Genome sequencing of severe acute respiratory syndrome COVID-19 EF.1 variant strain obtained from a Moroccan patient

Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome COVID-19 (SARS-CoV-2) strain obtained from a Moroccan patient. The detected strain EF.1 belongs to the BQ1.1 subvariant of the BA.5 Omicron variant.

TYK2, IFITM3, IFNAR2 and OAS3 single-nucleotide polymorphisms among severe COVID-19 ICU patients in Morocco

OBJECTIVES

This study aimed to explore the potential correlation between specific single nucleotide polymorphisms (TYK2, IFITM3, IFNAR2, and OAS3 variants) and the severity of COVID-19 in Moroccan patients.

METHODS

A genetic analysis was conducted on 109 patients with PCR-confirmed SARS-CoV-2 infection in Morocco. Among these patients, 46% were hospitalized in the intensive care unit, while 59% were not hospitalized. Importantly, all patients lacked known risk factors associated with COVID-19 severity. Genotyping was performed to identify variations in TYK2 rs74956615, IFITM3 rs12252, IFNAR2 rs2236757, and OAS3 rs10735079. Statistical analysis was applied using codominant, dominant and recessive logistic regression models to assess correlations with COVID-19 severity.

RESULTS

Our findings revealed no significant correlation between TYK2 rs74956615, IFITM3 rs12252, IFNAR2 rs2236757, and OAS3 rs10735079 with COVID-19 severity in Moroccan patients, as indicated in logistic regression models (p > .05). Interestingly, these results may offer insights into the mitigated impact of the COVID-19 pandemic and the reduced severity observed in SARS-CoV-2 infected patients in Morocco. Age, however, exhibited a significant correlation with severity (p < .001), with a trend towards increased likelihood of ICU admission with advancing age. Additionally, In the severe group, a higher proportion of patients were females (54%), indicating a statistically significant correlation with disease severity (p = .04). Nevertheless, female ICU patients aged above 60 years accounted for 37%, compared to 17% for males.

CONCLUSION

This study underscores the absence of a genetic association between the selected polymorphisms and COVID-19 severity in Moroccan patients. Advanced age emerges as the primary factor influencing the severity of COVID-19 patients without comorbidities. We recommend setting the threshold for advanced age at 60 years as a risk factor for severe forms of COVID-19.

Neutralising antibodies against SARS-CoV-2 give important information on Covid-19 epidemic evolution in Rabat, Morocco, March 2020-February 2021

Background

The SARS-CoV-2 is an extremely contagious and acute viral disease mainly affecting humans.

Objective

To estimate seroprevalence of SARS-CoV-2 neutralizing antibodies (NAbs) for illegible armed force individuals living in Rabat, Morocco.

Method

A convenience sample (N = 2662) was conducted from May 2020 to February 2021. We used the standard neutralization assay to quantify the NAbs titers. A serum was positive when the titer was 1:4. High positive NAbs titers were defined when ≥ 1:32.

Results

Demographic and socioeconomic status did not affect seroprevalence data. An overall seroprevalence of 24,9% was found. Sera from blood donors, young recruits and auto-immune population had lower NAbs titers. However, titers were above 1:16 in 9% of the population with high risk of SARS-CoV-2 exposure. Seropositivity increased over time with values reaching peaks after the epidemic waves (2.4% in May 2020; 16.2% in August 2020; 22.7% in December 2020 and 37% in February 2021).

Conclusion

And increase of NAbs was observed over time and correlated with the post-epidemic waves of COVID-19 in Morocco.

Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2

Here, we present the complete coding sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains that were recovered from a nasopharyngeal swab from a female patient and the second viral passage in cell culture. After testing, both strains were identified as BA.5.2.20, a subvariant of Omicron.

Novel nanostructure-coupled biosensor platform for one-step high-throughput quantification of serum neutralizing antibody after COVID-19 vaccination

COVID-19 vaccination efficacy depends on serum levels of the neutralizing antibodies (NAs) specific to the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Therefore, a high-throughput rapid assay capable of measuring the total SARS-CoV-2 NA level is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, vaccine development, and assessment. Here, we developed a novel nanoplasmonic immunosorbent assay (NanoPISA) platform for one-step rapid quantification of SARS-CoV-2 NAs in clinical serum samples for high-throughput evaluation of COVID-19 vaccine effectiveness. The NanoPISA platform enhanced by the use of nanoporous hollow gold nanoparticle coupling was able to detect SARS-CoV-2 NAs with a limit of detection of 0.2 pM within 15 min without washing steps. The one-step NanoPISA for SARS-CoV-2 NA detection in clinical specimens yielded good results, comparable with those obtained in the gold-standard seroneutralization test and the surrogate virus-neutralizing enzyme-linked immunosorbent assay. Collectively, the one-step NanoPISA might be a rapid and high-throughput NA-quantification platform for evaluating the effectiveness of COVID-19 vaccines.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

Genome Sequences of the Delta Variant (B.1.617.2) and the Kappa Variant (B.1.617.1) Detected in Morocco

Here, we report the identification and coding-complete genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from patients with COVID-19. The strains identified belong to variant of concern B.1.617.2 and variant of interest B.1.617.1.

Update on the resistance of Escherichia coli isolated from urine specimens in a Moroccan hospital: a review of a 7-year period

Introduction

Escherichia coli is the most commonly isolated species in both community and healthcare-associated infections. Our study's purpose was to determine the rates of antibiotic resistance of E. coli isolates in hospital and community populations, track the kinetics of resistance rates of E. coli isolates to major antibiotics, particularly those prescribed for urinary tract infections and study the occurrence and evolution of multi-resistant phenotypes.

Methods

We conducted a retrospective study at the Bacteriological Department of the Mohammed V Military Hospital of Instruction, over a period of 7 years. All isolates of E. coli from inpatients and outpatients were included. Identification of bacterial isolates was based on culture, morphological and biochemical identification characteristics. Antibiotic susceptibility was studied using the Mueller Hilton agar diffusion method by using OXOID® type antibiotic discs and interpreted according to the recommendations of EUCAST/CA-SFM 2019.

Results

The rate of resistance of E. coli isolates to 3^rd generation cephalosporins, imipenem and fluoroquinolones was 12%, 1% and 34%, respectively. The difference between the resistance rates of inpatient and outpatient E. coli isolates was statistically significant for most antibiotics (p<0.05). The rate of extended-spectrum beta-lactamase phenotype (ESBL) was 6.73%. The carbapenemase phenotype was 1.25%. The ESBL phenotype rate increased from 3% in 2012 to 11.16% in 2018.

Conclusions

The progression of the ESBL phenotype in both hospital and community settings, due to the increase in the resistance rate to 3^rd generation cephalosporin, is prompting a review of the strategy for the therapeutic management of urinary tract infections with these molecules as probabilistic treatment.

Complete Genome Sequence of a SARS-CoV-2 Strain Sampled in Morocco in May 2020, Obtained Using Sanger Sequencing

The complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain was obtained. The strain was isolated from a nasopharyngeal swab specimen from a female patient in Rabat, Morocco, with coronavirus disease 2019 (COVID-19). This strain belongs to clade 20A and has 12 mutations and 8 amino acid substitutions compared to the reference strain Wuhan/Hu-1/2019.

Early screening of autism spectrum disorder in general and pediatric practices, nurseries and early child care centers: Kitcat french study protocol using a two-stage procedure

Introduction

Early screening of children at-risk to develop Autism Spectrum Disorder (ASD) needs to be improved to propose early interventions. This detection should allow diagnosis of ASD before the age of 3. An early screening performed at the general practitioner of the family should facilitate accessibility to diagnosis and a better collaboration between professionals.

Objectives

Our primary objective is to estimate the positive predictive value of an early detection kit composed of 2 questionnaires (First screening: M-CHAT-R/F™ + CSBS DP™-ITC) and a confirmation of the detection with a phone call by a neuropsychologist. Patients with confirmed positive M-CHAT-R/F™ and/or CSBS DP™-ITC scores are referred to a level 2 team for pre-diagnosis and diagnosis assessment.

Methods

The KitCAT study is a cohort study of 1,700 children aged 16 to 24 months seen in routine care in general or pediatric practices, or in nurseries and child care centers.

Results

Seven hundred and five children have already been enrolled in the study. Twenty nine patients, ie 4.1%, (with a confirmed positive M-CHAT-R/F™ and/or CSBS DP™-ITC scores) were referred to a level 2 team where a pre-diagnosis assessment was conducted by using the following test: ADI-R, ADOS 2, BLR, WPPSI-IV and Vineland II. The diagnosis of ASD (using the same test than the pre-diagnosis) was confirmed for the first two patients aged of 3.

Conclusions

The preliminary results confirm that the use of 2 questionnaires may optimize the reliability of the screening. A thousand children are still needed for the final analysis and further results are expected.

Disclosure

No significant relationships.

A french adaptation of the vineland adaptive behavior scales VABS-II

Introduction

For populations with intellectual disability and autism spectrum disorder, it is essential to complete cognitive assessment with an adaptive behavior scale.

Objectives

To translate VABS-II from English to French and establish norms for the French population.

Methods

We used the Parent/Caregiver form in order to assess psychometric characteristics of the VABS-II and to develop norms for the French population. VABS-II comprises 4 domains, 11 subdomains, and an optional maladaptive behavior index. The French translation of the VABS-II followed standard cross-cultural translation methods. The study was performed in the Rhône-Alpes-Auvergne department comprising 12 % of France inhabitants and well representing the French general population.

Results

From 4576 VABS-II questionnaires distributed, 1707 were returned and 1654 were analyzed. The reason for exclusion was the impossibility to score one of the subdomains. From 174 questionnaires included in the test-retest, 95 were analyzed, and 79 questionnaires were excluded because 86 under 34 days, 8 > 3 months, and one participant that changed age group between test and retest. Scores based on French norms fluctuated around values based on US norms on all subdomains.

Conclusions

The French Vineland questionnaire is the single test with the adequate norms to allow identifying children with adaptive behavior difficulties. It should be used as a complement of the assessment of the intellectual quotient, according to DSM V, for the diagnosis of intellectual disabilities. It must be done in reference to the developmental and cultural standards specific to the environment in which the person is evolving.

Disclosure

No significant relationships.

Role of multidimensional evaluations in the support of school trajectories of children with mild to moderate intellectual disability

Introduction

There is a lack of objective evaluation with validated tools in school children with intellectual disability (ID). Standardized and validated tools, allowing children evaluations and follow-up, exist but are poorly used. Our action-study wishes to develop evaluation practices to better adapt to the specific needs of children with ID.

Objectives

We evaluated the multidimensional profiles (cognitive, adaptative and behavioral) of children with ID attending regular or adapted school system.

Methods

School children, aged 5 to 13 years old, with mild to moderate ID were enrolled in this French cohort study. The multidimensional evaluation consisted of a school evaluation grid proposed by the French educational system, a scale of school needs (GEVA-sco), an intellectual assessment (WISC IV), a behavior adaptative scale (Vineland II) and a behavior rating scale (the French Nisonger Child Behavior Rating Form (Nisonger CBRF)). The results of this multidimensional assessment were analyzed.

Results

Between November 2014 and June 2016, 121 children were enrolled, 3 children were lost to follow-up. Analysis was performed on 118 children. Seventy one (60.2 %) were male. Fifty-two (44.1%) were aged 6 to 9 years. Sixty-eight (57.6%) children were in regular schools and 50 (42.4%) in adapted schools. Children in regular schools had a higher mean IQ score (57.5) than children in adapted schools (43.5). The adaptative behavior profile of children in regular school is less severe than in children in adapted schools.

Conclusions

Multidimensional evaluations allow optimizing and personalizing support. Evaluation of adaptative behavior is more informative than cognitive profile which does not differentiate between children skills

Disclosure

No significant relationships.

Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment

The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.

BCG vaccine: a hope to control COVID-19 pandemic amid crisis

COVID-19 caused by the virus SARS-CoV-2 has gripped essentially all countries in the world, and has infected millions and killed hundreds of thousands of people. Several innovative approaches are in development to restrain the spread of SARS-CoV-2. In particular, BCG, a vaccine against tuberculosis (TB), is being considered as an alternative therapeutic modality. BCG vaccine is known to induce both humoral and adaptive immunities, thereby activating both nonspecific and cross-reactive immune responses in the host, which combined could effectively resist other pathogens including SARS-CoV-2. Notably, some studies have revealed that SARS-CoV-2 infectivity, case positivity, and mortality rate have been higher in countries that have not adopted BCG vaccination than in countries that have done so. This review presents an overview of the concepts underlying BCG vaccination and its nonspecific immuological effects and protection, resulting in 'trained immunity' and potential utility for resisting COVID-19.

Evidence for zoonotic transmission of species A rotavirus from goat and cattle in nomadic herds in Morocco, 2012-2014

Species A rotaviruses (RVAs) are a leading cause of diarrhea in children and in the young of a large variety of mammalian and avian host species. The purpose of this study was to identify RVA in nomadic goats and calves during severe diarrhea outbreaks in 2012 and 2014 in Bouaarfa, Morocco, and to characterize the complete genomic constellation of two bovine and caprine strains (S18 and S19) and their genetic relatedness with the human strain ma31 detected in 2011 in Morocco. Partial nucleotide sequencing of VP4 and VP7 genes for the twenty-two positive samples revealed three circulating genotypes: G6P[14], G10P[14], and G10P[5] with predominance of G6P[14] genotype. Full-genome sequencing for both strains S18 and S19 presented, respectively, the following genomic constellations: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3. Phylogenetic analyses and the analysis of the VP8* antigenic epitopes for S18, S19 and ma31 revealed a shared similarity with bovine, caprine, ovine and human strains from Morocco and other countries. The VP2 and NSP1 genes of the S19 strain were closely related to those of the cognate genes of the human ma31 strain, while the VP4 gene of S18 strain was closely related to the cogent gene of the ma31 strain. Our findings revealed cases of zoonotic transmission and confirmed the risk of emergence of new genotypes in some environments such as nomadic regions, where close physical proximity between human and livestock is common. The present study is novel in reporting whole-genome analyses of RVA isolates obtained from nomadic livestock in Morocco.

Evaluation of GeneXpert MTB/RIF system performances in the diagnosis of extrapulmonary tuberculosis

Background

Tuberculosis represents a serious public health problem and a significant diagnostic and therapeutic challenge worldwide. Molecular diagnostic techniques are crucial in the World Health Organization’s new tuberculosis control strategy.

This study aims to evaluate the performance of GeneXpert MTB/RIF (Cepheid Sunnyvale, CA, United States) in diagnosis of extra-pulmonary tuberculosis then compare it’s performance in detecting Rifampicin resistance to GenoType MTBDRplus (HAIN Life Sciences, Nehren, Germany).

Methods

Samples from pulmonary and/or extra-pulmonary origins were analysed in a 21 months retrospective study. Samples were sent to the bacteriology laboratory for Mycobacterium tuberculosis detection using conventional bacteriological and molecular methods (GeneXpert MTB/RIF and MTBDRplus). Sensitivity and specificity were calculated for the stained smear and GeneXpert according to culture (Gold Standard) as well as for GeneXpert MTB/RIF in both negative and positive microscopy tuberculosis cases. Data’s statistical analysis was performed with SPSS13.0 software.

Results

Seven hundred fourteen patients’ samples were analysed; the average age was 47.21 ± 19.98 years with a male predominance (66.4%). Out of 714 samples: 285 were from pulmonary and 429 were from extra-pulmonary origins. The positivity rates for microscopy, GeneXpert MTB/RIF and culture were 12.88, 20.59 and 15.82%, respectively. These rates were 18.9, 23.85 and 20.35% for pulmonary samples and 9.71, 18.41 and 12.82% for extra-pulmonary samples, respectively. The sensitivity and specificity of GeneXpert MTB/RIF were almost the same in both pulmonary and extra-pulmonary samples (78.2 and 90.4%) and (79,3 and 90.3%) respectively.

Rifampicin resistance rate found by GeneXpert MTB/RIF was 0.84%. Comparison of Rifampicin resistance obtained by GeneXpert MTB/RIF and Genotype MTBDRplus, showed 100% agreement between the two techniques for studied samples.

Conclusions

This confirms GeneXpert MTB/RIF advantage for tuberculosis diagnosis, particularly extra-pulmonary tuberculosis with negatively stained smear. The performance of GeneXpert and Genotype MTBDRplus are similar in detection of Rifampicin resistance. However, variability of detection performance according to tuberculosis endemicity deserves more attention in the choice of screening techniques of Rifampicin resistance, hence the interest of conducting comparative studies of detection performance under low and medium endemicity on large samples of tuberculosis populations.

Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field

The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.

The value of camels as sentinels for bluetongue virus in Morocco

A  serosurvey  was  conducted  to  determine  the  value  of  camels  (Camelus  dromedaries)  as sentinel animals for the detection of bluetongue virus (BTV) in Morocco. Between 2010 and 2013, camels from various localities in Morocco were randomly tested for antibodies against BTV  serotypes‑1,  ‑4,  ‑6,  ‑8,  ‑11,  ‑14,  and  ‑16.  Antibodies  against  1  or  more  serotypes  were detected in 41.8% of 537 camels tested with a competitive enzyme‑linked immunosorbent assay  (ELISA)  diagnostic  test.  Of  the  7  tested  serotypes,  only  BTV‑11  antibodies  were  not detected with serum neutralisation assays. This study not only confirms the epidemiological presence of BTV‑1, ‑4, and ‑8 in Morocco, but also presents the first evidence of BTV‑6, ‑14, and ‑16 in the country. As such, we conclude that camels would be ideal sentinel animals to determine the potential risk of BTV in Morocco.

First report and genetic characterization of porcine astroviruses of lineage 4 and 2 in diarrhoeic pigs in India

Porcine astroviruses (PAstVs) have extended their distribution globally and have a high prevalence; however, their clinical significance is still under investigation. Thus far, information about their prevalence and diversity in the Indian pig population is unknown. This study is the first report on the prevalence and genetic characterization of PAstVs in diarrhoeic piglets in India. From January 2013 to December 2017, 757 samples were screened using an RT-PCR assay and PAstV infection was detected in 17.6% (133/757) pigs. Of the 133 positive samples, 79 (59.4%) were positive for PAstV alone, whereas 54 (40.6%) were found to be co-infected with porcine rotavirus A (PoRVA). Phylogenetic analysis of RdRp/capsid gene region revealed high genetic heterogeneity among PAstV sequences, with a predominance of PAstV lineage 4 and detection of lineage 2. The lineage 4 PAstVs exhibited 61.2%-94.5% sequence similarity at the nucleotide level to other reported sequences, whereas lineage 2 strain shared 66.0%-71.6% sequence identity with cognate sequences of the same lineage. This is the first report on PAstV and circulation of lineages 4 and 2 in India. Further, phylogenetic analysis indicates a multiphyletic origin of PAstV strains and suggests cross-border circulation of PAstVs with a similar genetic configuration in Asian countries.

Introduction of a paediatric anaesthesia comic information leaflet reduced preoperative anxiety in children

BACKGROUND

The aim of the study was to determine whether the introduction of a paediatric anaesthesia comic information leaflet reduced preoperative anxiety levels of children undergoing major surgery. Secondary objectives were to determine whether the level of understanding of participants and other risk factors influence STAIC-S (State-Trait Anxiety Inventory for Children-State subscale) score in children.

METHODS

We performed a randomized controlled parallel-group trial comparing preoperative anxiety between two groups of children aged >6 and <17 yr. Before surgery, the intervention group received a comic information leaflet at home in addition to routine information given by the anaesthetist at least 1 day before surgery. The control group received the routine information only. The outcome measure was the difference between STAIC-S scores measured before any intervention and after the anaesthetist's visit. A multiple regression analysis was performed to explore the influence of the level of education, the anxiety of parents, and the childrens' intelligence quotient on STAIC-S scores.

RESULTS

One hundred and fifteen children were randomized between April 2009 and April 2013. An intention-to-treat analysis on data from 111 patients showed a significant reduction (P=0.002) in STAIC-S in the intervention group (n=54, mean=-2.2) compared with the control group (n=57, mean=0.90). The multiple regression analysis did not show any influence on STAIC-S scores of the level of education, parental anxiety, or the intelligence quotient of the children.

CONCLUSIONS

A paediatric anaesthesia comic information leaflet was a cheap and effective means of reducing preoperative anxiety, measured by STAIC-S, in children.

CLINICAL TRIALS REGISTRATION

NCT 00841022.

Prevalence of resistance to integrase strand-transfer inhibitors (INSTIs) among untreated HIV-1 infected patients in Morocco

Objective

The integrase strand-transfer inhibitors (INSTIs) are an important class in the arsenal of antiretroviral drugs designed to block the integration of HIV-1 cDNA into the host DNA through the inhibition of DNA strand transfer. In this study for the first time in Morocco, the complete HIV-1 integrase gene was analysed from newly diagnosed patients to evaluate the prevalence of natural polymorphisms and INSTIs resistance-associated mutations in the integrase gene.

Results

The 864pb IN coding region was successfully sequenced from plasma sample for 77 among 80 antiretroviral naïve patients. The sequences were interpreted for drug resistance according to the Stanford algorithm. Sixty samples were HIV-1 subtype B (78%), fourteen CRF02_AG (18%), two subtype C and one subtype A. Overall 81 of 288 (28%) amino acid IN positions presented at least one polymorphism each. We found 18 (36.73%), 42 (25.76%) and 21 (27.27%) of polymorphic residues assigned to the N-Terminal Domain, Catalytic Core Domaine and the C-Terminal Domain positions respectively. Primary INSTIs resistance mutation were absent, however secondary mutations L74IM, T97A were detected in four samples (5.2%). These results demonstrate that untreated HIV-1 infected Moroccans will be susceptible to INSTIs.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3492-5) contains supplementary material, which is available to authorized users.

Prevalence and molecular characterization of avian infectious bronchitis virus in poultry flocks in Morocco from 2010 to 2014 and first detection of Italy 02 in Africa

The aim of this study was to investigate the prevalence and diversity of infectious bronchitis virus (IBV) genotypes in poultry flocks in 16 areas of Morocco between 2010 and 2014. A total of 360 chicken flocks suspected of being infected by IBV were screened for the IBV N gene using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Flocks were classified into four groups according to their IBV vaccination programme. Group 1 contained unvaccinated birds. Group 2 received a single application of live H120 vaccine. Groups 3 and 4 birds received one or two booster vaccination(s), respectively, mostly using the H120 vaccine. The real-time RT-PCR results showed that 51.7% of the flocks were positive for the IBV genome with geographical disparities. Molecular characterization of IBV was performed on 50 RT-PCR positive samples by partially sequencing the S1 gene, including the hypervariable regions (nucleotides 705-1097). Two predominant genotypes were detected, with the Massachusetts type dominating (66%), among which 25% of the samples were identical to the H120 vaccine. The second most common genotype (present in 32% of the flocks) was surprisingly Italy 02, revealing the first detection of this genotype in Morocco and also in Africa. 793B, the predominant genotype in the late 1990s in Morocco, was only detected on one occasion and was identical to the 4/91 vaccine strain. This study highlights the high prevalence of IBV in poultry farms in Morocco and confirms its continuous dynamic changes and evolution.

Isolation and identification of group A rotaviruses among neonatal diarrheic calves, Morocco

Background

Group A rotaviruses (RVA) are the main cause of neonatal calve diarrhea (NCD) in Morocco. In this study, we isolated RVA strains from NCD clinical samples in order to support RVA disease control in Morocco. This isolation process constitutes a first step toward vaccine development.

Methods

Thirteen fecal samples were obtained from calves with a single episode of neonate calf diarrhea at three different dairies and two samples were collected from field during a severe NCD outbreak. Diagnosis of RVA infection was based on fecal immune-chromatographic rapid test and further evaluated for their hemagglutination (HA) activity. RVA isolation was carried out on MA104 cells after inoculates were treated with different concentrations of trypsin TPCK. All RVA isolates were confirmed by LSI VetMAX™ Triplex Ruminant Rotavirus & Coronavirus Real-Time PCR kit. G and P typing were determined by direct sequencing of the VP4 and VP7 amplicons.

Results

RVA isolation was achieved for nine clinical samples following one or two passages (60 %) and was properly depended on HA activity and trypsin treatment of inoculates. The first sign of CPE detected consisted of increased cell granularity, obscure cell boundaries, cell rounding, and eventual degeneration and detachment of cells. At lower TPCK concentration (3–10 μg/inoculum), no changes at the cellular level were observed, while cells activated with 25–30 μg of trypsin/inoculums, they degenerated and trypsin cytotoxicity was enhanced. Appreciable changes in cell’s morphology were detected with optimal trypsin concentration of 15–20 μg trypsin/inoculums. Data from qRT-PCR confirmed that unsuccessful cultivations have No-Ct, and all nine isolates have Ct values ranged between 12.17 and 24.69. Analysis sequencing revealed that field isolates were of G6 P[5] serotype and isolates from the dairy NCD samples were of G10 P[14] serotype.

Conclusions

To our knowledge, this is the first study in Morocco which reports the circulation of G10P[14] in NCD on dairy farms and G6P[5] in the field. Our study constitutes a crucial and a necessary step allowing preventive and veterinary medicine to support RVA disease controls in the country.

The single nucleotide polymorphism +936 C/T VEGF is associated with human epidermal growth factor receptor 2 expression in Moroccan breast cancer women

The vascular endothelial growth factor (VEGF), a potent regulator of angiogenesis, is involved in the development and progression of breast cancer (BC). The functional +936 C/T polymorphism of the VEGF-A gene has been implicated in BC susceptibility; however, published data are conflicting. In the current case-control study, we analyzed the association of the +936 C/T polymorphism with BC risk and tumor markers expression, human epidermal growth factor receptor 2 (HER2/neu) and caner antigen 15.3 (CA 15.3) in Moroccan women. We genotyped the DNA of 70 BC patients and 70 healthy women by TaqMan SNP assays. The χ(2) test and Fisher's exact test were used for statistical analyses. The overall results revealed that there is no association between the +936 C/T polymorphism and BC risk [p = 0.8; OR 0.87, 95 % CI (0.32-2.42)]. However, when we stratified the group of patients according to the status of tumor markers, a statistical significant association of +936 C/T SNP and HER2/neu expression was observed (p = 0.009). In contrast, no association with the other tumor marker, CA 15.3, was found (p = 0.090). Thus, the +936 C/T polymorphism seems to have a correlation with HER/neu expression in BC disease.

Cleavage site and Ectodomain of HA2 sub-unit sequence of three equine influenza virus isolated in Morocco

Background

The equine influenza (EI) is an infectious and contagious disease of the upper respiratory tract of horses. Two outbreaks were notified in Morocco during 1997 and 2004 respectively in Nador and Essaouira. The aims of the present study concern the amino acids sequences comparison with reference strain A/equine/Miami/1963(H3N8) of the HA2 subunit including the cleavage site of three equine influenza viruses (H3N8) isolated in Morocco: A/equine/Nador/1/1997(H3N8), A/equine/Essaouira/2/2004 (H3N8) and A/equine/Essaouira/3/2004 (H3N8).

Results

The obtained results demonstrated that the substitutions were located at Ectodomain (ED) and transmembrane domain (TD), and they have only one arginine in cleavage site (HA1-PEKQI-R³²⁹-GI-HA2). In the Ectodomain, the mutation N/154²/T deleted the NGT glycosylation site at position 154 for both strains A/equine/Essaouira/2/2004(H3N8) and A/equine/Essaouira/3/2004(H3N8). Except for mutation D/160²/Y of the A/equine/Nador/1/1997(H3N8) strain, the other mutations were involved in non conserved sites. While the transmembrane domain (TM) of the strain A/equine/Essaouira/3/2004(H3N8) exhibits a substitution at residue C/199²/F. For the A/equine/Nador/1/1997(H3N8) strain the HA2 shows a mutation at residue M/207²/L. Three Moroccan strains reveals a common substitution at the residue E/211²/Q located between transmembrane domain TM and the cytoplasmic domain (CD).

Conclusion

The given nature virulence of three Moroccan strains, the identified and reported mutations certainly played a permissive role of infection viral process.

No evidence for replication of a field strain of bluetongue virus serotype 1 in the blood of domestic dogs

The potential role of domestic dogs in the long-distance transmission of bluetongue virus (BTV) is currently unproven. This study set out, through an experimental infection study, to investigate whether domestic dogs mount a viraemia post-infection with a field strain of BTV serotype 1. All six experimentally infected dogs seroconverted within 14 days and viral RNA was detected in the blood of the dogs, albeit at significantly lower levels than that seen in domestic ruminants. There was no clear evidence for viral replication in the dogs as no increase in viral RNA was observed in, and it was not possible isolate virus from, the blood of the dogs. There was however evidence for a persistence of viral RNA in the blood of the dogs, which may be evidence for a low level of replication or could be indicative of persistence of the viral inoculum.

Range-reference determination of lymphocyte subsets in Moroccan blood donors

BACKGROUND

Information on lymphocyte populations (T, B, and Natural killer cells) and subpopulations (CD4 and CD8) in Morocco is scarce if not inexistent.

OBJECTIVE

To establish a reference value of these cells in 242 Moroccan young adult blood donors by flow cytometry.

RESULTS

Smokers had significantly higher total leukocyte count (p < 0.001), total lymphocyte count (p < 0.0001) and higher CD3+CD4+ cells (p < 0.0001). The percentage of CD3-CD56+ subsets was affected by smoking (p < 0.01). Our analysis positively correlate with previous observations of an increase of absolute CD4+ T cells, with no changes in other lymphocyte subset cells in smokers. The lymphocyte subpopulation distributions for all antigens were found to be similar to those reported in Saudi and Italian adults, while higher levels were reported for the same gender in other countries, especially Ghana and Kuwait.

CONCLUSION

The international classification standards of the HIV-infected subjects according to their rates of CD4 are applicable to the present study's population.

Experimental infection of alpine goats with a Moroccan strain of peste des petits ruminants virus (PPRV)

Peste des petits ruminants virus (PPRV) recently caused a serious outbreak of disease in Moroccan sheep and goats. Alpine goats were highly susceptible to PPRV with mortality rates approaching 100%, as opposed to local breeds of sheep which were less susceptible to the disease. The relative susceptibility of alpine goats was investigated through an experimental infection study with the Moroccan strain of PPRV. Severe clinical signs were observed in the alpine goats with virus being excreted through ocular, nasal and oral routes. No difference in the severity of the disease in goats was observed with different inoculation routes and transmission of the virus by direct contact was confirmed. This study confirmed the susceptibility of the alpine goat to PPRV infection and describes a challenge protocol that effectively and consistently reproduced severe clinical signs of PPR in experimentally infected goats.

[An ovarian mucinous borderline tumour with mixed mural nodules]

The occurrence of mural nodules in serous or mucinous ovarian tumours is not frequent. Mural nodule can be developed in benign, borderline or malignant tumours. They can be benign, malignant or mixed type. Thus the prognosis of the ovarian tumour can be dramatically modified by the presence if these nodules. Eighty-two cases of mural nodules were reported in the literature, among which we account four cases of mixed nodules type. We report an additional case of mixed type mural nodules of anaplastic carcinoma and sarcoma-like developed in an ovarian mucinous borderline tumour at a 60-year-old woman.We give details about the classification, the differential diagnosis and prognosis of theses nodules.

[Surgical treatment in De Quervain's tenosynovitis. About 20 cases]

INTRODUCTION

The De Quervain's tenosynovitis is an inadequacy into the first extensor compartment between the osteo-fibrous tunnel and the tendons. This mechanical conflict generates a tenosynovitis of the extensor pollicis brevis and the abductor pollicis longus tendons in first dorsal extensor compartment of the wrist.

PATIENTS AND METHODS

The authors report a retrospective study of 20 patients who have been treated by a longitudinal surgical approach. The mean age was 49 years old with a net female predominance. The Finkelstein's test was positive in all cases. All patients were treated operatively by incision of the sheath, which was sufficient to unwind the dorsal compartment tendons. The sheath palmar flap has been sutured with skin (Le Viet plasty) to avoid a further tendons luxation.

RESULTS

At three years follow-up, the functional results were good in all the patients. However, non-aesthetic scars were noticed in three patients. We did not notice neither a case of anesthesia of the radial nerve nor a tendinous luxation in our series.

DISCUSSION

The stenosing tenosynovitis of the first dorsal extensor compartment of the wrist is a relatively frequent pathology in the young woman. We use a longitudinal surgical approach to avoid the radial nerve lesions. Le Viet procedure using the palmar flap of the pulley fixed to the dermis works as a barrier and maintains the tendons sliding on the radial styloid groove.

Assessment of genotoxic effects related to chronic low level exposure to ionizing radiation using biomarkers for DNA damage and repair

The first objective of our study was to analyse whether biomarkers for genotoxic effects (DNA breaks and alkali-labile sites and micronucleus and non-disjunction frequencies) could be fully validated for biomonitoring workers chronically exposed to ionizing radiation (IR). Blood samples of controls and individuals chronically exposed to IR were analysed. The interindividual variation was reduced when the comet data were adjusted for interexperimental variation, but remained statistically significant. No differences were found between groups, either for smoking or for exposure status. The second objective was to determine whether the Comet assay can be used to evaluate global repair phenotype as a susceptibility biomarker for IR-induced DNA damage in nuclear workers. A pilot study was performed and blood from workers exposed or not to radiation was submitted to a challenging dose of gamma-rays. The repair kinetics of each individual donor were analysed by Comet assay at different time points and compared with the frequencies of biomarkers of genotoxic effects. There was a statistically significant interaction between biomarkers assessing the same damage (micronucleus and Comet assays). Multivariate analysis showed that micronucleus frequencies were positively influenced by age and the percentage of residual tail length was negatively influenced by the interaction between smoking and exposure status. The general conclusions from our study are: (i) a positive correlation exists between mechanistically related biomarkers; (ii) multivariate regression analysis confirmed that the interaction between smoking and exposure to IR negatively and statistically significantly influenced residual tail length; (iii) use of the Comet assay for the estimation of global repair phenotype with respect to IR is recommended because it is simple, fast and differences in in vitro repair capacity can be detected.

Validation and implementation of an internal standard in comet assay analysis

The comet assay is widely used to detect DNA damage in single cells. However, only moderate attention has been paid to the experimental variability of this assay, especially during electrophoresis. To take into account this variation and to be able to compare measurements from different electrophoretic runs, as would be necessary when large numbers of samples need to be analysed, it is important to integrate an internal standard into the assay. This study presents a first step in the validation and implementation of an internal standard in the alkaline comet assay. Untreated and ethyl methanesulfonate treated cells (K562 human erythroleukemia cell line) were used as negative and positive internal standards, respectively, in each electrophoresis run. Three steps were followed: (1) assessment of the different levels of variability which may influence the damage levels of the internal standards, (2) evaluation of the variability across separate electrophoresis runs on the quantification of DNA damage in the internal standards by three experimenters involved in different studies and (3) proposal of an adequate calculation system to integrate the internal standards into test sample data. The application of the two proposed models to samples from a human biomonitoring study is presented. The model which calibrates the measurements against the negative internal standard is the most useful since this negative standard was the most stable across experiments and among the three experimenters. The percentage of DNA in the tail is the most appropriate parameter to analyse induced DNA damage, because its interelectrophoresis and interexperimenter variation is less pronounced than that of tail length.

Analysis of chromosome loss and chromosome segregation in cytokinesis-blocked human lymphocytes: non-disjunction is the prevalent mistake in chromosome segregation produced by low dose exposure to ionizing radiation

The aim of the present work was to examine in human lymphocytes, firstly, whether in vitro gamma-rays as compared with X-rays also induce chromatid malsegregation and at higher frequencies than chromosome loss and, secondly, whether the cytokinesis-blocked micronucleus assay combined with fluorescence in situ hybridization might be useful for the biomonitoring of individuals exposed to ionizing radiation. After irradiation, the relative frequencies of centromere-positive micronuclei decreased from 39.2% at 0.1 Gy to 21. 63% at higher doses. There was no statistically significant increase in MNCen+ frequencies at doses below 1 Gy (0.1, 0.25 and 0.5 Gy), but a statistically significant increase at 1 (P < 0.05) and 2 Gy (P < 0.001) was observed for all the donors. No significant differences in baseline and gamma-ray-induced non-disjunction frequencies for chromosomes 1 (P = 0.9) and 17 (P = 0.8) between individuals were detected. For radiation-induced non-disjunction, lower doses (0.1, 0. 25 and 0.5 Gy) of gamma-rays did not induce a statistically significant increase in non-disjunction frequencies whereas 1 Gy and above clearly induced a statistically significant increase in the total non-disjunction frequencies for all the donors (P < 0.05 at 1 Gy and P < 0.0001 at 2 Gy). The aneugenic effect of radiation is less clearly dose dependent at the lower doses, suggesting an apparent threshold below which no change could be demonstrated. At high radiation doses the major mechanism for gamma-ray-induced aneuploidy is related to chromosome loss through non-disjunction, as has been demonstrated using X-rays, and not through the formation of micronuclei.

Inter-laboratory comparison of cytogenetic endpoints for the biomonitoring of radiological workers

PURPOSE

The evaluation of different cytogenetic endpoints of radiation damage for the biomonitoring of contract workers temporarily employed at nuclear power plants.

MATERIALS AND METHODS

Blood samples from six donors were irradiated in vitro with doses ranging from 0.1 to 2Gy 60Co gamma-rays. Compared were a conventional analysis for dicentrics, the conventional micronucleus (MN) assay, the centromere micronucleus assay using p82H and an alphaAllCen pancentromeric probe, and tricolour FISH with chromosome 2, 4 and 8 DNA probes for the scoring of translocations.

RESULTS

Agreement in the number of MN between Giemsa-and propidium iodine fluorescence-stained preparations was obtained. The control samples showed higher centromere positivity for the MN after FISH with the p82H probe compared with the alphaAllCen probe. The MN results with both probes showed a slight but systematic increase in the number of centromere-positive MN with dose, indicating that radiation, although principally clastogenic, also has aneuploidogenic properties. The values of the genomic translocation frequency (FG) derived from the observed translocation frequencies were systematically higher than the dicentric yields. Comparing the sensitivity of the different methods with restriction of the scoring time to 1 day for biomonitoring purposes, the centromere micronucleus assay had the lowest dose detection limit (0.1 to 0.2 Gy).

CONCLUSION

This study shows that at present only the centromere micronucleus assay can combine high sensitivity with a reasonable scoring time for the biomonitoring of relatively large populations.