Évolution des techniques de séquençage

La biologie analytique a connu depuis quelques années une grande révolution en conséquence des progrès technologiques de la biologie moléculaire appliquée au séquençage des génomes. En effet, connaître l’enchaînement complet des bases nucléotidiques qui constituent un génome, c’est connaître toute l’information nécessaire à la vie (du moins en théorie).Ce n’est que récemment, avec la mise en place des Programmes Génome, que de nombreux génomes, dont celui de l’être humain, sont aujourd’hui séquencés, et que d’autres génomes sont en voie de l’être dans des délais de plus en plus raccourcis. Ces réalisations spectaculaires, sont rendues possible grâce aux développements extraordinaires des techniques de séquençage que nous essayons de passer en revue dans cet article. Nous rappellerons dans un premier temps le principe de base et l’évolution des techniques traditionnelles (Sanger, Maxam et pyroséquençage). Nous discuterons les avantages et les inconvénients de chaque approche avant d’exposer la nouvelle génération de séquenceurs automatisés

Diversity of culturable moderately halophilic and halotolerant bacteria in a marsh and two salterns a protected ecosystem of Lower Loukkos (Morocco)

To study the biodiversity of halophilic bacteria in a protected wetland located in Loukkos (Northwest, Morocco), a total of 124 strains were recovered from sediment samples from a marsh and salterns. 120 isolates (98%) were found to be moderately halophilic bacteria; growing in salt ranges of 0.5 to 20%. Of 124 isolates, 102 were Gram-positive while 22 were Gram negative. All isolates were identified based on 16S rRNA gene phylogenetic analysis and characterized phenotypically and by screening for extracellular hydrolytic enzymes. The Gram-positive isolates were dominated by the genus Bacillus (89%) and the others were assigned to Jeotgalibacillus, Planococcus, Staphylococcus and Thalassobacillus. The Gram negative isolates were dominated by the genus Vibrio (41%) and the others were assigned to Halomonas, Psychrobacter, Marinobacterium, Pseudoalteromonas, Salinivibrio and Photobacterium. The growth of strains obtained under different physico-chemical conditions and the screening for hydrolytic enzymes showed a high diversity even within the same species

An autosomal recessive leucoencephalopathy with ischemic stroke, dysmorphic syndrome and retinitis pigmentosa maps to chromosome 17q24.2-25.3

Background Single-gene disorders related to ischemic stroke seem to be an important cause of stroke in young patients without known risk factors. To identify new genes responsible of such diseases, we studied a consanguineous Moroccan family with three affected individuals displaying hereditary leucoencephalopathy with ischemic stroke, dysmorphic syndrome and retinitis pigmentosa that appears to segregate in autosomal recessive pattern. Methods All family members underwent neurological and radiological examinations. A genome wide search was conducted in this family using the ABI PRISM linkage mapping set version 2.5 from Applied Biosystems. Six candidate genes within the region linked to the disease were screened for mutations by direct sequencing. Results Evidence of linkage was obtained on chromosome 17q24.2-25.3. Analysis of recombination events and LOD score calculation suggests linkage of the responsible gene in a genetic interval of 11 Mb located between D17S789 and D17S1806 with a maximal multipoint LOD score of 2.90. Sequencing of seven candidate genes in this locus, ATP5H, FDXR, SLC25A19, MCT8, CYGB, KCNJ16 and GRIN2C, identified three missense mutations in the FDXR gene which were also found in a homozygous state in three healthy controls, suggesting that these variants are not disease-causing mutations in the family. Conclusion A novel locus for leucoencephalopathy with ischemic stroke, dysmorphic syndrome and retinitis pigmentosa has been mapped to chromosome 17q24.2-25.3 in a consanguineous Moroccan family

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

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Systematic review and meta-analysis for the biotechnological production of THC in Morocco

Cannabinoids have promising therapeutic potential. Δ9-tetrahydrocannabinol (THC), the most important psychotropic active ingredient of Cannabis Sativa L, has been the subject of several chemical, pharmacological and biosynthetic studies. In this context, a meta-analysis of biotechnological processes applied to the production of recombinant cannabinoid THC worldwide was carried out. The objective was to highlight the potential of these processes on the Moroccan variety of Cannabis Sativa. The PubMed, ScienceDirect and Web of Science search motors were used to search for original scientific work presenting biotechnological tools used in the production of THC. The scientific articles exploited are those published before the end of 2020. Succinct analysis of the experimental work performed showed that expression of the gene encoding Cannabis Sativa L. THCA synthase was performed on prokaryotic and eukaryotic expression systems. Currently, no functional expression could be obtained in E. coli. Whereas, production of recombinant protein (THCA Synthase) associated with significant enzymatic activity was obtained in P. pastoris cultures (F. Saccharomycetaceae). The exploitation of the sequences showed the presence of a large similarity between the THCA Synthase gene of cannabis Sativa of the Moroccan variety and the mRNA precursor of the same gene reported in several studies. This will allow us to use a specific signal sequence of choice for an adopted expression host, in order to produce the recombinant THCA synthase enzyme from the Moroccan Cannabis Sativa L strain on P. pastoris cultures

Circulating microRNA profiles in Wilms tumour (WT): A systematic review and meta-analysis of diagnostic test accuracy.

BACKGROUND: Wilms tumour (WT) is caused by aberrant embryonic kidney development and associated with dysregulated expression of short, non-protein-coding RNAs termed microRNAs (miRNAs). At present, there is no reliable circulating biomarker of WT, and this remains an urgent unmet clinical need. Such biomarkers may assist diagnosis, subtyping/prognostication, and disease-monitoring. Here, we established the list of dysregulated circulating miRNAs in WT from the existing published literature. METHODS: Regardless of publication date, PubMed, Scopus, Web-of-Science, and Wiley online library databases were searched for English/French studies on WT circulating miRNAs. The PRISMA-compliant search was registered in PROSPERO. The QUADAS tool measured retained article quality. The meta-analysis assessed the sensitivity and specificity of miRNAs for WT diagnosis. RESULTS: Qualitative analysis included 280 samples (172 WT patients; 108 healthy controls) from five of 450 published articles. The study uncovered 301 dysregulated miRNAs (144 up-regulated, 143 down-regulated, 14 conflicting). The pooled sensitivity, specificity, and AUC of the 49 significantly dysregulated microRNAs from two studies was 0.67 [0.62; 0.73], 0.95 [0.92; 0.96] and 0.77 [0.73; 0.81] respectively, indicating a stronger diagnostic potential for WT. CONCLUSIONS: Circulating miRNAs show promise for WT diagnosis and prognosis. More research is needed to confirm these findings and determine associations with tumour stage/subtype. PROSPERO REGISTRATION NUMBER: CRD42022301597.MJM and NC recognise support from Bethany’s Wish, grant reference numbers CCLGA 2017 02 and CCLG 2022CIG10

Variability and genetic structure of a natural population of <em>Citrus psorosis virus</em>

International audienceIn this study, we examined the population structure and genetic diversity of Citrus psorosis virus (CPsV) in Morocco. Analysis of the coat protein partial sequences of 34 isolates collected in the three main citrus-growing areas of Morocco showed that CPsV grouped in three major groups, with low within-group nucleotide diversity. Analyses indicated that CPsV genetic diversity is not structured by the geographic origin of the CPsV isolates. The genetic variation resulting from mutations depends on evolutionary forces that have contributed to the shaping of the genetic structure and diversity of the CPsV populations analyzed here: negative selective pressure for amino acid variation, recombination between variants or mixed infection, genetic drift induced by the founder effect associated with the transmission process, and migration explained by the exchange of infected propagative plant material