Exploring characteristics and severity of road traffic injuries in Lebanon using emergency department hospital-based data.

In Lebanon, the lack of quality data on road traffic injuries (RTIs) led to the implementation of a hospital-based RTI surveillance system by the Ministry of Health in in private and public-run hospitals in the Bekaa governorate. This paper aims to describe the characteristics and severity of RTIs recorded over two years during the pilot phase. It also assesses the strengths and challenges of the surveillance system, highlighting areas for enhancement. The data collected from the Emergency department (ED) was used to conduct a retrospective analysis of population-based injuries hospitalized for road traffic crashes (RTC). Designated focal persons reported injuries weekly using a standardized form, which included demographic and crash-related variables, body lesions, and vital signs. Data were coded per the International Classification of Diseases (ICD-10), entered into Epidata, and analyzed using SPSS. The RTI surveillance system was assessed using Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis. Over two years, a total of 1576 cases of RTIs were reported. The male-to-female ratio was 2.16 and the majority of RTIs (44.4%) were recorded among those aged between 15 and 29 years old. From 2013 to 2015, a decrease of 0.7% in the revised trauma score (RTS < 4) was recorded. On the contrary, an increase of 3.9% in injury severity score (ISS) that ranged between 15 and 75 was reported. The probability of survival of an injured individual at one month was improved. The hospital-based surveillance system demonstrated strengths in structured data collection and ethical considerations but faced challenges like underreporting, limited coverage, and resource constraints. Recommendations for improvement include enhancing data quality and timely reporting, ultimately supporting evidence-based road safety interventions.

Pfizer-BioNTech (BNT162b2) Vaccine Effectiveness against Symptomatic Laboratory-Confirmed COVID-19 Infection among Outpatients in Sentinel Sites, Lebanon, July-December 2021.

On 14 February 2021, Lebanon implemented nationwide vaccination, offering the Pfizer-BioNTech (BNT162b2) vaccine to adults over 50 years of age. We estimated the effectiveness of the Pfizer-BioNTech vaccine in preventing symptomatic laboratory-confirmed COVID-19. We conducted a test-negative case-control (TND) study among symptomatic adults aged 50 years and older who presented with influenza-like illness (ILI) or COVID-19-like illness (CLI) in surveillance sentinel sites between 1 July and 31 December 2021. Unvaccinated participants did not receive any vaccine dose before symptom onset. Vaccinated participants received at least one dose within 14 days before onset of symptoms. We estimated vaccine effectiveness against symptomatic laboratory-confirmed COVID-19, adjusted for demographic and behavioral factors, using multivariable logistic regression. Out of 457 participants with symptoms, 150 (33%) were positive and 307 (67%) were negative for SARS-CoV-2. Adjusted vaccine effectiveness was 22% (95% CI: -70-65%) for those partially vaccinated and 44% (95% CI: 6-67%) for those fully vaccinated. Vaccination with two doses of the Pfizer-BioNTech vaccine was effective in preventing COVID-19 symptomatic illness in the older population. Vaccine effectiveness was lower for those partially vaccinated. We recommend enhancing vaccine uptake with at least one dose among risk groups for COVID-19 and keeping general recommendations on contact and droplet precautions in the general population.

Preparing for the next respiratory pathogen pandemic: using tabletop simulation exercises to strengthen national planning in Cook Islands, Costa Rica, Lebanon and Mongolia.

The Preparedness and Resilience for Emerging Threats (PRET) initiative takes an innovative mode-of-transmission approach to pandemic planning by advocating for integrated preparedness and response systems and capacities for groups of pathogens with common transmission pathways. The World Health Organization (WHO) launched this initiative in 2023 with the publication of PRET Module 1 addressing respiratory pathogens. Exercise PanPRET-1 is a customizable tabletop simulation exercise (TTX) package developed to complement PRET Module 1. The exercise scenario focuses on strengthening capacities for multisectoral coordination, risk communication and community engagement, and the triggers for operational decision-making. This article reports on the experiences of the first four countries to implement Exercise PanPRET-1: Cook Islands, Costa Rica, Lebanon and Mongolia. Exercise outcomes demonstrated that PanPRET-1 can be an effective tool for testing pandemic plans in a multisectoral forum and identifying opportunities to improve preparedness and response in key domains. In quantitative evaluations in Cook Islands, Costa Rica and Mongolia, high proportions of exercise participants indicated that multiple aspects of the exercise were well-designed and were beneficial for improving health emergency preparedness. Exercise participants in Lebanon provided qualitative feedback indicating that they found the exercise to be beneficial. Conducting a TTX and monitoring the implementation of action plans based on exercise findings facilitates a country-owned whole-of-society vision for pandemic planning. Countries are encouraged to incorporate TTX such as Exercise PanPRET-1 into a continuous cycle of activity to improve pandemic preparedness.

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.

Communicable Disease Surveillance in Lebanon during the Syrian Humanitarian Crisis, 2013-2019.

Lebanon has been one of the most affected countries by the Syrian humanitarian crisis. The national communicable disease surveillance was enhanced to detect outbreaks among Syrians. In this study, we aim to describe the findings of the communicable disease surveillance among Syrians in Lebanon, compare it to residents' data, and describe the implemented surveillance activities between 2013 and 2019. During the study period, data on communicable diseases was mainly collected through the routine national surveillance system and an enhanced syndromic surveillance system. Predefined case definitions and standard operating procedures were in place. Data collection included both case-based and disease-specific reporting forms. Descriptive data and incidence rates were generated. Information was disseminated through weekly reports. Activities were conducted in close collaboration with different partners. The most commonly reported diseases were: viral hepatitis A, cutaneous leishmaniasis, mumps, and measles. Hepatitis A incidence increased in 2013 and 2014 among Syrians as well as residents. For leishmaniasis, the incidence increased only among Syrians in 2013 and decreased after that. An outbreak of mumps was reported among Syrians between 2014 and 2016, with a peak in 2015 concomitant with a national outbreak. Outbreaks of measles were reported among Syrians and residents in 2013, 2018, and 2019. The infrastructure of the well-implemented surveillance system in Lebanon has been utilized to monitor the health status of Syrians in Lebanon, early detect communicable diseases among this population, and guide needed preventive and control measures. This highlights the importance of having a flexible surveillance system that can be adapted to emergencies and the importance of sharing results with involved partners.

Effectiveness of the Pfizer-BioNTech Vaccine against COVID-19-Associated Hospitalizations among Lebanese Adults ≥75 Years Old-Lebanon, April-May 2021.

In Lebanon, the nationwide vaccination against COVID-19 was launched in February 2021 using the Pfizer-BioNTech vaccine and prioritizing elderly people, persons with comorbidities, and healthcare workers. Our study aims to estimate the post-introduction vaccine effectiveness (VE) of the Pfizer-BioNTech vaccine in preventing COVID-19 hospitalizations among elderly people ≥75 years old in Lebanon. A case-control study design was used. Case patients were Lebanese, ≥75 years old, and hospitalized with positive PCR results during April-May 2021, and randomly selected from the database of the Epidemiological Surveillance Unit at the Ministry of Public Health (MOPH). Each case patient was matched by age and locality to two controls. The controls were hospitalized, non-COVID-19 patients, randomly selected from the MOPH hospital admission database. VE was calculated for fully (2 doses ≥14 days) and partially vaccinated (≥14 days of the first or within 14 days of the second dose) participants using multivariate logistic regression. A total of 345 case patients and 814 controls were recruited. Half were females, with a mean age of 83 years. A total of 14 case patients (5%) and 143 controls (22%) were fully vaccinated. A bivariate analysis showed a significant association with gender, month of confirmation/hospital admission, general health, chronic medical conditions, main income source, and living arrangement. After adjusting for a month of hospital admission and gender, the multivariate analysis yielded a VE of 82% (95% CI = 69-90%) against COVID-19-associated hospitalizations for those fully vaccinated and 53% (95% CI = 23-71%) for those partially vaccinated. Our study shows that the Pfizer-BioNTech vaccine is effective in reducing the risk for COVID-19-associated hospitalizations of Lebanese elderly people (≥75 years old). Additional studies are warranted to explore VE in reducing hospitalizations for younger age groups, as well as reducing COVID-19 infections.

Estimation of the influenza-associated respiratory hospitalization burden using sentinel surveillance data, Lebanon, 2015-2020.

Introduction: Influenza epidemics cause around 3 to 5 million cases of severe illness worldwide every year. Estimates are needed for a better understanding of the burden of disease especially in low- and middle-income countries. The objective of this study is to estimate the number and rate of influenza-associated respiratory hospitalizations in Lebanon during five influenza seasons (2015-2016 to 2019-2020) by age and province of residence in addition to estimating the influenza burden by level of severity. Methods: The severe acute respiratory infection sentinel surveillance system was used to compute influenza positivity from the influenza laboratory confirmed cases. The total of respiratory hospitalizations under the influenza and pneumonia diagnosis was retrieved from the Ministry of Public Health hospital billing database. Age-specific and province-specific frequencies and rates were estimated for each season. Rates per 100 000 population were calculated with 95% confidence levels. Results: The estimated seasonal average of influenza-associated hospital admission was 2866 for a rate of 48.1 (95% CI: 46.4-49.9) per 100 000. As for the distribution by age group, the highest rates were seen in the two age groups ≥65 years and 0-4 years whereas the lowest rate was for the age group 15-49 years. For the distribution by province of residence, the highest influenza-associated hospitalization rates were reported from the Bekaa-Baalback/Hermel provinces. Conclusion: This study shows the substantial burden of influenza in Lebanon mainly on high-risk groups (≥65 years and <5 years). It is crucial to translate these findings into policies and practices to reduce the burden and estimate the illness-related expenditure and indirect costs.

Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon.

BACKGROUND: The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. METHODS: We collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform. RESULTS: A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. CONCLUSION: This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

A framework for reconstructing transmission networks in infectious diseases.

In this paper, we propose a general framework for the reconstruction of the underlying cross-regional transmission network contributing to the spread of an infectious disease. We employ an autoregressive model that allows to decompose the mean number of infections into three components that describe: intra-locality infections, inter-locality infections, and infections from other sources such as travelers arriving to a country from abroad. This model is commonly used in the identification of spatiotemporal patterns in seasonal infectious diseases and thus in forecasting infection counts. However, our contribution lies in identifying the inter-locality term as a time-evolving network, and rather than using the model for forecasting, we focus on the network properties without any assumption on seasonality or recurrence of the disease. The topology of the network is then studied to get insight into the disease dynamics. Building on this, and particularly on the centrality of the nodes of the identified network, a strategy for intervention and disease control is devised.

The impact of vaccination on the burden of invasive pneumococcal disease from a nationwide surveillance program in Lebanon: an unexpected increase in mortality driven by non-vaccine serotypes.

BACKGROUND: The impact of pneumococcal conjugate vaccines (PCVs) on the burden of invasive pneumococcal disease (IPD) and serotype distribution was examined across age groups from data collected by the Lebanese Inter-Hospital Pneumococcal Surveillance Program. METHODS: Between 2005 and 2020, 593 invasive Streptococcus pneumoniae isolates were collected from 79 hospitals throughout Lebanon. Serotypes and antimicrobial resistance (AMR) profiles were identified, and trends compared over 3 eras: PCV7, post-PCV7/ pre-PCV13, and PCV13 eras. RESULTS: The prevalence of PCV7 serotypes decreased significantly from 43.6% in the PCV7 era to 17.8% during the PCV13 era (p<0.001). PCV13-only serotypes remained stable in the PCV13 compared to the post-PCV7 eras, especially serotypes 1 and 3, whereas non-vaccine types (NVT) increased throughout the study period, especially 24 and 16F. The mortality rate increased substantially from 12.5% (PCV7 era) to 24.8% (PCV13 era). A significant decrease in AMR was observed across the three study eras. CONCLUSION: PCVs substantially impacted IPD and AMR in vaccinated and unvaccinated populations despite an increase in mortality driven by NVT. Broadening the recommendation of vaccination to include older age-groups, using higher valency vaccines, and implementing stringent antimicrobial stewardship are likely to further impact the burden of IPD.

COVID-19 mortality surveillance in Lebanon.

Since the beginning of the COVID-19 pandemic, the Epidemiological surveillance program of the Lebanese Ministry of Public Health has launched a rapid surveillance system for collecting COVID-19-related mortality data. In this study, we document the Lebanese experience of COVID-19 mortality surveillance and provide an analysis of the epidemiological characteristics of confirmed deaths. The implementation of the rapid COVID-19 mortality surveillance system, data sources, and data collection were described. A retrospective descriptive analysis of the epidemiological characteristics of confirmed cases occurring in Lebanon between February 20, 2020, and September 15, 2021, was performed. Epidemiological curves of Covid-19 confirmed cases and deaths as well as the geographic distribution map of mortality rates were generated. Between February 21, 2020, and September 15, 2021, a total of 8163 COVID-19-related deaths were reported with a predominance of males (60.4%). More than 60% were aged 70 years or above. Of all deaths, 84% occurred at hospitals and 16% at home. The overall cumulative mortality rate was 119.6 per 100,000. The overall case fatality ratio (CRF) was 1.3%. Of the total deaths, 82.2% had at least one underlying medical condition. The top reported COVID-19 comorbidities associated with COVID-19-related deaths are cardiovascular diseases including hypertension (59.1%), diabetes (37.2%), kidney diseases including dialysis (11%), cancer (6.7%), and lung diseases (6.3%). The CFR was 30.9% for kidney diseases, 20.2% for cancer, 20.2% for lung diseases, 18.1% for liver diseases, 14% for diabetes, and 12.2% for cardiovascular diseases. Considering the limited human and financial resources in Lebanon due to the economic and political crisis, the rapid mortality surveillance system can be considered successful. Improving this system is important and would contribute to better detection of deaths from emerging and re-emerging diseases during health crises.

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.

Experience of field testing in Lebanon during the COVID-19 pandemic, January to August 2021.

Soon after detection of the first COVID-19 case in Lebanon, a testing strategy was developed aiming to early detect new cases and identify close contacts in order to implement isolation and quarantine measures, thus limiting disease transmission. Field-testing activities were initiated in March 2020, focusing on suspected cases and close contacts. The objective of this paper is to present data collected between the 1st and the 35th week of 2021 and discuss challenges and lessons learned. During the study period, testing activities were conducted in field sites covering all Lebanese districts and following a fixed schedule. Testing was provided free of charge for suspected/probable patients with COVID-19 and close contacts of positive cases. Nasopharyngeal specimens were collected and sent to designated laboratories for reverse transcription polymerase chain reaction testing. Results were received on a timely manner, within 48 hours. From the 1st to the 35th week of 2021, 1244 field-testing activities were conducted with an average of 37 testing activities per week. During this period, 71 542 samples were collected with an average of 2104 specimens per week. On average, activities covered 78% of the Lebanese districts. The average positivity rate for this period was 24% (15%-33%) in line with the virus circulation levels in the country. Timely development and implementation of a testing strategy is crucial during epidemics. The success of Lebanon's field-testing experience was mainly due to the timely adapted approach that covered all national territories, targeting all residents as well as high-risk groups in suburbs and remote areas.

Converting the existing disease surveillance from a paper-based to an electronic-based system using district health information system (DHIS-2) for real-time information: the Lebanese experience.

INTRODUCTION: The Ministry of Public Health in Lebanon is in the process of converting the surveillance reporting from a cumbersome paper-based system to a web-based electronic platform (DHIS-2) to have real-time information for early detection of alerts and outbreaks and for initiating a prompt response. OBJECTIVES: This paper aimed to document the Lebanese experience in implementing DHIS-2 for the disease surveillance system. It also targets to assess the improvement of reporting rates and timeliness of the reported data and to disclose the encountered challenges and opportunities. METHODOLOGY: This is a retrospective description of processes involved in the implementation of the DHIS-2 tool in Lebanon. Initially, it was piloted for the school-based surveillance in 2014; then its use was extended in May 2017 to cover other specific surveillance systems. This included all surveillance programs collecting aggregate data from hospitals, medical centers, dispensaries, or laboratories at the first stage. As part of the national roll-out process, the online application was developed. The customized aggregated-based datasets, organization units, user accounts, specific and generic dashboards were generated. More than 80 training sessions were conducted throughout the country targeting 1290 end-users including health officers at the national and provincial levels, focal persons who were working in all public and private hospitals, laboratories, and medical centers as well. Completeness and timeliness of reported data were compared before and after the implementation of DHIS-2. The unveiled challenges and the main lessons learned during the roll-out process were discussed. RESULTS: For laboratory-based surveillance, completeness of reporting increased from 70.8% in May to 89.6% in October. Timeliness has improved from 25 to 74%. For medical centers, an improvement of 8.1% for completeness and 9.4% in timeliness was recorded before and after training sessions. For zero reporting, completeness remains the same (88%) and timeliness has improved from 74 to 87%. The main challenges faced during the implementation of DHIS-2 were mainly infrastructural and system-related in addition to poor internet connectivity, limited workforce, and frequent changes to DHIS-2 versions. CONCLUSION: Implementation of DHIS-2 improved timeliness and completeness for aggregated data reporting. Continued on-site support, monitoring, and system enhancement are needed to improve the performance of DHIS-2.

Phased repatriation of Lebanese expatriates stranded abroad during coronavirus disease 2019 (COVID-19) pandemic.

BACKGROUND: The coronavirus disease (COVID-19) pandemic represents a serious worldwide threat. Stranded Lebanese citizens abroad appealed to the Lebanese government to embark on citizen repatriation missions. We aim to document the Lebanese experience in the repatriation of citizens during COVID-19 which allow us to disclose encountered challenges and lessons learned. METHODS: This is a retrospective description of processes involved in the phased repatriation of Lebanese citizens. The Mission consisted of 4 phases starting, April 5th until June 19th 2020. The prioritization of returnees was based on both medical and social risk assessment. The repatriation team was divided into four groups: the aircraft team, the airport team, the hotel team and the follow up team. On arrival, all returning citizens were tested using Polymerase chain Reaction (PCR) based technique, and were obliged to adhere to a mandatory facility quarantine for 24 to 48 h. Returning travelers who were tested positive for COVID-19 were transferred to the hospital. Those who were tested negative were urged to strictly comply with home-quarantine for a duration of 14 days. They were followed up on a daily basis by the repatriation team. RESULTS: Overall, 25,783 Lebanese citizens have returned home during the phased repatriation. The third phase ranked the uppermost in regard of the number of citizens repatriated. The total number of performed PCR tests at the airport upon arrival was 14,893 with an average percentage of around 1% positivity for COVID-19. On the other hand, more than 10,687 repatriates underwent external PCR requisite in the third and fourth phases. Two hundred seventy-two repatriates were tested positive for COVID-19 upon their arrival. CONCLUSION: Considering the limited human and financial resources besides the economic and political crisis, the overall repatriation mission could be considered as a successful experience. Such processes would not have been achieved without the professionalism of all involved stakeholders.

Calculating the serial interval of SARS-CoV-2 in Lebanon using 2020 contact-tracing data.

INTRODUCTION: The first detected case in Lebanon on 21 February 2020 engendered implementation of a nationwide lockdown alongside timely contact-tracing and testing. OBJECTIVES: Our study aims to calculate the serial interval of SARS-CoV-2 using contact tracing data collected 21 February to 30 June 2020 in Lebanon to guide testing strategies. METHODS: rRT-PCR positive COVID-19 cases reported to the Ministry of Public Health Epidemiological Surveillance Program (ESU-MOH) are rapidly investigated and identified contacts tested. Positive cases and contacts assigned into chains of transmission during the study time-period were verified to identify those symptomatic, with non-missing date-of-onset and reported source of exposure. Selected cases were classified in infector-infectee pairs. We calculated mean and standard deviation for the serial interval and best distribution fit using AIC criterion. RESULTS: Of a total 1788 positive cases reported, we included 103 pairs belonging to 24 chains of transmissions. Most cases were Lebanese (98%) and male (63%). All infectees acquired infection locally. Mean serial interval was 5.24 days, with a standard deviation of 3.96 and a range of - 4 to 16 days. Normal distribution was an acceptable fit for our non-truncated data. CONCLUSION: Timely investigation and social restriction measures limited recall and reporting biases. Pre-symptomatic transmission up to 4 days prior to symptoms onset was documented among close contacts. Our SI estimates, in line with international literature, provided crucial information that fed into national contact tracing measures. Our study, demonstrating the value of contact-tracing data for evidence-based response planning, can help inform national responses in other countries.

Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon.

BACKGROUND: In December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases of unknown origin in the city of Wuhan, China. Presently, it has almost reached 94 million cases worldwide. Lebanon on the brink of economic collapse and its healthcare system thrown into turmoil, has previously managed to cope with the initial SARS-CoV-2 wave. In this study, we sequenced 11 viral genomes from positive cases isolated between 2 February 2020 and 15 March 2020. METHODS: Sequencing data was quality controlled, consensus sequences generated, and a maximum-likelihood tree was generated with IQTREE v2. Genetic lineages were assigned with Pangolin v1.1.14 and single nucleotide variants (SNVs) were called from read files and manually curated from consensus sequence alignment through JalView v2.11 and the genomic mutational interference with molecular diagnostic tools was assessed with the CoV-GLUE pipeline. Phylogenetic analysis of whole genome sequences confirmed a multiple introduction scenario due to international travel. RESULTS: Three major lineages were identified to be circulating in Lebanon in the studied period. The B.1 (20A clade) was the most prominent, followed by the B.4 lineage (19A clade) and the B.1.1 lineage (20B clade). SNV analysis showed 15 novel mutations from which only one was observed in the spike region.

The Association Between the Syrian Crisis and Cutaneous Leishmaniasis in Lebanon.

INTRODUCTION: Displacement of refugees from highly endemic areas of leishmaniasis to adjacent countries is associated with the spread of Leishmania. Syria is a country with a known high endemicity for cutaneous leishmaniasis and the presence of Syrian refugees in Lebanon has contributed to the re-emergence of the disease. The aim of this article is to evaluate the burden of cutaneous leishmaniasis in Lebanon in view of the presence of a large number of Syrian refugees. METHODS: Data regarding all cases of leishmaniasis were collected from reports by the Lebanese Ministry of Public Health-Epidemiology Surveillance (LMPH-ESU), and the World Health Organization (WHO) between 2005 and 2018. All cases were reviewed in terms of area of residence, age and gender, clinical presentation, treatment, and outcome. An extensive literature review was conducted using "PubMed", "Medline", and "Google Scholar". RESULTS: The annual number of leishmaniasis cases recorded in Lebanon between 2005 and 2011 ranged between 0 and 6 cases. In 2012, this number increased to 1275 cases and dropped to 263 in 2018, where all those infected were Syrian refugees from Aleppo, with zero cases of local transmission. Seventy-two percent of cases were seen in patients aged < 20 years. The predominant species of Leishmania was L. tropica followed by L. major. CONCLUSION: Lebanon was affected by leishmaniasis following the Syrian crisis, and the influx of refugees to the country. Accurate disease monitoring and strategic training of healthcare personnel based within refugee camps are essential for proper containment. Preventative measures remain the best way to avoid both local and adjacent spread of leishmaniasis.

PulseNet Lebanon: An Overview of Its Activities, Outbreak Investigations, and Challenges.

Background: Foodborne diseases are still a major health issue in Lebanon, although some steps have been taken forward in food safety. To this purpose, PulseNet Lebanon, a foodborne diseases tracking network, was established in 2009, through the collaboration between the Ministry of Public Health (MoPH) and the American University of Beirut (AUB). Materials and Methods: Three papers published regarding the PulseNet project were summarized. Initially, clinical and food samples, collected within the surveillance network scope, were identified by using the respective API for Salmonella and Listeria spp. Salmonella spp. were further serotyped by using the Kauffman and White method. Campylobacter spp. were determined by the 16 S rRNA sequencing method. Antimicrobial susceptibility to a number of antibiotics was determined by using the disk diffusion method for Samonella and Campylobacter spp. Genomic diversity was determined by using pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD). Results: Results indicated that 290 clinical and 49 food isolates were identified as Salmonella. Serotyping revealed the prevalence of ten and seven serotypes in the clinical and food samples, respectively. Fifty-one isolates from chicken ceca and carcass were identified to be Campylobacter spp. Fifty-nine samples were identified to be Listeria monocytogenes. Antimicrobial susceptibility testing revealed a wide range of resistance among the different samples. PFGE showed a variation in pulsotypes among the Salmonella serotypes. PFGE also linked certain outbreaks to their food sources. This method also demonstrated 13 subtypes with 100% similarity among the L. monocytogenes isolates. Finally, the Camplyobcater spp. were grouped into nine clusters with a minimum similarity of 43.5% using RAPD. Conclusion: This summary of results shows the importance of implementing a "farm-to-fork" approach in the surveillance of foodborne disease outbreaks in Lebanon, allowing the detection of pathogens causing foodborne disease outbreaks in a timely fashion.

Enhancing surveillance for early detection of Zika virus infection: strategies for the countries of Eastern Mediterranean Region.

BACKGROUND: Zika virus infection (ZIKV) has caused major outbreaks in tropic and sub-tropic areas. No case from ZIKV has yet been reported in the countries of the Eastern Mediterranean Region (EMR) despite the presence of competent vector Aedes mosquitoes in many of these countries. AIMS: This study addresses appropriate surveillance strategies for early detection of ZIKV infection, which is important for EMR countries with established Aedes populations, but with no known or documented autochthonous transmission of ZIKV. METHODS: The WHO Regional Office for the Eastern Mediterranean developed a strategic framework for enhancing surveillance for ZIKV infection in EMR countries with established Aedes populations through a consultative process and review of available evidence. RESULTS: The framework calls for enhancing surveillance for early detection of ZIKV infection using a combination of both syndromic and event-based surveillance approaches. CONCLUSIONS: Enhancing surveillance for ZIKAV would require no shift in the existing system. A number of considerations would be required to integrate this syndromic and event-based surveillance approaches within the existing system.