A phased strengthening of laboratory capacity in the Eastern Mediterranean Region during the COVID-19 pandemic.

The Eastern Mediterranean Region (EMR) faces ongoing challenges in its public health system due to limited resources, logistical issues, and political disruptions. The COVID-19 pandemic accelerated the need for stronger laboratory capacities to handle the increased demand for testing. In a phased response, EMR countries utilized the National Influenza Centers to rapidly establish and scale molecular testing for SARS-CoV-2, the causative agent of COVID-19. The expansion of capacity included strong collaborations between public health bodies and private and academic sectors to decentralize and expand testing to the subnational level. To ensure that the quality of testing was not impacted by rapid expansion, national and subnational laboratories were enrolled in external quality assurance programs for the duration of the response. Implementation of genomic surveillance was prioritized for variant tracking, leading to the establishment of regional sequencing reference laboratories and the distribution of MinION sequencing platforms to complex emergency countries who previously had limited experience with pathogen sequencing. Challenges included a lack of technical expertise, including in implementing novel diagnostic assays and sequencing, a lack of bioinformatics expertise in the region, and significant logistical and procurement challenges. The collaborative approach, coordinated through the WHO Eastern Mediterranean Regional Office, enabled all 22 countries to achieve SARS-CoV-2 diagnostic capabilities, highlighting the pivotal role of laboratories in global health security.

Learning From COVID-19: What Would It Take to Be Better Prepared in the Eastern Mediterranean Region?

The COVID-19 transmission in the Eastern Mediterranean Region (EMR) was influenced by various factors such as conflict, demographics, travel and social restrictions, migrant workers, weak health systems, and mass gatherings. The countries that responded well to COVID-19 had high-level political commitment, multisectoral coordination, and existing infrastructures that could quickly mobilize. However, some EMR countries faced challenges due to political instability and fragile health systems, which hindered their response strategies. The pandemic highlighted the region's weak health systems and preparedness, fragmented surveillance systems, and lack of trust in information sharing. COVID-19 exposed the disruption of access and delivery of essential health services as a major health system fragility. In 2020, the World Health Organization (WHO) conducted a global pulse survey, which demonstrated that the EMR experienced the highest disruption in health services compared to other WHO regions. However, thanks to prioritization by the WHO and its member states, significant improvement was observed in 2021 during the second round of the WHO's National Pulse Survey. The pandemic underscored the importance of political leadership, community engagement, and trust and emphasized that investing in health security benefits everyone. Increasing vaccine coverage, building regional capacities, strengthening health systems, and working toward universal health coverage and health security are all priorities in the EMR. Emergency public health plays a key role in preparing for and responding to pandemics and biological threats. Integrating public health into primary care and investing in public health workforce capacity building is essential to reshaping public health and health emergency preparedness.

Rapid response teams in the Eastern Mediterranean Region: Results from the baseline survey of country-level capacities, operations and outbreak response capabilities.

The aim of this study is to assess WHO/Eastern Mediterranean region (WHO/EMR) countries capacities, operations and outbreak response capabilities. Cross-sectional study was conducted targeting 22 WHO/EMR countries from May to June 2021. The survey covers 8 domains related to 15 milstones and key performance indicators (KPIs) for RRT. Responses were received from 14 countries. RRTs are adequately organised in 9 countries (64.3%). The mean retention rate of RRT members was 85.5% ± 22.6. Eight countries (57.1%) reported having standard operating procedures, but only three countries (21.4%) reported an established mechanism of operational fund allocation. In the last 6 months, 10,462 (81.9%) alerts were verified during the first 24 h. Outbreak response was completed by the submission of final RRT response reports in 75% of analysed outbreaks. Risk Communication and Community Engagement (RCCE) activities were part of the interventional response in 59.5% of recent outbreaks. Four countries (28.6%) reported an adequate system to assess RRTs operations. The baseline data highlights four areas to focus on: developing and maintaining the multidisciplinary nature of RRTs through training, adequate financing and timely release of funds, capacity and system building for implementing interventions, for instance, RCCE, and establishing national monitoring and evaluation systems for outbreak response.

Deployment of COVID-19 vaccine in the WHO Eastern Mediterranean Region 2021-23: How do we switch to a life course approach?

In 2020-2021, all countries of the WHO Eastern Mediterranean Region [EMR] introduced COVID-19 vaccine with inequalities in coverage across countries. As for 2023, we reviewed subsequent progress in deployment, coverage, acceptance, and integration. As of 31 December 2023, coverage in EMR reached 51% for primary series and 19 % for the first booster, higher in high income countries (77 % and 44 %, respectively) than in upper middle-income countries (49 % and 20 %), Advance Market Commitment [AMC] non-Gavi eligible countries (47 % and 15 %) and AMC Gavi eligible countries (49 % and 16 %). Thirteen countries measured coverage among healthcare workers (76 % and 43 %, respectively) and 15 among elderly (69 % and 38 %, respectively). Three rounds of the regional Knowledge, Attitudes, and Practices [KAP] survey on COVID-19 vaccine acceptance in 2021-2022 indicated that acceptance increased from 20 % in June-July 2021 to 62 % in October-November 2021, and 77 % in June-July 2022. Those unvaccinated but intending to be vaccinated decreased from 60 % to 23 % and 11 %, respectively. Unvaccinated without intention to be vaccinated decreased from 15 % to 10 % and 11 %, respectively. Twenty out of 22 countries in the region had completely or partially integrated COVID-19 vaccination into the Expanded Programme on Immunization [EPI] and Primary Health Care [PHC]. Overall, challenges to reach high-risk groups persisted as the population was less concerned about Omicron variant of the SARS-CoV-2 virus. Countries should build on the trust, momentum, and lesson-learned generated from COVID-19 vaccination to get the highest risk groups vaccinated and switch from a time bound and project type approach to a sustainable and long-term approach for COVID-19 vaccine delivery that would be integrated into the routine EPI and PHC.

Strengthening laboratories in response to outbreaks in humanitarian emergencies and conflict settings: Results, challenges and lessons from expanding PCR diagnostic capacities for COVID-19 testing in Yemen.

BACKGROUND: When the COVID-19 pandemic was declared, Yemen, a country facing years of conflict had only one laboratory with PCR testing capacity. In this article, we describe the outcome of the implementation of molecular based diagnostics platform in Yemen and highlight the key milestones the country went through to increase access to testing for its populations residing in a geographically vast and politically divided country. METHODS: A retrospective assessment of COVID-19 laboratory response activities was done detailing the needs assessment process, timelines, geographical coverage, and outcomes of the activities. Laboratory data was analyzed to construct the geographical locations of COVID-19 testing laboratories and the numbers of tests performed in each facility to highlight the demands of testing for travelers. Finally, we discuss the impact these activities had in enabling the movement of people across international borders for economic gains and in delivery of critical humanitarian aid. OUTCOME: PCR testing capacities in Yemen significantly improved, from one laboratory in Sanaa in April 2020 to 18 facilities across the country by June 2022. In addition, the number of functional Real-Time PCR thermocyclers increased from one to 32, the PCR tests output per day improved from 192 to 6144 tests per day. Results from analysis of laboratory data showed there were four peaks of COVID-19 in Yemen as October 2022. The majority of laboratory tests were performed for travelers than for medical or public health reasons. Demand for laboratory testing in Yemen was generally low and waned over time as the perceived risk of COVID-19 declined, in parallel with rollout of the COVID-19 vaccines. DISCUSSION/CONCLUSION: The successful expansion of laboratory testing capacity was instrumental in the control and management of COVID-19 cases and critical in the implementation of public response strategies, including restrictions on gathering. Laboratory testing also facilitated the movement of humanitarian agencies and delivery of aid and enabled hundreds of thousands of Yemeni nationals to travel internationally. By virtue of these outcomes, the impact of laboratory strengthening activities was thus felt in the health sector and beyond.

An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study.

Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.