels and facilities. *
  3. Conduct regular reviews of specimen transportation systems to confirm that specimens are being transported promptly and in a manner that maintains safety and specimen quality. *
  4. Establish a system to collect and test specimens from hard-to-reach areas. *
  5. Organize and support training programmes on M&E of specimen referral and transport system, for all relevant stakeholders (e.g. courier companies, customs, animal health and environment officers, etc.). *
  6. Conduct SimEx/AAR/IAR (as relevant), with relevant sectors, to assess the functionality of specimen referral systems in health facilities (including public and private) at all levels. *

05 SUSTAINABLE CAPACITY

  1. Conduct training exercises to develop a pool of shippers that is trained on infectious substances and is always available, including for international shipments. *
  2. Allocate sustainable funding to maintain national standards of specimen collection, handling, preservation, protection, transportation, disposal, packaging, and import and export procedures. *
  3. Implement a national mechanism for collecting safety data and incident reporting for any transport incidents involving infectious substances. *
  4. Share experiences in specimen referral and transport system and engage the country in peer-to-peer learning programmes at the subnational, national and international levels. *

Benchmark 9.2

Laboratory quality system is in place

Objective To ensure laboratory quality implementation

01 NO CAPACITY

  1. There are no quality standards for laboratories in place or under development.

02 LIMITED CAPACITY

  1. Establish an independent unit or laboratory working group at the national level to oversee laboratory services and develop national laboratory strategy and quality standards. *
  2. Develop minimum standards for certification or licensing, using international standards adapted to local settings, as part of the laboratory regulation system. *
  3. Develop a roadmap for laboratory inspections, licensing and accreditation, in line with the national laboratory strategy. *
  4. Identify and map laboratories (public and private sector) based on prevailing national standards for licensing, certification and accreditation at all levels. *
  5. Establish a quality assessment programme for national or central laboratories for diagnostics of diseases with epidemic potential. *
  6. Develop and disseminate SOPs, along with checklist(s), for maintaining laboratory quality standards in both public and private health sectors. *
  7. Identify modules that include laboratory quality standards in the curricula of undergraduate and postgraduate studies in relevant fields (e.g. medicine, laboratory technicians and other relevant health workers) and propose revisions and updates as needed. *
  8. Identify existing legal frameworks for laboratory quality management system as applicable to all relevant laboratories. *
  9. Map existing quality standards in relevant sectors.
  10. Provide basic training on quality assessment for focal points from relevant sector laboratories (e.g animal, agriculture, etc.).

03 DEVELOPED CAPACITY

  1. Develop and publish national guidance on registration procedures for in vitro diagnostic devices and other relevant devices. *
  2. Establish a national quality assessment programme for peripheral laboratories testing for diseases with epidemic potential. *
  3. Implement a system of inspecting and licensing laboratories, including using local adaptations of international standards and norms and obtaining required funding and human resources, including training/retraining of laboratory staff in the inspection of laboratories according to minimum standards. *
  4. Implement minimum standards for certification or licensing using international standards adapted to the local setting, develop a system for regulation of laboratories, and allocate sufficient funding and human resources for implementation. *
  5. Update undergraduate and postgraduate curricula of relevant fields (e.g. medicine, laboratory technicians and other relevant health workers) to include laboratory quality standards in relevant modules. *
  6. Train and/or retrain health workers on laboratory quality principles and procedures.
  7. Identify minimum standards to obtain licenses for laboratories in relevant sectors.
  8. Enhance laboratory quality management system involving experts from relevant sectors.
  9. Provide advanced trainings on international laboratory standards (e.g. ISO) and other standards for implementation of quality assessment systems in relevant sectors

04 DEMONSTRATED CAPACITY

  1. Implement a mandatory licensing programme for national and subnational public health laboratories (including laboratories in the private sector) and issue licenses in conformity with national quality standards. *
  2. Implement national quality standards for both public and private sector laboratories that align with international norms and standards. *
  3. Conduct quality assurance programmes for all core tests. *
  4. Design a domestic external quality assessment programme for all priority tests or oversee testing with international external quality assessment schemes. *
  5. Conduct planned or unannounced quality assessments and inspections of public and private laboratories, in line with the national laboratory strategy and involving relevant sectors (including human and animal health, food safety, security, energy, water and sanitation, waste management, agriculture, etc.). *
  6. Support operational research programmes to generate evidence on laboratory quality management systems to improve laboratory quality at all levels. *
  7. Conduct regular M&E for laboratory quality assurance programmes *
  8. Obtain WHO accreditation for selected laboratories for disease specific testing (e.g. polio, HIV genotyping, measles, etc.).
  9. Implementation of laboratory licensing processes by relevant sectors.

05 SUSTAINABLE CAPACITY

  1. Accredit all national reference laboratories in line with international standards (e.g. ISO 15189 for health laboratories). *
  2. Update existing laboratory strategies, guidelines and procedures for laboratory quality based on lessons learned from M&E activities. *
  3. Implement a national external quality assurance programme including microbiology, virology, serology, parasitology, etc. in relevant sector laboratories (public and private). *
  4. Organize corrective actions based on the results of external quality assessments and recommendations from reviews and supervisions *
  5. Improve the national plan for quality management system compliance at all levels in public and private laboratories through continuous quality improvement, based on analysis of country experiences. *
  6. Allocate sustainable funding for laboratory quality assurance programmes. *
  7. Share experiences in laboratory quality management system and engage the country in peer-to-peer learning programmes at the subnational, national and international levels. *
  8. Comply with external quality assurance programmes and implement recommendations
  9. Accredit all national reference laboratories in accordance with international standards in relevant sectors.

Benchmark 9.3

Laboratory testing for detection of priority diseases is in place

Objective To strengthen laboratory testing capacities for detection of priority diseases

01 NO CAPACITY

  1. Country has not taken a risk-based approach to determine testing modalities for priority diseases.
  2. Testing for priority diseases relies only on point of care testing (POCT) and/or other simple testing modalities such as microscopy.

02 LIMITED CAPACITY

  1. Review or develop a list of priority diseases for the country and update (compile) supporting evidence to perform a national risk assessment for each disease. *
  2. Develop surveillance data and prioritization methods and a national laboratory testing strategy for each priority disease based on risk assessment findings. *
  3. Map/list all laboratories in the country performing public health functions and/or testing for priority diseases. *
  4. Assess laboratory algorithms, standards and testing capacities (including equipment inventory) in all laboratories for all identified priority diseases. *
  5. Implement rapid testing (antigen and antibody), microscopy, and serological and/or molecular assays for detecting select endemic and priority diseases, based on national testing algorithms. *
  6. Develop a plan for conducting assessment visits in national reference laboratories (for priority diseases) to assess capacities in conformity with the national testing strategy, and produce a capacity-building plan for each laboratory to address identified gaps. *
  7. Identify (and train, if necessary) a pool of individuals capable of performing assessment visits, and provide ongoing support to national reference laboratories to ensure the implementation of capacity building plans. *
  8. Develop and disseminate testing SOPs along with quality control SOPs for all core tests for priority diseases. *
  9. Establish clear SOPs and necessary agreements with international laboratories to perform diagnostic and confirmatory testing of specimens and support outbreak detection and responses when local capacity is not available. *
  10. Develop hands-on training curricula for laboratory staff that includes task-based training, refresher training and mentoring in relevant technical and administrative areas for priority diseases. *
  11. Review law, legislation and regulations relevant to laboratory capacities to perform one or more tests for detection of priority diseases, at national and subnational levels. *
  12. Develop a mechanism for sharing laboratory testing information between relevant sectors.
  13. Develop animal health laboratory capacities to detect zoonotic diseases of national importance (e.g. equipment, infrastructure, human resources, training, etc.).
  14. For animal health sector: Assess regulations, legislation, policies for diagnostic services by animal health laboratories, Develop a laboratory system strategy for animal health laboratories including tier-specific roles, Put in place basic level of field-based testing (e.g. pen side rapid kits),Provide training on a few diagnostic procedures including serological testing, Provide basic training or preliminary advocacy on laboratory leadership and management conducted (e.g. Global Laboratory Leadership Programme),Access to reagents, equipment, consumables and procurement by animal health laboratories

03 DEVELOPED CAPACITY

  1. Review or update or develop national laboratory policies to reflect strategies and procedures developed for testing priority diseases. *
  2. Train and equip laboratories from relevant sectors involved in laboratory detection of the country’s endemic and priority diseases, based on the national testing algorithms and national laboratory administrative and technical structures. *
  3. Supply required equipment to support laboratory tests for priority diseases (such as molecular testing, bacterial culture with AST and access to sequencing, etc.) based on laboratory level in the tiered laboratory network and adhere to recommended maintenance procedures. *
  4. Develop a plan for conducting assessment visits in subnational laboratories that test for priority diseases to assess capacities in conformity with the national testing strategy and produce a capacity-building plan for each laboratory to address identified gaps. *
  5. Identify (and train, if necessary) a subnational pool of individuals capable of performing assessment visits and provide ongoing support to national reference laboratories to ensure the implementation of capacity-building plans. *
  6. Implement national proficiency and quality assurance processes for all tests conducted for the country’s endemic and priority diseases. *
  7. Develop capacity for in-country production and procurement processes for acquiring necessary media and reagents to perform laboratory tests for priority diseases. *
  8. Provide funding to implement capacity-building plans for national reference laboratories performing testing for priority diseases as well as ongoing monitoring and assessment visits to assure implementation. *
  9. Establish mechanisms and protocols for timely and appropriate sharing of information generated by laboratory testing in relevant sectors, especially linking laboratory data with surveillance and risk assessment. *
  10. Identify essential tests that the country is currently unable to perform, and prioritize developing that capacity within one year (with domestic or donor funding). *
  11. Conduct SimEx or AAR (as relevant) to test the functionality of laboratory testing capacities for detecting priority diseases at the national level. *
  12. Map laboratory capacity in relevant sectors for testing human specimens during emergencies.
  13. Conduct proficiency testing in animal health laboratories for priority zoonotic diseases and encourage pairing of laboratories between human and animal health sectors.
  14. Draft or review regulations, legislation and policies for animal health laboratories to ensure that they contain essential elements of diagnostic services, including but not limited to: Regular participation in regional laboratory networks and collaboration with regional laboratories when national testing capacities are not available, Trainings on diagnostic techniques, including molecular and sequencing capacities (or access to these capacities) and other areas such as laboratory leadership, Available resources for procurement of reagents, equipment and consumables by animal health laboratories.

04 DEMONSTRATED CAPACITY

  1. Equip subnational laboratories to perform public health functions/testing for all priority diseases using advanced tests (e.g. molecular/nucleic acid tests, bacterial culture, AST, etc.). *
  2. Implement routine sequencing of laboratory samples for endemic and priority diseases as part of national laboratory strategic plan activities and during outbreaks. *
  3. Establish sustainable procurement and stock management systems for laboratory reagents and consumables for all endemic and priority diseases during routine operations and outbreaks. *
  4. Implement assessment and oversight plans for capacity-building in both national reference laboratories and subnational laboratories performing testing for priority diseases. *
  5. Establish collaboration agreements to outsource testing for priority diseases to laboratories in other countries or the private sector when required. *
  6. Conduct SimEx and AAR (as relevant) to test the functionality of laboratory testing capacities for detection of priority diseases at both national and subnational levels. *
  7. Assess laboratory capacity in relevant sectors to test human specimens during emergencies.
  8. Equip and train animal health laboratories to diagnose zoonotic diseases that are not currently present in the country but are present in the region.
  9. Implement regulations, legislation and policies in animal health laboratories for: Essential elements of diagnostic services with underdeveloped capacity, Full implementation of laboratory networking for animal health laboratories strategy, sharing of data, expertise and information among animal health laboratory network.
  10. Participate in external quality assurance programmes (EQAP) for some priority diseases.

05 SUSTAINABLE CAPACITY

  1. Review and update the available evidence base, risk assessments and testing strategies for priority diseases, based on national surveillance and collection of priority data. *
  2. Secure sustainable national financing for the laboratory system to support ongoing testing of priority diseases. *
  3. Conduct regular inventory and replenish the national strategic stockpile of products and devices to perform tests for the detection of all priority diseases in the event of a health emergency. *
  4. Monitor turnaround times for confirming new, emerging, unknown and high consequence pathogens (including the use of metagenomic and whole genome sequencing) and implement improvement actions regularly. *
  5. Review and update national training curricula to align with current testing capacities and priorities. *
  6. Maintain a consistent pool of individuals available to perform assessment visits in national and subnational laboratories performing testing for priority diseases, with appropriate resources to support ongoing capacity-building efforts. *
  7. Document and share country experiences in laboratory testing for priority diseases and engage the country in peer-to-peer learning programmes at the subregional, national and international levels. *
  8. Participate in reviewing and updating the available evidence base, risk assessments and testing strategies for priority diseases that have risk of potential spill over.
  9. Document and share experiences in laboratory testing for detecting priority zoonotic diseases.

Benchmark 9.4

An effective national diagnostic network is in place

Objective To establish an effective national diagnostic network

01 NO CAPACITY

  1. No evidence of use of rapid and accurate point-of-care, farm-based diagnostics and/or laboratory-based diagnostics, and no tier-specific diagnostic testing strategies are documented.

02 LIMITED CAPACITY

  1. Develop a national laboratory policy or regulation that formalizes a tiered diagnostic structure and enables collaboration, information sharing and specimen referral between different tiers of the system, relevant sectors and private laboratories. *
  2. Develop a tiered laboratory network structure to test and monitor the country’s priority diseases, ensuring efficient linkages between tiers along the national referral system. *
  3. Identify existing point of care and rapid diagnostic tests that are available in-country for the detection of priority diseases. *
  4. Assess the feasibility for procurement, validation and use of new point of care and rapid diagnostic tests for priority diseases that are not currently available in-country. *
  5. Develop national guidance on the initial evaluation and field validation/quality assurance requirements for all new point of care tests, rapid diagnostic tests and/or in vitro diagnostics introduced for priority diseases. *
  6. Develop a legal basis for strengthening collaboration between public and private sector laboratories and partner agencies at both national and subnational levels. *
  7. Identify international laboratories with testing capacity for confirmatory diagnostic testing if such capacities are not currently available in-country. *
  8. Assess national diagnostic capacity and use findings to develop a national plan for strengthening national diagnostic capacity, taking into accoutavailable resources within the national health system administration at all levels.
  9. Provide a national laboratory policy that identifies expected capacities at each level of the animal health laboratory system.
  10. Assess and map animal health laboratories as part of the national diagnostic network.
  11. Develop a legal basis to strengthen collaboration between laboratories of relevant sectors

03 DEVELOPED CAPACITY

  1. Develop and disseminate SOPs for tiered testing for each priority disease, including point of care and rapid diagnostic tests and specimen referral systems, ideally within the framework of a national laboratory policy for each priority disease. *
  2. Develop in-service training plans for all staff that align with national tiered testing approaches and include task-based training, refresher training, and mentoring in relevant technical and administrative areas. *
  3. Allocate resources (human and material) to conduct appropriate diagnostic testing at the subnational level in line with the SOPs for tiered testing or national laboratory policy. *
  4. Conduct SimEx and AAR (as relevant) to monitor and evaluate functionality of the national diagnostic network in routine systems and during health emergencies. *
  5. Develop a real-time laboratory information management system (LIMS) that can be deployed across the tiered network and interoperable with other health information management systems.
  6. Collect data from diagnostic networks across the country, share with relevant national authorities including epidemiology departments, and collate with all other health data for regular analysis and planning.
  7. Develop mechanisms for availability, accessibility and affordability of laboratory material for all laboratories in the national diagnostic network, including public and private laboratories.
  8. Incorporate animal health laboratories into the laboratory networking strategy, including tier-specific roles and responsibilities.

04 DEMONSTRATED CAPACITY

  1. Monitor the implementation of point of care and rapid diagnostic tests using national guidance for field validation and quality assurance processes. *
  2. Develop and implement a plan to increase national testing capacity for all priority diseases, including cross-training national laboratory staff in different testing methods. *
  3. Establish real-time data sharing with national authorities including epidemiological departments and surveillance and response systems. *
  4. Review stockpiles of diagnostics for priority diseases and ensure stock replenishment and rotation according to anticipated expiration dates of reagents. *
  5. Implement in-service training by ensuring appropriate task-based training, for example using a continuting professional education programme. *
  6. Allocate sustainable funding for laboratory procurement, capacity-building and point-of-care diagnostics *
  7. Adopt LIMS across the tiered network and within the health system for all priority diseases in the country and support laboratory data reporting by electronic-based methods.
  8. Develop and implement plans to increase national testing capacity for all priority diseases in relevant sectors to support human health laboratory during emergencies.
  9. Implement the laboratory networking strategy for animal health at the national level, with established linkages between animal health surveillance units and laboratories.

05 SUSTAINABLE CAPACITY

  1. Secure sustainable financing for all tiers of the national laboratory system to support ongoing testing and sequencing of all endemic and priority diseases in the country. *
  2. Develop capacities to conduct advanced molecular and serological testing for confirmation of priority diseases, including the ability to conduct molecular subtyping. *
  3. Revise and update strategies, guidelines, operational plans and SOPs for the national diagnostic laboratory network based on lessons learned and ensure implementation of recommendations from M&E activities conducted. *
  4. Share experiences in management of a national diagnostic network and engage the country in peer-to-peer learning programmes at the subregional, national and international levels.. *
  5. Use analysed data results from diagnostic networks and to provide evidence to support adjustment of NHPSPs.
  6. Document and share lessons learned and best practices in delivering laboratory services during health emergencies in relevant sectors, including private and animal health.
  7. Connect animal health and other relevant laboratory networks to regional and global networks.
  8. Regularly conduct simulations, such as joint laboratory exercises, to assess and review strategies in place.

* Participation and contribution of other sectors to action.

Tools

  • World Health Organization, Clinical and Laboratory Standards Institute WHO Collaborating Center and Center for Disease Control and Prevention. Laboratory quality management system handbook. Geneva: World Health Organization; 2011 (https://www.who.int/publications/i/ item/9789241548274).
  • Laboratory Quality Stepwise Implementation Tool [website]. Geneva: World Health Organization; 2015 (https://extranet.who.int/lqsi/content/ homepage).
    WHO LQSI tool in the form of a website that provides a stepwise plan to guide medical laboratories toward implementing a quality management system in compliance with ISO 15189 or national standard with similar requirements.
  • Stepwise implementation of a quality management system for a health laboratory. Cairo: WHO Regional Office for the Eastern Mediterranean; 2016
    (https://apps.who.int/iris/handle/10665/249570).
  • Methodology for Prioritizing Severe Emerging Diseases for Research and Development. Geneva: World Health Organization; 2017 (https://cdn.who.int/
    media/docs/default-source/blue-print/prioritizing-methodology.pdf?sfvrsn=a8e808c_4).
    WHO guidance to identify global disease threats; methods can be applied to identifying priority diseases for laboratory testing in countries.
  • Strengthening Laboratory Management Toward Accreditation (SLMTA) [website]. Atlanta: Centers for Disease Control and Prevention (https://www. slmta.org/).
    A structured quality improvement program that teaches laboratory managers how to implement practical quality management systems in resource- limited settings.
  • Laboratory Quality Management System Training Toolkit. Geneva: World Health Organization; 2023 (https://extranet.who.int/hslp/content/LQMS- training-toolkit).
    WHO toolkit to train laboratory managers, senior biologists and technologists in quality management systems Stepwise implementation of a quality management system for a health laboratory. WHO EMRO publication adapting the ISO 15189 standard to the context and realities of resource-limited countries, where the requirements of the ISO standard may be too stringent to implement.
  • PVS Pathway [website]. Paris: World Organisation for Animal Health; 2023 (https://www.woah.org/en/what-we-offer/improving-veterinary-services/ pvs-pathway/targeted-support/sustainable-laboratory-support/oie-pvs-pathway-laboratory-reports/).

  • Strengthening veterinary diagnostic capacities: the FAO Laboratory Mapping Tool. Rome: Food and Agriculture Organization of the United Nations; 2016 (https://www.fao.org/documents/card/en/c/e13cf0b7-c8f4-4ff7-b340-439f40c677ec/).

  • The selection and use of essential in vitro diagnostics - TRS 1031. Geneva: World Health Organization; 2021 (https://www.who.int/publications/i/ item/9789240019102).
  • Simulation exercises [website]. Geneva: World Health Organization; 2023 (https://www.who.int/emergencies/operations/simulation-exercises).
  • WHO simulation exercise manual: a practical guide and tool for planning, conducting and evaluating simulation exercises for outbreaks and public health emergency preparedness and response. Geneva: World Health Organization; 2017 (https://apps.who.int/iris/handle/10665/254741).
  • Guidance for after action review (AAR). Geneva: World Health Organization; 2019 (https://apps.who.int/iris/handle/10665/311537).
  • Guidance for conducting a country COVID-19 intra-action review. Geneva: World Health Organization; 2020 (https://apps.who.int/iris/ handle/10665/333419).