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

Les modes alternatifs de règlement des conflits dans le droit des contrats

El-Hakim Jacques. Les modes alternatifs de règlement des conflits dans le droit des contrats. In: Revue internationale de droit comparé. Vol. 49 N°2, Avril-juin 1997. pp. 347-357

Cloning and sequence analysis of human calcyphosine complementary DNA

Calcyphosine, initially identified as thyroid protein p24, is a calcium-binding protein containing four EF-hand domains. It was first cloned and characterized in the dog and corresponds to R2D5 antigen in rabbit. Using the canine calcyphosine cDNA sequence as a probe, we have isolated its human counterpart from a thyroid cDNA library. The two sequences display a high degree of conservation, both at nucleotide and deduced amino acid levels. Sequence comparison with other proteins showed that the closest homologue of calcyphosine is the crustacean CCBP-23 protein. Northern blot analysis revealed that calcyphosine messenger RNA is much less abundant in human than in canine thyrocytes. Western blot experiments indicated that the amount of protein is also dramatically reduced in man compared to dog.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

The NRC 3-D Laser Tracking System: IIT's Contribution to the International Space Station Project

Advances in the 3D sensing of dynamics and unstructured environments require the development of intelligent systems, algorithms, and methods to replace or at least minimize the human intervention to the 3D acquisition process. From the user point of view, most existing 3D acquisition systems still require static techniques that can be considered archaic when compared to current 2D still cameras and video. For dynamically uncontrolled environments, the dynamics of the 3D system is becoming very important. Space applications provide an initial impetus to reach this objective, for uncontrolled and harsh environments. This paper will summarize the work that the National Research Council of Canada has pursued in the development of sensing, dynamic tracking, and intelligent acquisition systems for space applications.Les progr\ue8s r\ue9alis\ue9s dans la d\ue9tection 3D d'environnements dynamiques et non structur\ue9s exigent la mise au point de m\ue9thodes, d'algorithmes et de syst\ue8mes intelligents dans le but de remplacer ou d'au moins r\ue9duire au minimum l'intervention humaine dans le processus d'acquisition 3D. Du point de vue de l'utilisateur, les syst\ue8mes d'acquisition 3D exigent encore, dans la plupart des cas, des techniques statiques qu'on peut consid\ue9rer comme archa\uefques lorsqu'on les compare aux vid\ue9os et aux appareils photo 2D actuels. Dans le cas des environnements sans contr\uf4le dynamique, la dynamique des syst\ue8mes 3D devient tr\ue8s importante. Les applications spatiales donnent l'\ue9lan initial pour atteindre cet objectif dans le cas des environnements non contr\uf4l\ue9s et difficiles. Le pr\ue9sent document r\ue9sumera le travail que le CNRC a men\ue9 pour mettre au point des syst\ue8mes de d\ue9tection, de poursuite dynamique et d'acquisition intelligente en vue d'applications spatiales.NRC publication: Ye

Laser Range Imaging in Archaeology: Issue and Results

Archaeology is emerging as one of the key areas of applications for laser range imaging. This particular context imposes a number of specific constraints on the design and operations of range sensors. In this paper, we discuss some of the issues in designing and using laser range sensor systems for archaeology. Results obtained on remote archaeological sites will serve to illustrate these considerations.L'arch\ue9ologie est l'un des nouveaux domaines importants d'application de l'imagerie par t\ue9l\ue9m\ue9trie laser. Son contexte particulier impose un certain nombre de contraintes sur la conception et le fonctionnement des t\ue9l\ue9m\ue8tres. Dans cette communication, nous discutons certains des probl\ue8mes propres \ue0 la conception et l'utilisation de syst\ue8mes de t\ue9l\ue9m\ue9trie laser en arch\ue9ologie. Nous illustrons ces observations, \ue0 partir de r\ue9sultats obtenus sur des sites arch\ue9ologiques \ue9loign\ue9s.NRC publication: Ye

Real World Modelling Through High Resolution Digital 3D Imaging of Objects Structures

NRC publication: Ye

Crohn’s Disease is associated with Toll-like receptor (TLR)-4 polymorphism Asp299Gly: Further evidence for a deficient bacterial recognition in the triggering of the disease

info:eu-repo/semantics/publishe

Cyclosporine bone remodeling effect prevents steroid osteopenia after kidney transplantation

Cyclosporine bone remodeling effect prevents steroid osteopenia after kidney transplantation.BackgroundIt is well established that prednisone above 7.5 mg/day may induce osteopenia in association with decreased bone formation. In contrast, the effect of cyclosporine on bone remodeling and bone mineral density (BMD) is controversial. Multiple confounding factors explain this controversy, especially after renal transplantation.MethodsFifty-two renal transplanted patients never exposed to aluminum while on dialysis were selected because they had no rejection and no hypercalcemia for 24 months while being treated with low dose prednisone/cyclosporine A (daily dose at 10 mg and 4.8 mg/kg, respectively, beyond 3 months). Bone remodeling markers (BRMs; plasma osteocalcin, bone and total alkaline phosphatases for formation, and urinary pyridinolines for resorption) were sequentially measured together with plasma creatinine, intact parathyroid hormone (PTH) and 25 OH vitamin D and cyclosporine from day 0 to 24 months. BMD was measured at 3, 6, 12, and 24 months by quantitative computerized tomography (QCT) at the lumbar spine and by double-energy x-ray absorptiometry (DEXA) at this site, as well as at the femoral neck, radius shaft, and ultradistal (UD) radius.ResultsPlasma concentrations of creatinine, PTH, and 25 OH vitamin D initially decreased and stabilized beyond three months at 137 μmol/L, 1.5 the upper limit of normal (ULN) and 11 ng/mL, respectively. All BRM increased significantly above the ULN at six months and then decreased. The BMD Z score at three months was low at all sites measured by DEXA and QCT. Follow-up measurements showed stability of absolute value and of Z score at all sites measured by DEXA. A comparison of the lumbar QCT Z score, which was available in 42 patients at 3 and 24 months, showed an increase in 28 and a decrease in 14, so that the increase for the whole group was significant (P < 0.04). Compared with patients with a decreased Z score, those with an increased Z score had significantly higher cyclosporine and lower prednisone dosages and a greater BRM increase at six months, whereas age, sex ratio, and plasma creatinine, PTH and 25 OH vitamin D were comparable and stable from months 3 through 24. The mean trough level of cyclosporine for the first six months was positively correlated to osteocalcin and total alkaline phosphatase increase at six months, and both bone formation and resorption marker increases were significantly correlated to the lumbar QCT Z score increase at 24 months.ConclusionsCombined low-dose prednisone and cyclosporine immunosuppression are associated with a stabilization of BMD measured at all sites with DEXA 3 to 24 months after renal transplantation and with a prevention of age-related loss of vertebral trabecular bone, as shown by the significant increase in lumbar spine QCT Z score. It is suggested that cyclosporine, together with the decrease of prednisone dosage but independent of renal function, PTH, and vitamin D status, contributes to a transient stimulation of bone remodeling at six months, which counterbalances the deleterious effect of prednisone on bone formation and BMD

Active Optical 3-D Imaging for Heritage Applications

NRC publication: Ye