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

Monte Carlo Calculation of the X-Ray Depth Distributions in an Aluminum Target

A Monte-Carlo simulation of inelastic scattering process developed by Terrissol has been modified and used to calculate X-Ray depth distributions. The elastic scattering is modelled using the Mott collision cross-section and the Hartree-Fock atomic potential. The validity of this model is discussed in a comparison between the Monte-Carlo results and experimental data describing the energy distribution of backscattered electrons and energy loss data

Analytical description of mirror plot in insulating target

International audienceA method has been developed to link the geometry of the trapped charge distribution within irradiated insulators to the mirror plot shape, in a scanning electron microscope. We give a detailed analysis of the geometrical optic approximation which is used to evaluate the mirror image formation. We establish then analytical mirror relations obtained for diverse trapped charge distributions such as homoïdal charge distribution, bipunctual and cylindrical ones. Knowledge of the charge distribution first moments enables us to investigate then their effect on the first terms of the mirror expression limited development. Finally, we apply these analytical expressions to evaluate certain characteristics of the charge distribution from an experimental mirror plot

Contribution à l'étude des effets de charge sur l'émission X des matériaux isolants non métallisés

International audienceThe presence of charges perturbs the microanalysis-X on insulator samples. Attempt to suppress these effects have been fruitless and a better understanding of the charge phenomenon is the only way to a clear interpretation of the results of a microanalysis-X.From a simulation of the charges implanted by an electron beam on an insulator target, we compute, as a fuction of the integrated dose, the caracteristics of the emitted X-rays, such as the generating function phi(rho z) or the intensity of caracteristic lines. We underline the role of the electric field on the primary beam and on the electron trajectories in the target. These results allow the analysis of experimentally measured X-rays. Our studies on the effects of the diameter of the probe and on the exposure time led us to establish the best conditions for the successful microanalysis-X of an insulator

Space charge in irradiated insulators: mirror method

International audienceA scanning electron microscope mirror method analysis has been developed to study the geometry of the trapped charge distribution within irradiated insulators. Several authors have noted that the optical geometrical approximation is an appropriate model to illustrate the mirror image formation. Nevertheless, some results have shown that it is not possible to use such model in the case of anisotropic material in which we can observe an elliptic mirror image. In this paper, we propose a new theoretical model to explain the formation of such elliptic mirror, which confirms the electric charge delocalization

HLA Class III: A susceptibility region to systemic lupus erythematosus in Tunisian population

<div><p>Background and objectives</p><p>Short tandem repeats (STR) are usually used as informative polymorphic markers for genetic mapping and for disease susceptibility analysis. The involvement of these microsatellite markers localized in the MHC region was reported in many auto-immune diseases.</p><p>In this study we analyzed for the first time eight polymorphisms of microsatellite loci at the HLA region: D6S291, D6S273, TNFa, b and c, MICA, D6S265 and D6S276, in Tunisian systemic lupus erythematosus (SLE) patients.</p><p>Materials and methods</p><p>We performed a case control study in which the microsatellite loci were amplified using specific primers labeled with NED, VIC, PET or 6-FAM and analyzed using GeneScan software 3.7. For the statistical analysis, we used SPSS software and we performed a sub-haplotype scoring test using the haplo.stats software developed in the R language.</p><p>Results</p><p>We found that two mean associated regions existed; the most statistically significant encompassed the 3 TNF markers (p = 0.0003, OR = 19.34); the latter covered the DR region. In fact, when scoring haplotypes in 3 marker- sliding windows, the p value increased as we moved away from the TNF region and decreased again when we approached the DRB1 locus. We also established for the first time the negative association between alleles of D6S291 and SLE. The majority of clinical and serological correlations were noted with TNF alleles.</p><p>Conclusion</p><p>Our results confirm the association between TNF and DRB1 polymorphisms and SLE. The association between alleles of D6S291 and SLE needs however to be verified by the analysis of other markers beyond this region.</p></div

Clinical and serological associations with STR markers.

<p>Clinical and serological associations with STR markers.</p

Characteristics of studied STR.

<p>Characteristics of studied STR.</p

Allelic distribution of STR markers.

<p>Allelic distribution of STR markers.</p

Clinical and immunological manifestations in our patients.

<p>Clinical and immunological manifestations in our patients.</p