A Multilingual Tool for Standardized Laboratory Biosafety and Biosecurity Assessment and Monitoring.

Control of infectious diseases requires the handling of infectious materials by both clinical and public health laboratories with exposure risks for laboratory personnel and environment. A comprehensive tool for assessing the capacity to manage these risks could enable the development of action plans for mitigation. Under the framework of the Global Health Security Agenda action package for biosafety and biosecurity, the authors developed a tool dedicated to assessing laboratory biosafety and biosecurity. The Biosafety and Biosecurity Laboratory Assessment Tool (BSS LAT) assesses the status of all laboratory biosafety core requirements across 10 different modules. It consists of a standardized spreadsheet-based tool that provides automatic scoring. It is designed to support national, regional, and global efforts to strengthen biosafety in clinical, public health, and veterinary laboratories. The BSS LAT was first used in Burkina Faso in collaboration with the African Society for Laboratory Medicine and the US Centers for Disease Control and Prevention to support the country in strengthening their biorisk management system. Since then, it has been successfully used in other countries (ie, Armenia, Burundi, Cameroon, Ghana, Guinea, Kazakhstan, Liberia), various settings (medical and veterinary laboratories), and translated into several languages (eg, English, French, Russian). The BSS LAT is a multipurpose tool that assists with standardization of biosafety and biosecurity requirements for all laboratories working with infectious materials, serves as a self-assessment guide for laboratories to develop improvement plans and reinforce capacities, and serves as a training guide for individual laboratories and networks or at the national level. The BSS LAT can also be used as a monitoring tool for the assessment of biosafety and biosecurity across all laboratories working with infectious materials at the national, regional, and global levels.

Strengthening laboratory biosafety in Liberia during the COVID-19 pandemic: Experience from the Global Laboratory Leadership Programme.

Background: The Global Laboratory Leadership Programme (GLLP) has biosafety and biosecurity as one of its core competencies and advocates for a One Health approach involving all relevant sectors across the human-animal-environment interface to empower national laboratory systems and strengthen health security. Decentralization of SARS-CoV-2 testing in Liberia coupled with an increase in the number of COVID-19 infections among laboratory professionals raised biosafety concerns. In response, a set of trainings on laboratory biosafety was launched for lab personnel across the country under the framework of the GLLP. The goal was to deliver a comprehensive package for laboratory biosafety in the context of SARS-CoV-2 through active learning. Methods: Three one-day workshops were conducted between September and October 2020, training personnel from human, animal and environmental laboratories through a One Health approach. Concepts critical to laboratory biosafety were delivered in an interactive engagement format to ensure effective learning and retention of concepts. Pre- and post-training assessments were performed, and a paired t-test was used to assess knowledge gain. Results: Of the 67 participants, 64 were from the human health sector, one from veterinary sector and two from environmental health sector. The average pre-test score was 41%. The main gaps identified were failure to acknowledge surgical antisepsis as a form of hand hygiene and recognition of PPE as the best risk control measure. The average post-test score was 75.5%. The mean difference of pre-test and post-test scores was statistically significant (p-value <0.001). Participants indicated satisfaction with the workshop content, mode of delivery and trainers' proficiency. Conclusions: The workshops were impactful as evidenced by significant improvement (34.5%) in the post-test scores and positive participant feedback. Repeated refresher trainings are vital to addressing the gaps, ensuring compliance, and promoting biosafety culture. GLLP's approach to cultivating multisectoral national laboratory leaders ready to take responsibility and ownership for capacity building provides a sustainable solution for attaining strong national laboratory systems better prepared for health emergencies and pandemics like COVID-19.

National Biosafety Management System: A Combined Framework Approach Based on 15 Key Elements.

The pervasive nature of infections causing major outbreaks have elevated biosafety and biosecurity as a fundamental component for resilient national laboratory systems. In response to international health security demands, the Global Health Security Agenda emphasizes biosafety as one of the prerequisites to respond effectively to infectious disease threats. However, biosafety management systems (BMS) in low-medium income countries (LMIC) remain weak due to fragmented implementation strategies. In addition, inefficiencies in implementation have been due to limited resources, inadequate technical expertise, high equipment costs, and insufficient political will. Here we propose an approach to developing a strong, self-sustaining BMS based on extensive experience in LMICs. A conceptual framework incorporating 15 key components to guide implementers, national laboratory leaders, global health security experts in building a BMS is presented. This conceptual framework provides a holistic and logical approach to the development of a BMS with all critical elements. It includes a flexible planning matrix with timelines easily adaptable to different country contexts as examples, as well as resources that are critical for developing sustainable technical expertise.

Field Epidemiology and Laboratory Training Program, Where Is the L-Track?

Background: Modifications of the Field Epidemiology Training Program (FETP) curricula to include a laboratory track (L-Track), to become Field Epidemiology and Laboratory Training Program (FELTP), began in 2004 in Kenya. The L-Track offered candidates training on laboratory competencies in management, policy, quality systems, and diagnostic methods as well as epidemiology, disease surveillance and outbreak response. Since then several FELTPs have discontinued the L-Track and instead offer all candidates, epidemiologists and laboratorians, a single FETP curriculum. Reasons for these changes are reported here. Methods: A questionnaire was sent to directors of 13 FELTP programs collecting information on the status of the programs, reasons for any changes, basic entry qualifications, source institutions and where residents were post enrollment or after graduation. Data from previous CDC internal assessments on FELTP L-Track was also reviewed. Results: Out of the 13 FELTPs included, directors from 10 FELTPs sent back information on their specific programs. The FELTPs in Kenya, Mozambique, Cameroon and Kazakhstan and Mali have discontinued a separate L-Track while those in Ghana, Georgia, Nigeria, Rwanda, and Tanzania continue to offer the separate L-Track. Reasons for discontinuation included lack of standardized curriculum, unclear strategies of the separate L-Track, and funding constraints. Two countries Kenya and Tanzania reported on the career progression of their graduates. Results show 84% (Kenya) and 51% (Tanzania) of candidates in the FELTP, L-Track were recruited from national/regional medical health laboratories. However post-graduation, 56% (Kenya) and 43% (Tanzania) were working as epidemiologists, program managers, program coordinators, or regulatory/inspection boards. Professional upward mobility was high; 87% (Kenya) and 73% (Tanzania) residents, reported promotions either in the same or in new institutions. Conclusions: The FELTP L-Track residents continue to offer critical contributions to public health workforce development with high upward mobility. While this may be a reflection of professional versatility and demand of the FELTP graduates, the move from core laboratory services underscores the challenges in filling and retaining qualified staff within the laboratory systems. Results suggest different strategies are needed to strengthen laboratory management and leadership programs with a clear focus on laboratory systems and laboratory networks to meet current and future clinical and public health laboratory workforce demands.

Laboratory Response to Ebola - West Africa and United States.

The 2014-2016 Ebola virus disease (Ebola) epidemic in West Africa highlighted the need to maintain organized laboratory systems or networks that can be effectively reorganized to implement new diagnostic strategies and laboratory services in response to large-scale events. Although previous Ebola outbreaks enabled establishment of critical laboratory practice safeguards and diagnostic procedures, this Ebola outbreak in West Africa highlighted the need for planning and preparedness activities that are better adapted to emerging pathogens or to pathogens that have attracted little commercial interest. The crisis underscored the need for better mechanisms to streamline development and evaluation of new diagnostic assays, transfer of material and specimens between countries and organizations, and improved processes for rapidly deploying health workers with specific laboratory expertise. The challenges and events of the outbreak forced laboratorians to examine not only the comprehensive capacities of existing national laboratory systems to recognize and respond to events, but also their sustainability over time and the mechanisms that need to be pre-established to ensure effective response. Critical to this assessment was the recognition of how response activities (i.e., infrastructure support, logistics, and workforce supplementation) can be used or repurposed to support the strengthening of national laboratory systems during the postevent transition to capacity building and recovery. This report compares CDC's domestic and international laboratory response engagements and lessons learned that can improve future responses in support of the International Health Regulations and Global Health Security Agenda initiatives.The activities summarized in this report would not have been possible without collaboration with many U.S. and international partners (http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/partners.html).

Ebola Laboratory Response at the Eternal Love Winning Africa Campus, Monrovia, Liberia, 2014-2015.

West Africa experienced the first epidemic of Ebola virus infection, with by far the greatest number of cases in Guinea, Sierra Leone, and Liberia. The unprecedented epidemic triggered an unparalleled response, including the deployment of multiple Ebola treatment units and mobile/field diagnostic laboratories. The National Institute of Allergy and Infectious Diseases and the Centers for Disease Control and Prevention deployed a joint laboratory to Monrovia, Liberia, in August 2014 to support the newly founded Ebola treatment unit at the Eternal Love Winning Africa (ELWA) campus. The laboratory operated initially out of a tent structure but quickly moved into a fixed-wall building owing to severe weather conditions, the need for increased security, and the high sample volume. Until May 2015, when the laboratory closed, the site handled close to 6000 clinical specimens for Ebola virus diagnosis and supported the medical staff in case patient management. Laboratory operation and safety, as well as Ebola virus diagnostic assays, are described and discussed; in addition, lessons learned for future deployments are reviewed.

The Merits of Malaria Diagnostics during an Ebola Virus Disease Outbreak.

Malaria is a major public health concern in the countries affected by the Ebola virus disease epidemic in West Africa. We determined the feasibility of using molecular malaria diagnostics during an Ebola virus disease outbreak and report the incidence of Plasmodium spp. parasitemia in persons with suspected Ebola virus infection.

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak.

Ebola Virus Diagnostics: The US Centers for Disease Control and Prevention Laboratory in Sierra Leone, August 2014 to March 2015.

In August 2014, the Viral Special Pathogens Branch of the US Centers for Disease Control and Prevention established a field laboratory in Sierra Leone in response to the ongoing Ebola virus outbreak. Through March 2015, this laboratory tested >12 000 specimens from throughout Sierra Leone. We describe the organization and procedures of the laboratory located in Bo, Sierra Leone.

Clinical inquiries regarding Ebola virus disease received by CDC--United States, July 9-November 15, 2014.

Since early 2014, there have been more than 6,000 reported deaths from Ebola virus disease (Ebola), mostly in Guinea, Liberia, and Sierra Leone. On July 9, 2014, CDC activated its Emergency Operations Center for the Ebola outbreak response and formalized the consultation service it had been providing to assist state and local public health officials and health care providers evaluate persons in the United States thought to be at risk for Ebola. During July 9-November 15, CDC responded to clinical inquiries from public health officials and health care providers from 49 states and the District of Columbia regarding 650 persons thought to be at risk. Among these, 118 (18%) had initial signs or symptoms consistent with Ebola and epidemiologic risk factors placing them at risk for infection, thereby meeting the definition of persons under investigation (PUIs). Testing was not always performed for PUIs because alternative diagnoses were made or symptoms resolved. In total, 61 (9%) persons were tested for Ebola virus, and four, all of whom met PUI criteria, had laboratory-confirmed Ebola. Overall, 490 (75%) inquiries concerned persons who had neither traveled to an Ebola-affected country nor had contact with an Ebola patient. Appropriate medical evaluation and treatment for other conditions were noted in some instances to have been delayed while a person was undergoing evaluation for Ebola. Evaluating and managing persons who might have Ebola is one component of the overall approach to domestic surveillance, the goal of which is to rapidly identify and isolate Ebola patients so that they receive appropriate medical care and secondary transmission is prevented. Health care providers should remain vigilant and consult their local and state health departments and CDC when assessing ill travelers from Ebola-affected countries. Most of these persons do not have Ebola; prompt diagnostic assessments, laboratory testing, and provision of appropriate care for other conditions are essential for appropriate patient care and reflect hospital preparedness.

Recombinant viruses initiated the early HIV-1 epidemic in Burkina Faso.

We analyzed genetic diversity and phylogenetic relationships among 124 HIV-1 and 19 HIV-2 strains in sera collected in 1986 from patients of the state hospital in Ouagadougou, Burkina Faso. Phylogenetic analysis of the HIV-1 env gp41 region of 65 sequences characterized 37 (56.9%) as CRF06_cpx strains, 25 (38.5%) as CRF02_AG, 2 (3.1%) as CRF09_cpx, and 1 (1.5%) as subtype A. Similarly, phylogenetic analysis of the protease (PR) gene region of 73 sequences identified 52 (71.2%) as CRF06_cpx, 15 (20.5%) as CRF02_AG, 5 (6.8%) as subtype A, and 1 (1.4%) was a unique strain that clustered along the B/D lineage but basal to the node connecting the two lineages. HIV-2 PR or integrase (INT) groups A (n = 17 [89.5%]) and B (n = 2 [10.5%]) were found in both monotypic (n = 11) and heterotypic HIV-1/HIV-2 (n = 8) infections, with few HIV-2 group B infections. Based on limited available sampling, evidence suggests two recombinant viruses, CRF06_cpx and CRF02_AG, appear to have driven the beginning of the mid-1980s HIV-1 epidemic in Burkina Faso.

Strengthening public health laboratory capacity in Thailand for International Health Regulations (IHR) (2005).

INTRODUCTION: Thailand conducted a national laboratory assessment of core capacities related to the International Health Regulations (IHR) (2005), and thereby established a baseline to measure future progress. The assessment was limited to public laboratories found within the Thai Bureau of Quality and Safety of Food, National Institute of Health and regional medical science centres. METHODS: The World Health Organization (WHO) laboratory assessment tool was adapted to Thailand through a participatory approach. This adapted version employed a specific scoring matrix and comprised 16 modules with a quantitative output. Two teams jointly performed the on-site assessments in December 2010 over a two-week period, in 17 public health laboratories in Thailand. The assessment focused on the capacity to identify and accurately detect pathogens mentioned in Annex 2 of the IHR (2005) in a timely manner, as well as other public health priority pathogens for Thailand. RESULTS: Performance of quality management, budget and finance, data management and communications was considered strong (>90%); premises quality, specimen collection, biosafety, public health functions, supplies management and equipment availability were judged as very good (>70% but ≤90%); while microbiological capacity, staffing, training and supervision, and information technology needed improvement (>60% but ≤70%). CONCLUSIONS: This assessment is a major step in Thailand towards development of an optimized and standardized national laboratory network for the detection and reporting of infectious disease that would be compliant with IHR (2005). The participatory strategy employed to adapt an international tool to the Thai context can also serve as a model for use by other countries in the Region. The participatory approach probably ensured better quality and ownership of the results, while providing critical information to help decision-makers determine where best to invest finite resources.

Integrated Disease Investigations and Surveillance planning: a systems approach to strengthening national surveillance and detection of events of public health importance in support of the International Health Regulations.

The international community continues to define common strategic themes of actions to improve global partnership and international collaborations in order to protect our populations. The International Health Regulations (IHR[2005]) offer one of these strategic themes whereby World Health Organization (WHO) Member States and global partners engaged in biosecurity, biosurveillance and public health can define commonalities and leverage their respective missions and resources to optimize interventions. The U.S. Defense Threat Reduction Agency's Cooperative Biological Engagement Program (CBEP) works with partner countries across clinical, veterinary, epidemiological, and laboratory communities to enhance national disease surveillance, detection, diagnostic, and reporting capabilities. CBEP, like many other capacity building programs, has wrestled with ways to improve partner country buy-in and ownership and to develop sustainable solutions that impact integrated disease surveillance outcomes. Designing successful implementation strategies represents a complex and challenging exercise and requires robust and transparent collaboration at the country level. To address this challenge, the Laboratory Systems Development Branch of the U.S. Centers for Disease Control and Prevention (CDC) and CBEP have partnered to create a set of tools that brings together key leadership of the surveillance system into a deliberate system design process. This process takes into account strengths and limitations of the existing system, how the components inter-connect and relate to one another, and how they can be systematically refined within the local context. The planning tools encourage cross-disciplinary thinking, critical evaluation and analysis of existing capabilities, and discussions across organizational and departmental lines toward a shared course of action and purpose. The underlying concepts and methodology of these tools are presented here.

HIV-2 protease sequences of subtypes A and B harbor multiple mutations associated with protease inhibitor resistance in HIV-1.

BACKGROUND: HIV-1 protease inhibitors (PI) have been used for treating HIV-2-infected persons but little is known about amino acid mutations associated with PI resistance in HIV-2 and whether they are similar to those seen in HIV-1. OBJECTIVE: To determine the frequency of HIV-1 PI resistance-associated mutations in PI-naive HIV-2-infected individuals. DESIGN: Using PCR, protease genes were amplified from 76 individuals, directly sequenced, phylogenetically subtyped, and translated into amino acids to analyze PI-associated major and minor mutations. RESULTS: Of the 76 HIV-2 sequences, 68% belonged to subtype A and 32% to subtype B. All sequences contained at least four codon changes giving substitutions at 10, 30, 32, 36, 46, 47, 71 or 77. The frequency of these mutations was similar in subtype A and B viruses. Two major resistance-conferring mutations, 30N and 46I, were identified in one (1%) and 68 (89%) specimens, respectively. Minor mutations 10V/I, 32I, 36I, 47V, and 71V were predominant (89%-100%), followed by the rare mutation 77I (1%). Of the 76 strains, 89% harbored multiple PI resistance-associated substitutions comprising both the major 46I and minor mutations: 10V/I, 32I, 36I, 46I, 47V, 71V (76%); 10V, 32I, 36I, 46I, 47V (9%); and 10V, 32I, 36I, 46I, 47V 71V, 77I (1.3%), 10V, 32I, 46I, 47V, 71V (1.3%), and 10V, 30N, 32I, 36I, 46I, 47V, 71V (1.3%). The remaining 11% of the sequences had patterns with only minor mutations: 10V, 32I, 36I, 47V, 71V (9%) and 10V, 32I, 36I, 47V (1.3%). CONCLUSIONS: The high frequency of multiple PI-associated substitutions represent natural polymorphisms occurring in HIV-2 strains of subtypes A and B. Phenotypic and clinical studies are needed to determine the relevance of these substitutions.

Evaluation of rapid HIV test kits on whole blood and development of rapid testing algorithm for voluntary testing and counseling centers in Ethiopia.

Five simple and rapid HIV antibody detection assays viz. Determine, Capillus, Oraquick, Unigold and Hemastrip were evaluated to examine their performance and to develop an alternative rapid test based testing algorithm for voluntary counseling and testing (VCT) in Ethiopia. All the kits were tested on whole blood, plasma and serum. The evaluation had three phases: Primary lab review, piloting at point of service and implementation. This report includes the results of the first two phases. A total of 2,693 specimens (both whole blood and plasma) were included in the evaluation. Results were compared to double Enzyme Linked Immuno-Sorbent Assay (ELISA) system. Discordant EIA results were resolved using Western Blot. The assays had very good sensitivities and specificities, 99-100%, at the two different phases of the evaluation. A 98-100% result agreement was obtained from those tested at VCT centers and National Referral Laboratory for AIDS (NRLA), in the quality control phase of the evaluation. A testing strategy yielding 100% [95% CI; 98.9-100.0] sensitivity was achieved by the sequential use of the three rapid test kits. Direct cost comparison showed serial testing algorithm reduces the cost of testing by over 30% compared to parallel testing in the current situation. Determine, Capillus/Oraquick (presence/absence of frefrigeration) and Unigold were recommended as screening, confirmation and tiebreaker tests, respectively.

Human immunodeficiency virus type 1 group m protease in cameroon: genetic diversity and protease inhibitor mutational features.

To establish a baseline for monitoring resistance to protease inhibitors (PIs) and examining the efficacy of their use among persons in Cameroon infected with human immunodeficiency virus type 1 (HIV-1), we analyzed genetic variability and PI resistance-associated substitutions in PCR-amplified protease (PR) sequences in strains isolated from 110 HIV-1-infected, drug-naïve Cameroonians. Of the 110 strains, 85 were classified into six HIV-1 PR subtypes, A (n = 1), B (n = 1), F (n = 4), G (n = 7), H (n = 1), and J (n = 7), and a circulating recombinant form, CRF02-AG (n = 64). PR genes from the remaining 25 (23%) specimens were unclassifiable, whereas 2% (7 of 301) unclassifiable PR sequences were reported for a global collection. Two major PI resistance-associated mutations, 20M and 24I, were detected in strains from only two specimens, whereas secondary mutations were found in strains from all samples except one strain of subtype B and two strains of CRF02-AG. The secondary mutations showed the typical PI resistance-associated pattern for non-subtype B viruses in both classifiable and unclassifiable PR genes, with 36I being the predominant (99%) mutation, followed by 63P (18%), 20R (15%), 77I (13%), and 10I or 10V (11%). Of these mutations, dual and triple PI resistance-associated substitutions were found in 38% of all the Cameroonian strains. Compared with classifiable PR sequences, unclassifiable sequences had significantly more dual and triple substitutions (64% versus 30%; P = 0.004). Phenotypic and clinical evaluations are needed to estimate whether PI resistance during antiretroviral drug treatment occurs more rapidly in individuals infected with HIV-1 strains harboring multiple PI resistance-associated substitutions. This information may be important for determination of appropriate drug therapies for HIV-1-infected persons in Cameroon, where more than one-third of HIV-1 strains were found to carry dual and triple minor PI resistance-associated mutations.