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

Quantification of thermo-halotolerant alkaline protease activity derived from Bacillus licheniformis strains isolated from extreme environments in Morocco

Proteases; especially alkaline proteases, constitute the most used group of enzymes in industry. The wide scope of their application requires varying properties; most commonly stability throughout the conditional changes that would occur during the various industrial processes. This study aimed to identify the potentially interesting bacterial strains obtained from Moroccan extreme environment, and evaluate their proteolytic activity under the various growing conditions. In this study, the impact of temperature and salinity on the alkaline protease activity (pH 11) of 33 Bacillus strains deposited in the Moroccan Coordinated Culture Collection, which originated from the various extreme environments from Morocco, was studied. Bacterial identification to the species level was performed using 16S rRNA gene sequencing and MultiLocus Sequence Typing (MLST), a technique that is much more precise and can identify the bacteria to the strain level. Strain B950 showed a relatively stable protease activity at the tested extreme conditions (i.e., 130.8 U/ ml at 60 °C and 10 % NaCl). On the other hand, strain B961 displayed a better overall activity at either high temperature (140.8 U/ ml) or salinity (137 U/ ml); however, it was not as stable as when grown under both extreme conditions. Regarding identity of the bacterial strains, they were all representatives of Bacillus licheniformis; although B950 and B961 strains belonged to Sequence Types 3 and 5, respectively

Use of rpoB gene phylogenetic marker-based distinction of abiotic stress tolerant and plant-growth promoting Bacillus paralicheniformis isolates from their closely related Bacillus licheniformis

Bacillus paralicheniformis is a new identified species, which was distinguished from Bacillus licheniformis in 2015 through extensive phylogenomic and phylogenetic analyses. In this context, this study aimed to achieve a clear identification of the active plant-growth promoting rhizobacteria (PGPR) B. paralicheniformis isolates among the closely related B. licheniformis through molecular typing, helping for the development of clearly-identified PGPR isolates to be used as biofertilizers. A total of 15 rhizobacteria were isolated from the olive rhizosphere soils. These bacterial isolates exhibited various proprieties in terms of abiotic stress tolerance, biofilm formation under stress conditions, and enzyme activities (i.e., lipases, cellulases, and proteases). In addition, several PGP traits such as phosphate solubilization and the production of siderophores and indol-3 acetic acid were also observed. Molecular identification through 16S rRNA sequencing initially identified all the isolates as Bacillus spp. The multi-locus sequence typing (MLST) scheme, using six housekeeping genes (adk, ccpA, recF, rpoB, sucC, and spo0A) had unveiled distinct allelic profiles resulting in 13 unique sequence types (ST). Notably, a comprehensive analysis indicated no exact allele matches existed between the examined isolates and those documented in the PubMLST database. Among the six housekeeping genes, we noticed that rpoB gene (RNA polymerase, subunit beta) had multiple polymorphic sites that were bordered by conserved sequences. Furthermore, the phylogenetic analysis based on rpoB had identified clusters indicating distinct phylogenetic relationships between B. paralicheniformis and B. licheniformis, and successfully differentiated the two species from a pool of 90 strains. The rpoB partial sequence proved to be effective for accurate species discrimination

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

Establishing African genomics and bioinformatics programs through annual regional workshops

The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.</p

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

Effectiveness of Sinopharm’s BBIBP-CorV Booster Vaccination against COVID-19-Related Severe and Critical Cases and Deaths in Morocco during the Omicron Wave

Objective: This study investigates the effectiveness of the 1st booster dose against COVID-19 severe and critical hospitalizations and deaths occurring due to the Omicron wave in Morocco. Participants/methods: This study uses nationally representative data on COVID-19 from 15 December 2021 to 31 January 2022. The aim is to investigate the effectiveness of the inactivated COVID-19 vaccine BBIBP-CorV (Sinopharm) 1st booster dose against the Omicron wave in Morocco using real-world data established from nationally representative statistics on COVID-19 cases, deaths and vaccinations. Statistical Analyses: The screening method was used to estimate vaccine effectiveness against COVID-19 severe or critical hospitalization and COVID-19-related deaths. The data were grouped by, age subgroup, sex, week, and geographical area and were analyzed using binary logistic regression with an offset for vaccine coverage. Results: The overall BBIBP-CorV VE estimate is 89% (95% CI 85 to 92) effective in curbing COVID-19 deaths, and 81% (95% CI 78 to 84 in curbing COVID-19 severe/critical hospitalizations. Death-related VE estimate was 86% (95% CI 81 to 90) for patients aged ≥65 years, 96% (95% CI 90 to 98) for those aged <65 years, 95% (95% CI 88 to 98) in no-risk factor patients, 91% (95% CI 85 to 94) with 1 risk factor, 90% (95% CI 83 to 95) with 2 risk factors, and 72% (95% CI 52 to 84) in patients with 3 risk factors and more. Severe/critical hospitalization VE estimate was 78% (95% CI 74 to 82) for patients aged ≥65 years, 87% (95% CI 82 to 90) for those aged <65 years, 86% (95% CI 80 to 90) in no-risk factor patients, 80% (95% CI 73 to 84) with 1 risk factor, 80% (95% CI 70 to 85) with 2 risk factors, and 80% (95% CI 68 to 86) in patients with 3 risk factors and more. Conclusions: BBIBP-CorV boosters are effective in increasing protection against the Omicron variant-related COVID-19 deaths and severe/critical hospitalizations. The protection is reduced with older age and higher risk factors. These findings emphasize the importance of targeted vaccination strategies for different demographic groups and underscore the protective benefits of the first booster BBIBP-CorV vaccine