Cross-species spill-over potential of the H9N2 bat influenza A virus.

In 2017, a novel influenza A virus (IAV) was isolated from an Egyptian fruit bat. In contrast to other bat influenza viruses, the virus was related to avian A(H9N2) viruses and was probably the result of a bird-to-bat transmission event. To determine the cross-species spill-over potential, we biologically characterize features of A/bat/Egypt/381OP/2017(H9N2). The virus has a pH inactivation profile and neuraminidase activity similar to those of human-adapted IAVs. Despite the virus having an avian virus-like preference for α2,3 sialic acid receptors, it is unable to replicate in male mallard ducks; however, it readily infects ex-vivo human respiratory cell cultures and replicates in the lungs of female mice. A/bat/Egypt/381OP/2017 replicates in the upper respiratory tract of experimentally-infected male ferrets featuring direct-contact and airborne transmission. These data suggest that the bat A(H9N2) virus has features associated with increased risk to humans without a shift to a preference for α2,6 sialic acid receptors.

Role of research Laboratories in pandemic and epidemic response in the Eastern Mediterranean Region: Experiences from COVID-19, avian influenza, and MERS-CoV.

We share the experience of research laboratories in the Eastern Mediterranean Region (EMR) that contributed to preparedness and response to highly pathogenic avian influenza (HPAI), Middle-East respiratory syndrome coronavirus (MERS-CoV), and coronavirus disease (COVID-19). Research groups in the region were pivotal in identifying, characterizing the pathogens and describing their evolution, distribution, transmission routes, and the immunological profile of exposed populations. They demonstrated the capacity to develop and test antivirals and potential vaccines. The EMR experience is a model of how national systems can work with researchers to improve regional preparedness and response to future epidemics and pandemics.

Detection of Coronaviruses in Bats in Lebanon during 2020.

Bats are considered the main reservoir of coronaviruses (CoVs), and research evidence suggests the essential role of bats in the emergence of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoV) and SARS-CoV-2. SARS-CoV-like viruses have been recently detected in bats in different countries. In 2020, we conducted surveillance for CoVs among six different bat species in Lebanon. Of 622 swab specimens taken, 77 tested positive. Alpha- and Beta- CoVs were identified in samples collected from different species. Our results show that SARS-like coronaviruses circulate in bats in this region, and we provide new data on their genetic diversity. The interaction between the spike of the detected SARS-CoV-like viruses and the human angiotensin-converting enzyme 2 (hACE2) receptor could be crucial in understanding the origin of the epidemic. The 3D protein structure analysis revealed that the receptor-binding domains of the SARS-like virus identified in Lebanon bind to the hACE2 protein more efficiently than to the spike of the SARS-CoV-2 strain. The spike of the detected SARS-CoV-like viruses does not contain the recognition site of furin at the cleavage site. Thus, our study highlights the variety of bat coronaviruses in Lebanon and suggests the zoonotic potential for other SARS-CoV-like viruses.

State and situation of avian influenza in the Eastern Mediterranean Region.

Avian influenza viruses have had a significant burden of disease on animal and public health in countries of the Eastern Mediterranean Region. In this review, we aimed at describing the state of avian influenza in the region from 2011 to 2021. We gathered information available through the peer-reviewed scientific literature, public gene sequence depositories, OIE World Animal Health Information System platform, World Health Organization FluNet, Joint External Evaluation reports, and governmental, Food and Agriculture Organization of the United Nations, and World Organization for Animal Health websites. We used an interdisciplinary perspective consistent with the One Health approach to perform a qualitative synthesis and making recommendations. Analysis showed that although avian influenza research in the Eastern Mediterranean Region has gained more attention during the last decade, it was limited to only few countries and to basic science research. Data highlighted the weakness in surveillance systems and reporting platforms causing underestimation of the actual burden of disease among humans and animals. Inter-sectoral communication and collaboration for avian influenza prevention, detection, and response remain weak. Influenza surveillance at the human-animal interface and the application of the One Health paradigm are lacking. Countries' animal health and public health sectors rarely publish their surveillance data and findings. This review suggested that surveillance at the human-animal interface, research, and reporting capacities should be enhanced to improve understanding and control of avian influenza in the region. Implementing a rapid and comprehensive One Health approach for zoonotic influenza in the Eastern Mediterranean Region is recommended.

Designing and validating a One Health Research Translation Framework through literature-based case studies in Egypt.

Within One Health, research translation is a dynamic process involving collaboration and communication between the human, animal, and environmental health sectors to create and apply research findings to address health threats at the human-animal-environment interface. Research translation is essential for the creation of evidence-based policies and programs for the prevention and control of infectious diseases and other health threats, and thus is an important component of a robust national capacity to effectively prevent, control, and mitigate biological incidents. However, there is a lack of conceptual guidance and training materials for research translation in a One Health context. To address this need, we developed a novel One Health Research Translation Framework that describes an iterative process for research and policy stakeholders to collaborate to design and implement research applications addressing One Health zoonotic disease challenges. In addition, we developed accompanying training materials to validate the Framework and facilitate capacity building for understanding and applying research translation concepts to zoonotic disease threats. The training materials consist of exercises to map One Health communication pathways and literature-based case studies on research translation to address zoonotic disease concerns. The Framework and training materials were piloted with Egyptian One Health stakeholders at a workshop in Cairo in 2018. The outcomes of the workshop validated the comprehensiveness and applicability of the Framework and training materials, as participants were able to demonstrate a firm understanding of research translation processes and successfully apply research translation and One Health concepts to real-world zoonotic disease scenarios. Overall, the Framework and accompanying training materials address an important gap in capacity building for One Health stakeholders and are valuable tools for strengthening research translation networks that promote development of innovative, evidence-based solutions to One Health zoonotic disease threats.

Insights into Genetic Characteristics and Virological Features of Endemic Avian Influenza A (H9N2) Viruses in Egypt from 2017-2021.

From 2010 to 2013, genotype I avian influenza A(H9N2) viruses of the G1-lineage were isolated from several poultry species in Egypt. In 2014, novel reassortant H9N2 viruses were detected in pigeons designated as genotype II. To monitor the subsequent genetic evolution of Egyptian A(H9N2) viruses, we characterized the full genomes of 173 viruses isolated through active surveillance from 2017 to 2022. In addition, we compared the virological characteristics and pathogenicity of representative viruses. Phylogenetic analysis of the HA indicated that all studied sequences from 2017-2021 were grouped into G1-like H9N2 viruses previously detected in Egypt. Phylogenetic analysis indicated that the Egyptian A(H9N2) viruses had undergone further reassortment, inheriting four genes (PB2, PB1, PA, NS) from genotype II, with their remaining segments deriving from genotype I viruses (these viruses designated as genotype III). Studying the virological features of the two most dominant genotypes (I and III) of Egyptian H9N2 viruses in vitro and in vivo indicated that both replicated well in mammalian cells, but did not show any clinical signs in chickens, ducks, and mice. Monitoring avian influenza viruses through surveillance programs and understanding the genetic and antigenic characteristics of circulating H9N2 viruses are essential for risk assessment and influenza pandemic preparedness.

Prevalence and determinants of SARS-CoV-2 neutralizing antibodies in Lebanon.

According to the Lebanese Ministry of Public Health, more than 1,053,000 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been confirmed in Lebanon so far. The actual number of cases is likely to be higher. We conducted a serological study from October 2020 to April 2021 to estimate the prevalence of SARS-CoV-2 neutralizing antibodies and identify associated factors. Serum samples as well as demographic, health, and behavioral data were collected from 2,783 subjects. Sera were tested by microneutralization assay. Neutralizing antibodies were detected in 58.9% of the study population. The positivity rate increased over the study period. It was highest among the group who remained at work during the COVID-19 pandemic and in peri-urban areas with limited adherence to preventive measures. Sex and age were associated with positivity. Reported previous COVID-19, exposure to a COVID-19 patient in the family, and attending gatherings were associated with increased prevalence. Not taking any precautionary measures against COVID-19 was a risk factor, whereas precautionary measures such as working from home and washing hands were protective. The high neutralizing antibody seroprevalence rates detected in this study emphasize the high transmission rate of SARS-CoV-2 infection in the community. Adherence to preventive measures and non-pharmaceutical interventions imposed by the government is recommended.

Incidence and seroprevalence of seasonal influenza a viruses in Egypt: Results of a community-based cohort study.

BACKGROUND: H1N1 and H3N2 influenza A viruses circulate in people as seasonal influenza viruses. Data on influenza infection rates and circulation in demographic subpopulations in Egypt are limited. In this study, we aimed to determine the incidence and seroprevalence of seasonal influenza A virus infections in a cohort of rural Egyptians between 2017 and 2020. METHODS: A total of 2383 subjects were enrolled from 390 households in five study sites in Northern Egypt. Informed consents were obtained. Sera were collected from participants on an annual basis (Baseline: 2016-2017, Follow up 1: 2017-2018, Follow up 2: 2018-2019, and Follow up 3: 2019-2020) to determine seroprevalence of antibodies against H1N1 and H3N2 viruses by hemagglutination inhibition assay and to estimate incidence based on seroconversion. RESULTS: Seropositivity against H1N1 was over 40% and over 60% against H3N2. The high seroprevalence was due to natural infection because participants were mostly unvaccinated. Seropositive participants were younger than seronegative participants indicating that the infection rate is higher in children. Incidence of both viruses ranged from 4% to 28% depending on study year. The incidence and seroprevalence of H3N2 and H1N1 infections at Follow up 1, 2, and 3 showed an increase at Follow up 2 observed for all age categories corresponding to season 2018-2019, at which the vaccine efficacy was the lowest worldwide compared with preceding and following seasons. CONCLUSIONS: This cohort study provided estimates of influenza A infection rates among rural Egyptians. We recommend updating influenza vaccination programs to focus on such populations.

Avian influenza surveillance at the human-animal interface in Lebanon, 2017.

BACKGROUND: Avian influenza viruses (AIVs) cause severe diseases in poultry and humans. In Lebanon, AIV H9N2 was detected in 2006 and 2010 and H5N1 was detected in 2016. AIM: To evaluate the current circulating AIVs in Lebanon at the human-animal interface. METHODS: A total of 1000 swabs were collected from poultry from 7 Lebanese governorates between March and June 2017. Swabs were screened for influenza infection. Haemagglutinin and neuraminidase AIV subtypes were determined for positive samples. Gene segments were cloned and sequenced. Blood was collected from 69 exposed individuals. Serological studies were performed to test sera for antibodies against AIV. RESULTS: In chickens, 0.6% were positive for AIV H9N2. Sequences obtained clustered tightly with those of Israeli origin as well as Lebanese H9N2 viruses from 2010. All human samples tested negative. CONCLUSION: We recommend regular surveillance for AIVs in poultry using a One Health approach.

Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016-2018.

Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016-2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.

Co-infection with different serotypes of FMDV in vaccinated cattle in Southern Egypt.

During 2015-2016 period, an outbreak of foot-and-mouth disease virus (FMDV) was observed in cattle in four governorates of the upper of Egypt. The infection was extended to the vaccinated cattle. A total of 54 mouth swabs and serum samples were collected from vaccinated cattle for serological and virological investigation. The typical clinical signs of FMDV infection were observed in all cattle under investigation. All samples were positive for FMDV using molecular methods, while the serological method showed 85% positive of tested samples. Typing of FMDV-positive samples using serotype-specific primers showed that 51.8% of samples were serotype O, 9.2% were serotype A, and 18.5% were SAT 2. Surprisingly, co-infections of serotypes A/SAT 2 (12.9%) and O/SAT 2 (7.4%) were also detected. By geographical location, the 3 serotypes A, O, and SAT2 were detected in all four governorates. The phylogenetic assessment of the detected viruses showed that two distinct groups of FMDV serotype O of East Africa-3 (EA-3) topotype were most closely related to circulating viruses in Sudan, as well as FMDV strains belonging to the topotype VII of serotype SAT 2. The detected SAT 2 strains clustered in separate clades in topotype VII, indicating new incursions. The VP1 signatures and protein sequences of some characterized viruses were analyzed. Multiple mutations were detected in VP1. Therefore, to enhance the control of FMD in Egypt, we recommend establishing an active surveillance system to characterize newly emerging virus strains/serotypes and subsequently updating vaccine strains.

BRCA mutation screening and patterns among high-risk Lebanese subjects.

BACKGROUND: Previous studies have suggested that the prevalence of BRCA1 and 2 mutations in the Lebanese population is low despite the observation that the median age of breast cancer diagnosis is significantly lower than European and North American populations. We aimed at reviewing the rates and patterns of BRCA1/2 mutations found in individuals referred to the medical genetics unit at the American University of Beirut. We also evaluated the performance of clinical prediction tools. METHODS: We retrospectively reviewed the cases of all individuals undergoing BRCA mutation testing from April 2011 to May 2016. To put our findings in to context, we conducted a literature review of the most recently published data from the region. RESULTS: Two-hundred eighty one individuals were referred for testing. The prevalence of mutated BRCA1 or 2 genes were 6 and 1.4% respectively. Three mutations accounted for 54% of the pathogenic mutations found. The BRCA1 c.131G > T mutation was found among 5/17 (29%) unrelated subjects with BRCA1 mutation and is unique to the Lebanese and Palestinian populations. For patients tested between 2014 and 2016, all patients positive for mutations fit the NCCN guidelines for BRCA mutation screening. The Manchester Score failed to predict pathogenic mutations. CONCLUSION: The BRCA1 c.131G > T mutation can be considered a founder mutation in the Lebanese population detected among 5/17 (29%) of individuals diagnosed with a mutation in BRCA1 and among 7/269 families in this cohort. On review of recently published data regarding the landscape of BRCA mutations in the Middle East and North Africa, each region appears to have a unique spectrum of mutations.

A novel cystic fibrosis gene mutation c.2490insT in a Palestinian patient: A case report and review of the literature.

We report the case of a 19-year-old male patient of Palestinian descent, who presented with a 1-year history of recurrent Pseudomonas aeruginosa respiratory infections, weight loss, chronic diarrhea, and a normal chloride sweat test. A panel for common cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations test was also negative. Cystic fibrosis (CF) was still clinically suspected thus, full CFTR gene sequencing was performed, which revealed a homozygous unreported mutation c.2490insT (GenBank accession number: BankIt2019289 seq1 MF167456). Both parents were also found to be heterozygous for this mutation. This case highlights the importance of clinical evaluation and the need for extensive genetic investigation when dealing with a genetic disease with wide variability in a clinical presentation such as CF.

Genotype/Phenotype Correlation in Primary Congenital Glaucoma Patients in the Lebanese Population: A Pilot Study.

BACKGROUND: The incidence of primary congenital glaucoma (PCG) varies among geographic regions and ethnic groups. The frequency of PCG in Lebanon and identification of disease-causing mutations have not been studied previously. PURPOSE: To investigate the role of Cytochrome P1B1 (CYP1B1) gene and Myocillin (MYOC) gene mutations in PCG in the Lebanese population and study possible genotype/phenotype correlations. METHODS: Patients with unilateral or bilateral PCG diagnosed at the American University of Beirut Medical Center and their first-degree relatives (parents and siblings) were screened for CYP1B1 and MYOC mutations. Demographic and phenotypic characteristics were recorded. Phenotypic characteristics pertaining to disease severity and outcomes were compared. RESULTS: Eighteen Lebanese families (66 subjects) with at least one member affected with PCG were included in this study. Mutations in the CYP1B1 gene were detected in 6 families (33%). Five previously described mutations (p.R444Q; p.E229K; p.R469W; p.G61E; p.M1T) and one new single nucleotide deletion were identified (1793delC). Patients in whom CYP1B1 mutations were detected tended to have a more severe phenotype as evidenced by earlier age at diagnosis, higher rate of bilateral disease, and higher number of glaucoma surgeries than those in whom no CYP1B1 mutations were present. MYOC gene mutations were not detected in any patients. CONCLUSION: The rate of CYP1B1 mutations in Lebanese patients with PCG is lower than that reported in other Arab and Middle Eastern populations and suggests other genes are responsible for PCG in the remainder.

Ellis-van Creveld Syndrome: Mutations Uncovered in Lebanese Families.

Background. Ellis-van Creveld (EvC) syndrome is a rare, autosomal recessive disorder characterized by short stature, short limbs, growth retardation, polydactyly, and ectodermal defects with cardiac anomalies occurring in around 60% of cases. EVC syndrome has been linked to mutations in EVC and EVC2 genes. Case Presentation. We report EvC syndrome in two unrelated Lebanese families both having homozygous mutations in the EVC2 gene, c.2653C>T (p.(Arg885(*))) and c.2012_2015del (p.(Leu671(*))) in exons 15 and 13, respectively, with the latter being reported for the first time. Conclusion. Although EvC has been largely described in the medical literature, clinical features of this syndrome vary. While more research is required to explore other genes involved in EvC, early diagnosis and therapeutic care are important to achieve a better quality of life.

Incidence of alpha-globin gene defect in the Lebanese population: a pilot study.

BACKGROUND: It is well established that the Mediterranean and Arab populations are at high risk for thalassemias in general and for alpha-thalassemia in particular. Yet, reports on alpha-thalassemia in Lebanon are still lacking. In this study, we aim at assessing the incidence of alpha-thalassemia in the Lebanese population. METHODS: 230 newborns' dried blood cards remaining from routine neonatal screening at the American University of Beirut Medical Center were collected for DNA extraction. Samples were screened for the 21 most common α-globin deletions and point mutations reported worldwide, through multiplex Polymerase Chain Reaction (PCR) and Reverse-Hybridization technique. RESULTS: Upon analyses, the carrier rate of α-thalassemia was found to be 8%. Two mutations detected the -α(3,7) single gene deletion found in 75% of cases and the nongene deletion α2 IVS1 [-5nt] in the remaining samples. CONCLUSION: This study is the first dedicated to investigate α-thalassemia trait incidence in Lebanon. Data obtained demonstrates a high carrier rate in a relatively, highly consanguineous population; it also highlighted the presence of two common mutations. These results may be of an important impact on premarital and newborn screening policies in our country.

Alpha thalassemia allelic frequency in Lebanon.

BACKGROUND: Hemoglobinopathies are the most common reported monogenic disorders worldwide. It is well established that Mediterranean and Arab countries are high risk areas for thalassemia in general, and for alpha thalassemia in particular. Reports of alpha thalassemia gene mutations from the Lebanese population are limited. PROCEDURE: We investigated the spectrum of alpha thalassemia mutations in a sample of 70 unrelated Lebanese families. Six different mutations of alpha thalassemia gene were identified. RESULTS: The most prevalent mutations were the single gene deletion -α(3.7) (43%) and the non-gene deletion α2 IVS1 [-5nt] (37%). The double deletional determinant -(MED) was detected only in 14% of thalassemic chromosomes. CONCLUSION: We determined the mutational spectrum of alpha thalassemia which might be used in the future for molecular investigations of the disease in susceptible patients in our population.