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Leishmania (L.) infantum strains, isolated from varying hosts and clinical manifestations (cutaneous, visceral and canine leishmaniasis), were investigated in order to understand the genetic polymorphisms within this species in Algeria and Tunisia. Two DNA-based typing methods were tested in order to evaluate their effectiveness against Multilocus enzyme electrophoresis (MLEE), widely considered as the reference method for Leishmania parasite typing. On the other hand, MLEE is cumbersome, high-cost, time consuming and frequently does not detect intra-species genetic polymorphisms. In this work, we used two molecular target regions to discriminate L. infantum strains, Internal transcribed spacer 1 (ITS1) and the cysteine proteinase B (cpb). The ITS1 region offers good resolution for Leishmania discrimination but does not spotlight intra-species polymorphisms. In contrast, cpbE and cpbF PCR-Sequencing demonstrated a certain variability within CL and VL Algerian and Tunisian L. infantum isolates. Following phylogenetic analyses of 44 L. infantum isolates, two main groups were identified, a group with 39 bp deletion in the cpb sequence, composed of cutaneous, visceral and canine isolates from both countries with no significant clinical or geographic distribution; these samples were typed as MON-1, MON-24, and MON-80 zymodemes. A second group which presents a clear clusterization of Tunisian cutaneous strains belonging to the L. infantum MON-24. This group, with no deletion in the mature domain of the cpb gene sequence, should be further explored with a higher number of samples.

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds' differentiation level (Wright's fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.

Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.

Cutaneous leishmaniasis (CL) remains one of the world's most prevalent neglected diseases, particularly in developing countries. Identification of the involved Leishmania species is an important step in the diagnosis and case management process. In this study, we tested simple, rapid, and highly sensitive loop-mediated isothermal amplification (LAMP) assays for Leishmania DNA species-specific detection from cutaneous lesions. Two LAMP assays, targeting cysteine protease B (cpb) gene, were developed to detect and identify Leishmania major and Leishmania tropica species. Loop-mediated isothermal amplification specificity was examined using DNA samples from other Leishmania species and Trypanosoma species. No cross-reactions were detected. The developed LAMP assays exhibited sensitivity with a detection limit of 20 fg and 200 fg for L. major and L. tropica, respectively. Both tests were applied on clinical samples of CL suspected patients living in endemic Tunisian regions and compared with kinetoplast DNA quantitative PCR (qPCR), microscopic, and conventional cpb-based polymerase chain reaction (PCR) assays. Our LAMP tests were able to discriminate between L. major and L. tropica species and showed a sensitivity of 84% and a specificity of 100%. However, when compared with the performance of the diagnostic tests with latent class analysis (LCA), our LAMP assays show a sensitivity of 100%. These assays can be used as a first-line molecular test for early diagnosis and prompt management of CL cases in public health programs.

Introduction : Le cancer est à l’origine de détresse psychologique alourdissant les morbidités des patients. Le cancer colorectal constitue un problème de santé publique de par son ampleur et sa gravité, en plus de son retentissement psychologique chez les patients et chez leur entourage. Notre objectif est de déterminer la prévalence de la dépression et de l’anxiété chez un groupe de patients tunisiens atteints de cancer colorectal et d’en rechercher les éventuelles relations avec les données cliniques. Patients et méthodes : Nous avons mené une étude observationnelle longitudinale prospective durant six mois (de mars à août 2017) colligeant tous les patients présentant un cancer colorectal et suivis à la consultation d’oncologie médicale au CHU Farhat-Hached à Sousse (Tunisie). En plus d’une grille à remplir par l’enquêteur se rapportant aux données épidémiologiques et cliniques du patient après l’entretien et la consultation du dossier médical, la mesure de l’anxiété et de la dépression a été faite à l’aide d’un autoquestionnaire validé en langue arabe : l’Hospital Anxiety and Depression Scale (HADS). La saisie et l’analyse des données ont été faites par le logiciel SPSS V20.0. Résultats : Cinquante-deux patients ont accepté de répondre à notre questionnaire. Ils étaient répartis en 28 femmes et 24 hommes ; l’âge moyen était de 57 ± 13 ans, la durée moyenne de la maladie était de 3,2 ± 1 ans. Les patients inclus dans l’étude étaient au stade métastatique (stade IV) de leur maladie dans 27%des cas. Nos patients ont bénéficié d’un traitement curatif dans 54 % des cas, d’une chirurgie de la tumeur primitive dans 88,6 %, d’une chimiothérapie dans 94,3 %, d’une radiothérapie dans 34,6 %, et 15,5 % ont reçu le cetuximab. La dépression détectée auprès de nos patients était douteuse dans 17,3 %et certaine dans 13,5 %. L’anxiété était douteuse chez 13,5 % et certaine dans 7,5 %. Une corrélation positive significative a été mise en évidence entre d’une part la symptomatologie dépressive et d’autre part le stade métastatique de la maladie (r = 0,741, p = 0,042), la présence de stomie (r = 0,811 ; p = 0,005), la fatigue (r = 0,720 ; p = 0,005) et les effets indésirables à type de nausée et vomissement (r = 0,653 ; p = 0,045). Conclusion : Il existe une forte prévalence de la dépression et de l’anxiété chez les patients atteints de cancer colorectal dans notre travail. Ces troubles psychiques devraient être systématiquement recherchés afin de préconiser une prise en charge adéquate de ces patients dans leur parcours de soins.

Summary The novel coronavirus disease‐2019 (Covid‐19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost‐effective methodology. The advent of the loop‐mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point‐of‐care test for the diagnosis of Covid‐19 in endemic areas, especially for low‐ and middle‐income countries.

African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].

Drafting and writing a data management plan (DMP) is increasingly seen as a key part of the academic research process. A DMP is a document that describes how a researcher will collect, document, describe, share, and preserve the data that will be generated as part of a research project. The DMP illustrates the importance of utilizing best practices through all stages of working with data while ensuring accessibility, quality, and longevity of the data. The benefits of writing a DMP include compliance with funder and institutional mandates; making research more transparent (for reproduction and validation purposes); and FAIR (findable, accessible, interoperable, reusable); protecting data subjects and compliance with the General Data Protection Regulation (GDPR) and/or local data protection policies. In this review, we highlight the importance of a DMP in modern biomedical research, explaining both the rationale and current best practices associated with DMPs. In addition, we outline various funders’ requirements concerning DMPs and discuss open-source tools that facilitate the development and implementation of a DMP. Finally, we discuss DMPs in the context of African research, and the considerations that need to be made in this regard.

Cutaneous leishmaniasis (CL) remains one of the world’s most prevalent neglected diseases, particularly in developing countries. Identification of the involved Leishmania species is an important step in the diagnosis and case management process. In this study, we tested simple, rapid, and highly sensitive loop-mediated isothermal amplification (LAMP) assays for Leishmania DNA species-specific detection from cutaneous lesions. Two LAMP assays, targeting cysteine protease B (cpb) gene, were developed to detect and identify Leishmania major and Leishmania tropica species. Loop-mediated isothermal amplification specificity was examined using DNA samples from other Leishmania species and Trypanosoma species. No cross-reactions were detected. The developed LAMP assays exhibited sensitivity with a detection limit of 20 fg and 200 fg for L. major and L. tropica, respectively. Both tests were applied on clinical samples of CL suspected patients living in endemic Tunisian regions and compared with kinetoplast DNA quantitative PCR (qPCR), microscopic, and conventional cpb-based polymerase chain reaction (PCR) assays. Our LAMP tests were able to discriminate between L. major and L. tropica species and showed a sensitivity of 84% and a specificity of 100%. However, when compared with the performance of the diagnostic tests with latent class analysis (LCA), our LAMP assays show a sensitivity of 100%. These assays can be used as a first-line molecular test for early diagnosis and prompt management of CL cases in public health programs.

Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD.

Pharmacogenomics studies the impact of genetic variation on drug response. The discipline is crucial in order to improve healthcare worldwide and an important stepping stone toward a future of personalized medicine. Pharmacogenomics generally involves single- to multigene variation investigations, and, although a great deal of progress has been made in the last decades, significant barriers prevent the utilization of pharmacogenomics to its full potential. These barriers include both financial and technical/analytical considerations, which are further complicated by the varied reporting methods employed by pharmacogenomics researchers and clinicians. Therefore, standardizing the manner in which pharmacogenomics investigations are reported can significantly contribute to resolving the existing analytical concerns, and thus, the Minimum Information required for a DMET experiment (MIDE) pharmacogenomics was designed to challenge the reporting variance in experiments employing microarray technology, specifically with regard to pharmacogenomics. The following chapter provides a brief overview of pharmacogenomics research, standardization within the field, and an in-depth look into the MIDE pharmacogenomics standard. Notably, the MIDE standard is adaptable to other pharmacogenomics applications and is available along with several other pharmacogenomics standards on the FAIRsharing (Findable, Accessible, Interoperable, Reproducible Sharing) resource. Standardization across pharmacogenomics applications is crucial in order to enhance the findability, accessibility, interoperability, and reusability of pharmacogenomics studies, ultimately enhancing the quality of such studies and promoting collaboration between independent bodies involved in the science.

Leishmaniasis, a public health problem in Tunisia, are diseases caused by different Leishmania species. Cutaneous leishmaniasis is present from the North to the South under different forms, due to Leishmania (L.) major, L. infantum or L. tropica. Whereas, Psammomys (P.) obesus is the confirmed reservoir host of L. major, those of L. tropica and dermotropic L. infantum wait to be identified. Importantly, P. vexillaris species have been recently highlighted; however, no studies have been carried out to explore its potential role in leishmaniasis epidemiology. Seventy two rodents were collected from Central and South-West of Tunisia between 2007 and 2010. Using several methods, 43 animals were identified as P. obesus and 29 as P. vexillaris. Leishmania kinetoplast DNA was detected in liver samples by real-time PCR in 18 P. obesus and in 8 P. vexillaris. Then, the direct sequencing of the amplified internal transcribed spacer 1, allowed the identification of L. infantum DNA in five P. obesus and in three P. vexillaris, as well as L. tropica DNA in three other P. vexillaris. Whereas, PCR fluorescent fragment length analysis of the 7 spliced leaders, allowed identifying L. major among infected P. obesus and P. vexillaris, and interestingly co-infection (L. major/L. infantum) among two P. obesus. We report here for the first time, the infection of P. obesus, from Central Tunisia, by L. infantum. Suggesting that P. obesus the known reservoir host of L. major, may also serve as reservoir host for L. infantum and thus play a role in the spread of sporadic cutaneous or visceral leishmaniasis in this region. Of equal importance, this work establish for the first time, the natural infection of P. vexillaris by different Leishmania species, suggesting its potential epidemiological role as reservoir host.

ObjectiveThis project aimed to develop and propose a standardised reporting guideline for kidney disease research and clinical data reporting, in order to improve kidney disease data quality and integrity, and combat challenges associated with the management and challenges of ‘Big Data’.MethodsA list of recommendations was proposed for the reporting guideline based on the systematic review and consolidation of previously published data collection and reporting standards, including PhenX measures and Minimal Information about a Proteomics Experiment (MIAPE). Thereafter, these recommendations were reviewed by domain-specialists using an online survey, developed in Research Electronic Data Capture (REDCap). Following interpretation and consolidation of the survey results, the recommendations were mapped to existing ontologies using Zooma, Ontology Lookup Service and the Bioportal search engine. Additionally, an associated eXtensible Markup Language schema was created for the REDCap implementation to increase user friendliness and adoption.ResultsThe online survey was completed by 53 respondents; the majority of respondents were dual clinician-researchers (57%), based in Australia (35%), Africa (33%) and North America (22%). Data elements within the reporting standard were identified as participant-level, study-level and experiment-level information, further subdivided into essential or optional information.ConclusionThe reporting guideline is readily employable for kidney disease research projects, and also adaptable for clinical utility. The adoption of the reporting guideline in kidney disease research can increase data quality and the value for long-term preservation, ensuring researchers gain the maximum benefit from their collected and generated data.

The management and analyses of large datasets is one of the grand challenges of modern biomedical research. Establishing methods to harmonise and standardise data collection, reporting, sharing and the employed data dictionaries, can support the resolution of these challenges whilst improving research quality, data quality and integrity, allowing sustainable knowledge transfer through re-usability, interoperability, reproducibility. The current project aimed to develop and propose a standardised reporting guideline for stroke research and clinical data reporting. Through systematic consolidation and harmonization of published data collection and reporting standards, several recommendations were drafted for the proposed guideline. These recommendations were reviewed by domain-researchers and clinicians using an online survey, developed in REDCap. The survey was completed by 20 international stroke-specialists, majority of respondents were based in Africa (10), followed by America, Europe and Australia (10). Of these respondents; the majority were working as dual clinician-researchers (57%) with more than 10 years’ experience in the field (78%). Data elements within the reporting standard were classified as participant-, study- and experiment-level information, further subdivided into essential or optional information, and defined using existing ontologies. The proposed reporting guideline can be employed for research utility and adapted for clinical utility as well. It is accompanied with an associated XML schema for REDCap implementation, to increase the user friendliness of data capturing, sharing, reporting and governance. Ultimately, the adoption of common reporting in stroke research has the potential to ensure that researchers gain the maximum benefit from their generated data and data collections.

The webinars series form part of the regular activities of any scientific consortium that aims to strengthen research activities and foster collaborations amongst the different partners. The webinars are intended to foster the exchange of ideas, build potential collaborations across multiple disciplines and enabling the participation and sharing of knowledge in current research. The Ten Simple Rules for organizing a webinar series can be summarized as follow: The webinar coordination team assists with all the planning and logistics for hosting a webinar (Rule 1); Choosing webinar themes requires mapping of the target audience needs and interest (Rule 2); Drafting a webinar planning checklist through regular planning meetings as well as post webinar meetings (Rule 3); Decentralized webinar organization of tasks and resources through accessible shared space (Rule 4); Planing early and settling on the provisional dates and times of the webinar events along with their themes (Rule 5); Choosing and settling on convenient and user friendly webinar platform (Rule 6); Approaching and confirming potential speakers (Rule 7); Obtaining the webinar title, abstract and presenter’s biography for creating the webinar announcement through emails and social media channels (Rule 8); Allocating time for the platform orientation (Rule 9); and Keeping close-up track of webinar metrics for regular assessment and evaluation (Rule 10). These Ten Simple Rules shared with the computational biology community will help those who have not yet ventured into training through webinars to learn from our experience. In our experience, the feedback from the post-webinar surveys clearly demonstrate that webinars are an effective way to create a two-way conversation between presenters and participants via a web-based platform.

International audience; : We developed a Leishmania infantum specific LAMP assay that was carried out using a set of, six primers targeting the cysteine protease B multi copy gene of L. infantum. Our result shows that we, successfully detect the L. infantum DNA and that amplification is specific as no cross reaction was seen, with L. major, L. tropica, L. turanica, L. aethiopica, L. tarentolae, L. gerbilii, Trypanosoma cruzi or, human genomic DNA. When compared to conventional cpb based PCR, the sensitivity of LAMP assay, was higher with a detection limit of 50fg/μl of genomic L. infantum parasite DNA. Accurate and rapid, diagnosis of canine leishmaniasis (CanL) is an important issue that allows early treatment and, prevents transmission. Our developed LAMP assay was used to evaluate occurrences of Leishmania infantum in seventy five (75) dogs from the field. Blood samples were used to perform LAMP assay, classical PCR, IFAT and microscopy that was used as gold standard. The IFAT in addition to, microscopy, are the basic techniques used for CanL diagnosis at the School of Veterinary Medicine, where we obtained our samples. Compared to molecular methods, the serology (IFAT) test shows the, best sensitivity (88.57%) with, however, a much lower specificity (52.5%) due to a relatively high, number of false-positive results (22 animals). The PCR assay shows a low sensitivity (37.14%) and, specificity around (82.5%). Our LAMP assay shows a suitable sensitivity (54%) and a good specificity, (80%), with however, positive (70%) and negative (66%) predictive values. Furthermore, the best, positive likelihood ratio (LR+) was obtained by LAMP assay (2.7). This technique presents the highest, kappa value (with a fair agreement of 0.34). Moreover, the relative stability of the reagents indicates, that LAMP may be a good alternative to a conventional PCR, especially under field conditions. Finally in, a brief cost evaluation, the LAMP assay compares favorably with other molecular diagnostic tests. This, is the first study that evaluates the L. infantum specific LAMP alongside other diagnostics tools for, CanL. Our results indicate a suitable sensitivity and specificity for the developed LAMP assay that could, has usefulness application on dogs and human L. infantum diagnosis.

International audience; Background: Theileria annulata is an economically important cattle disease in North Africa that occurs in subtropical and tropical areas. Accurate and rapid, molecular diagnosis of tropical theileriosis is an important issue that allows early treatment and, prevents transmission. We developed and validated a Theileria annulata specific LAMP assay targeting the cytochrome b multicopy gene, in order to increase the DNA detection sensitivity. Methods: The methodology was used to evaluate the occurrences of T. annulata in 88 field samples collected in Northern Tunisia during 2013-2014. The speci-ficity and sensitivity of the LAMP assays were compared to conventional cyto-chrome b PCR and routine microscopy commonly used on naturally infected cattle blood samples. Results: The PCR assay showed a sensitivity of 70% and specificity around 75%. Our LAMP assay showed a suitable sensitivity 78.7% and specificity 87.5%, with, however, positive (98.4%) and negative (29.1%) predictive values. Conclusion: The LAMP assay is a simple and convenient diagnostic tool for tropical theileriosis. Moreover, LAMP does not require experienced staff and specialized equipment for sampling procedures and it is practical outside laboratories and can be used for field diagnosis.