Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens

Our knowledge of the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes of this diversity remain elusive in the eukaryotic viromes of terrestrial animals. This situation hinders hypothesis-driven tests of virome influence on host physiology. Here, we compare taxonomic diversity between different spatial scales in the eukaryotic virome of the mosquito Culex pipiens. This mosquito is a vector of human pathogens worldwide. The experimental design involved sampling in five countries in Africa and Europe around the Mediterranean Sea and large mosquito numbers to ensure a thorough exploration of virus diversity. A group of viruses was found in all countries. This core group represented a relatively large and diverse fraction of the virome. However, certain core viruses were not shared by all host individuals in a given country, and their infection rates fluctuated between countries and years. Moreover, the distribution of coinfections in individual mosquitoes suggested random co-occurrence of those core viruses. Our results also suggested differences in viromes depending on geography, with viromes tending to cluster depending on the continent. Thus, our results unveil that the overlap in taxonomic diversity can decrease with spatial scale in the eukaryotic virome of C. pipiens. Furthermore, our results show that integrating contrasted spatial scales allows us to identify assembly patterns in the mosquito virome. Such patterns can guide future studies of virome influence on mosquito physiology.

Prevalence and Patterns of EGFR Mutations in Non-small Cell Lung Cancer in the Middle East and North Africa

Objectives

This study aims to analyze the prevalence and spectrum of epidermal growth factor receptor (EGFR) mutations within the Middle East and North Africa region, compare the findings to other parts of the world, and explore the geographic disparities of EGFR mutations across the region.

Methods

We conducted a literature search using the terms “[EGFR] AND [mutation] AND [Non-Small Cell Lung Cancer] AND [Middle East OR North Africa]”, using PubMed, Science Direct, Web of science, Embase, Scopus, and Google scholar.

Results

A total of 15 eligible studies were included and 6122 patients with non-small cell lung cancer (NSCLC) were analyzed. Male patients were predominant in all of the considered studies, accounting for 70.4%. Of the included patients, 65.6% were smokers and 88.3% had been diagnosed with adenocarcinoma. Overall, EGFR mutations prevalence was 17.2%. In the Middle East, the reported frequency was 16.5%, ranging from 11.3% in Lebanon to 29.7% in the Gulf region. In North Africa, the prevalence of EGFR mutations was 18%, ranging from 17.5% in Egypt to 21.5% in Morocco. The most prevalent mutations were the exon 19 deletions (46.7%) followed by exon 21 substitutions (31.1%). Exon 20 alterations were detected in 10.8% of the analyzed cases, whereas exon 18 mutations were reported in 3.4% of the EGFR-mutated patients. There was 1.1% of patients that had concurrent EGFR mutations. Overall, EGFR mutation prevalence was higher in females [females vs males: 29.7% vs 5.9%, P<.001], non-smokers [non-smokers vs smokers: 31.3% vs 9.6%, P<.001], and patients with adenocarcinoma [adenocarcinoma vs non-adenocarcinoma: 18.8% vs 6.5%, P<.001].

Conclusion

EGFR mutation prevalence among the Middle East and North Africa populations is slightly higher than that seen in NSCLC patients of Caucasian ethnicity but is lower than that identified in Asian NSCLC patients. The distribution of these mutations varies considerably throughout the region.

Identification of a novel pathogenic variant in PALB2 and BARD1 genes by a multigene sequencing panel in triple negative breast cancer in Morocco

Pathogenic variants (PVs) in BRCA genes have been mainly associated with an increasing risk of triple negative breast cancer (TNBC). The contribution of PVs in non-BRCA genes to TNBC seems likely since the processing of homologous recombination repair of double-strand DNA breaks involves several genes. Here, we investigate the susceptibility of genetic variation of the BRCA and non-BRCA genes in 30 early-onset Moroccan women with TNBC. Methods: Targeted capture-based next generation sequencing (NGS) method was performed with a multigene panel testing (MGPT) for variant screening. Panel sequencing was performed with genes involved in hereditary predisposition to cancer and candidate genes whose involvement remains unclear using Illumina MiSeq platform. Interpretation was conducted by following the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) criteria. Results: PVs were identified in 20% (6/30) of patients with TNBC. Of these, 16.7% (5/30) carried a BRCA PV [10% (3/30) in BRCA1, 6.7% (2/30) in BRCA2] and 6.6% (2/30) carried a non-BRCA PV. The identified PVs in BRCA genes (BRCA1 c.798_799delTT, BRCA1 c.3279delC, BRCA2 c.1310_1313del, and BRCA2 c.1658T>G) have been reported before and were classified as pathogenic. The identified founder PVs BRCA1 c.798_799del and BRCA2 c.1310_1313delAAGA represented 10% (3/30). Our MGPT allowed identification of several sequence variations in most investigated genes, among which we found novel truncating variations in PALB2 and BARD1 genes. The PALB2 c.3290dup and BARD1 c.1333G>T variants are classified as pathogenic. We also identified 42 variants of unknown/uncertain significance (VUS) in 70% (21/30) of patients with TNBC, including 50% (21/42) missense variants. The highest VUS rate was observed in ATM (13%, 4/30). Additionally, 35.7% (15/42) variants initially well-known as benign, likely benign or conflicting interpretations of pathogenicity have been reclassified as VUS according to ACMG-AMP. Conclusions: PALB2 and BARD1 along with BRCA genetic screening could be helpful for a larger proportion of early-onset TNBC in Morocco.

Identification of Eilat virus and prevalence of infection among Culex pipiens L. populations, Morocco, 2016

Eilat virus (EILV) is described as one of the few alphaviruses restricted to insects. We report the record of a nearly-complete sequence of an alphavirus genome showing 95% identity with EILV during a metagenomic analysis performed on 1488 unblood-fed females and 1076 larvae of the mosquito Culex pipiens captured in Rabat (Morocco). Genetic distance and phylogenetic analyses placed the EILV-Morocco as a variant of EILV. The observed infection rates in both larvae and adults suggested an active circulation of the virus in Rabat and its maintenance in the environment either through vertical transmission or through horizontal infection of larvae in breeding sites. This is the first report of EILV out of Israel and in Culex pipiens populations.

Consumption of antibacterial molecules in broiler production in Morocco

Monitoring the use of antibacterial agents in food-producing animals is crucial in order to reduce antimicrobial resistance, selection and dissemination of resistant bacterial strains, and drug residues in the animal food products. The broiler production sector is considered a great consumer of antibacterials and incriminated in the rise of antimicrobial resistance level in zoonotic bacterial pathogens such as Escherichia coli, Salmonella and Campylobacter. Following recommendations from the OIE and WHO, a survey was conducted about the use and consumption of several antibacterial agents in Moroccan broiler flocks. More than 5 million broilers were randomly surveyed at the prescriber level, that is, via the veterinary clinics involved in their health management. The results showed that 93% of the flocks received at least one antibacterial treatment of minimum 3 days duration. Enrofloxacin, colistin and trimethoprim/sulphonamides were the most used antibacterials followed by oxytetracycline, florfenicol and amoxicillin. Oxytetracycline, enrofloxacin and colistin were overdosed in most of the administration, while amoxicillin and the combination of trimethoprim/sulphonamides were under-dosed. The total amount of antibacterial consumed in the survey was 63.48 mg/kg and the Animal Level of Exposure to Antimicrobials (ALEA) was 94.45%. The reasons for this frequent use were related mainly to the poor quality of broiler production management. Chicks and animal feed provided to producers were of variable quality. Management of rearing stock density was often poor and biosecurity inadequate, and broilers were challenged by a high prevalence of infectious diseases.

Serological evidence of West Nile Virus infection among humans in the southern Provinces of Morocco

Introduction: The objective of this study was to determine the prevalence of West Nile Virus infection in the southern provinces of Morocco. Methodology: A total of 250 sera, collected during 2012 in the province of Dakhla, were analyzed by microneutralisation assay. Results: WNV-neutralizing antibodies were detected in 13 samples (5.2%). The participants with WNV-specific antibodies were significantly younger than the rest of the population (p = 0.009). The positivity rate was higher among women (6.3%) than men (3.6%) (p = 0.26). Conclusions: This is the first serological evidence of WNV infection among humans in the southern provinces of Morocco.

Evolution of the hemagglutinin gene of the influenza A(H1N1)pdm09 virus in Morocco during two influenza seasons 2009-2011

To study genetic evolution of Moroccan influenza A(H1N1)pdm09 virus strains, we conducted a molecular characterization of the hemagglutinin gene subunit 1 (HA1) of 36 influenza A(H1N1)pdm09 virus strains. The stains were collected from patients in Rabat and Casablanca during two influenza seasons 2009-2010 and 2010-2011. Nucleotide and amino acid sequences of 14 influenza A(H1N1)pdm09 virus strains from 2009 to 2010 were ~97 and 99 %, respectively, similar to the reference strain A/California/07/2009 (H1N1). Phylogenetic analysis of 22 influenza A(H1N1)pdm09 virus strains from 2010 to 2011 revealed a co-circulation of three well-described different genetic groups. Most important, none of the identified groups showed significant changes at the antigenic site of the virus HA1 subunit which may alter the efficacy of California/07/2009 (H1N1) vaccine.

Mutation screening of the BRCA1 gene in early onset and familial breast/ovarian cancer in Moroccan population

Worldwide variation in the distribution of BRCA mutations is well recognised, and for the Moroccan population no comprehensive studies about BRCA mutation spectra or frequencies have been published. We therefore performed mutation analysis of the BRCA1 gene in 121 Moroccan women diagnosed with breast cancer. All cases completed epidemiology and family history questionnaires and provided a DNA sample for BRCA testing. Mutation analysis was performed by direct DNA sequencing of all coding exons and flanking intron sequences of the BRCA1 gene. 31.6 % (6/19) of familial cases and 1 % (1/102) of early-onset sporadic (< 45 years)were found to be associated with BRCA1 mutations. The pathogenic mutations included two frame-shift mutations (c.798_799delTT, c.1016dupA), one missense mutation (c.5095C>T),and one nonsense mutation (c.4942A>T). The c.798_799delTT mutation was also observed in Algerian and Tunisian BC families, suggesting the first non-Jewish founder mutation to be described in Northern Africa. In addition, ten different unclassified variants were detected in BRCA1, none of which were predicted to affect splicing. Most unclassified variants were placed in Align-GVGD classes suggesting neutrality. c.5117G>C involves a highly conserved amino acid suggestive of interfering with function (Align-GVGD class C55), but has been observed in conjunction with a deleterious mutation in a Tunisian family. These findings reflect the genetic heterogeneity of the Moroccan population and are relevant to genetic counselling and clinical management. The role of BRCA2 in BC is also under study.