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

Nouveau modèle structural des membranes Nafion ®, polymère de référence pour l'application pile à combustible basse température

au micromètre en relation avec les propriétés de transport, est primordiales pour l'optimisation des systèmes pile à combustible H2/O2. Nous Une compréhension globale de la structure des membranes ionomères Nafion® de l'Ångström proposons un nouveau modèle structural de type fibrillaire, basé sur l'agrégation des chaînes polymères, permettant d'expliquer de façon continue le processus d'hydratation de la membrane sèche à la suspension colloïdale. Par le biais de techniques de diffusion de rayonnement aux petits angles (RX & neutrons) et de microscopie (AFM & TEM) nous avons étudié l'organisation du polymère sur une large gamme d'échelle et de teneur en eau. Les corrélations entre les propriétés de transport et la structure ont été discutées. L'analyse des expériences de membranes sous contraintes a permis de conforter notre modèle et a mis en évidence l'effet de l'orientation sur la conduction protonique.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

In vivo measurement of the size of oil bodies in plant seeds using a simple and robust pulsed field gradient NMR method

International audienceAn easy to implement and convenient method to measure the mean size of oil bodies (OBs) in plant seeds is proposed using a pulsed field gradient nuclear magnetic resonance (PFGNMR) approach. PFGNMR is a well-known technique used to study either free or restricted diffusion of molecules. As triacylglycerols (TAG) are confined in OBs, analysis of their diffusion properties is a well-suited experimental approach to determine OB sizes. In fact, at long diffusion time, TAG mean squared displacement is limited by the size of the domain where these molecules are confined. In order to access the OB size distribution, strong intensities of magnetic field gradients are generally required. In this work we demonstrate for the first time that a standard liquid-phase NMR probe equipped with a weak-intensity gradient coil can be used to determine the mean size of OBs. Average sizes were measured for several seeds, and OB diameters obtained by PFGNMR were fully consistent with previously published values obtained by microscopy techniques. Moreover, this approach provided evidence of TAG transfer through the network of interconnected OBs, which is dependent on the ability of adjacent membranes to open diffusion routes between OBs. The main advantage of the NMR method is that it does not require any sample preparation and experiments are performed with whole seeds directly introduced in a standard NMR tube

Water sub-diffusion in membranes for fuel cells.

International audienceWe investigate the dynamics of water confined in soft ionic nano-assemblies, an issue critical for a general understanding of the multi-scale structure-function interplay in advanced materials. We focus in particular on hydrated perfluoro-sulfonic acid compounds employed as electrolytes in fuel cells. These materials form phase-separated morphologies that show outstanding proton-conducting properties, directly related to the state and dynamics of the absorbed water. We have quantified water motion and ion transport by combining Quasi Elastic Neutron Scattering, Pulsed Field Gradient Nuclear Magnetic Resonance, and Molecular Dynamics computer simulation. Effective water and ion diffusion coefficients have been determined together with their variation upon hydration at the relevant atomic, nanoscopic and macroscopic scales, providing a complete picture of transport. We demonstrate that confinement at the nanoscale and direct interaction with the charged interfaces produce anomalous sub-diffusion, due to a heterogeneous space-dependent dynamics within the ionic nanochannels. This is irrespective of the details of the chemistry of the hydrophobic confining matrix, confirming the statistical significance of our conclusions. Our findings turn out to indicate interesting connections and possibilities of cross-fertilization with other domains, including biophysics. They also establish fruitful correspondences with advanced topics in statistical mechanics, resulting in new possibilities for the analysis of Neutron scattering data

Microphase Structure of Poly(N-isopropylacrylamide) Hydrogels As Seen by Small- and Wide-Angle X-ray Scattering and Pulsed Field Gradient NMR

International audienceAbove the lower critical solution temperature Tc (ca. 34 °C), poly(N-isopropylacrylamide) hydrogels become weakly hydrophobic and undergo microphase separation. Macroscopic deswelling, however, is extraordinarily slow, the out-of equilibrium state of the gel being conserved for many days. In this article the structure of the microphase-separated state above Tc is probed by small-angle X-ray scattering and by pulsed field gradient NMRof the protons of water, both in the water phase and in the polymer-rich phase. Above Tc the gel comprises two microphases, separated by smooth interfaces. The cavities occupied by the water phase form a connected network. The diffusion rate of the water molecules in this phase varies from one cavity to another and can be described by a Gaussian distribution. Water molecules belonging to the polymer-rich phase are also mobile, but their self-diffusion coefficient D is greatly diminished. Absence of compartmentalization of the water phase implies that the slow deswelling rate of the gel is not due to trapping of the water phase

NMR 1D-imaging of water infiltration into mesoporous matrices

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Water crystallization inside fuel cell membranes probed by X-ray scattering

International audienceWater properties in ionomer membranes at sub-zero temperatures are investigated as a function of water volume fraction using a micro X-ray beam scanning the membranes along their thicknesses. The influence of both the size of confinement and the membrane nature on water behavior is analyzed. The study is focused on Nafion ® membranes at different water contents to tune the size of water confinement and on water-saturated sulfonated polyimide (sPI) membrane. The scattering curves show that water does not crystallize inside Nafion ® membrane up to a characteristic size of water confinement of 3 nm. Water does crystallize inside Nafion ® for characteristic size of ionic domains larger than 5 nm, i.e. for hyperswollen state. In order to predict qualitatively the freezing occurrence of water in the Nafion ® matrix, the Gibbs-Thomson model was considered; both the effect of confinement and acidity were taken into account. In this context, the water-Nafion ® interfacial tension was determined using a contact angle experiment. The model is in accordance with a water crystallization occurring inside Nafion ® provided that it is highly swollen. However, water behavior is also strongly dependent on the nature of the membrane. In the case of water-saturated sulfonated polyimide, a hydrocarbon based membrane, water does not crystallize upon cooling but does not desorb upon annealing in contrast to Nafion ® membrane exposed to the same external conditions (temperature and relative humidity). Hence, the host-water interaction appears as a crucial parameter to take into account to describe properly the sorption-desorption and freezing phenomena

QENS investigation of proton confined motions in hydrated perfluorinated sulfonic membranes and self-assembled surfactants

We report on QuasiElastic Neutron Scattering (QENS) investigations of the dynamics of protons and water molecules confined in nanostructured perfluorinated sulfonic acid (PFSA) materials, namely a commercial Aquivion membrane and the perfluorooctane sulfonic acid (PFOS) surfactant. The former is used as electrolyte in low-temperature fuel cells, while the latter forms mesomorphous self-assembled phases in water. The dynamics was investigated as a function of the hydration level, in a wide time range by combining time-of-flight and backscattering incoherent QENS experiments. Analysis of the quasielastic broadening revealed for both systems the existence of localized translational diffusive motions, fast rotational motions and slow hopping of protons in the vicinity of the sulfonic charges. The characteristic times and diffusion coefficients have been found to exhibit a very similar behaviour in both membrane and surfactant structures. Our study provides a comprehensive picture of the proton motion mechanisms and the dynamics of confined water in model and real PFSA nanostructures

QENS investigation of proton confined motions in hydrated perfluorinated sulfonic membranes and self-assembled surfactants

International audienceWe report on QuasiElastic Neutron Scattering (QENS) investigations of the dynamics of protons and water molecules confined in nanostructured perfluorinated sulfonic acid (PFSA) materials, namely a commercial Aquivion membrane and the perfluorooctane sulfonic acid (PFOS) surfactant. The former is used as electrolyte in low-temperature fuel cells, while the latter forms mesomorphous self-assembled phases in water. The dynamics was investigated as a function of the hydration level, in a wide time range by combining time-of-flight and backscattering incoherent QENS experiments. Analysis of the quasielastic broadening revealed for both systems the existence of localized translational diffusive motions, fast rotational motions and slow hopping of protons in the vicinity of the sulfonic charges. The characteristic times and diffusion coefficients have been found to exhibit a very similar behaviour in both membrane and surfactant structures. Our study provides a comprehensive picture of the proton motion mechanisms and the dynamics of confined water in model and real PFSA nanostructures