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

L'étude de la méthode de l'impact par plaque comme précurseur des phénomènes physiques et des processus chimiques

This manuscript aims at characterizing a new device based on a plate impact on a liquid surface to generate cavitation and evaluate its potential to induce chemical reactions. The device is composed of a reactor containing a liquid that a piston hits due to pressure difference. This impact generates a strong and uniform pressure increase in the medium followed by a depressurization. We show that the gas/vapor layer trapped between the piston and the liquid free surface influences the pressure peaks and frequencies generated in the medium. High-speed camera visualization shows that depressurization activates nucleation sites leading to bubble appearance in the solution. Bubbles expand and collapse intensively generating high velocity jets under some conditions. We also investigate the response of pre-existing bubbles. We identify a critical bubble radius that depends on the impact height, external pressure and piston’s characteristics. Bubbles with an initial radius larger than the critical one collapse at the moment of impact while smaller bubbles are only activated after it (under tension). Significant differences are observed in the pressure recordings after the impact depending on the presence/absence of large bubbles. We finally study the oxidation of phenol. We show that impacting on pure water is incapable of generating radical species responsible of the degradation. By adding hydrogen peroxide as an oxidant we show that the molecule is decomposed under certain conditions. In general, the amount of hydrogen peroxide required to initiate a significant oxidation decreases when increasing the intensity of the impact on which the degradation rate mainly depends.Ce manuscrit a pour but d'étudier un nouveau dispositif générateur de cavitation dont le potentiel favorable à l'intensification de réactions chimiques est évalué. Ce dispositif est constitué d'une plaque mobile qui frappe un liquide contenu dans un réacteur. L'impact génère une forte augmentation de pression dans le milieu suivi d'une dépressurisation. Nous montrons que la couche de gaz/vapeur piégée entre le piston et la surface du liquide influence les pics de pression et les fréquences générées dans le milieu. La visualisation à l'aide d'une caméra rapide montre que la dépressurisation active les sites de nucléation à l'origine des bulles de cavitation qui grandissent et implosent en générant occasionnellement des jets de grande vitesse. Nous étudions aussi la réponse de bulles préexistantes. Nous identifions un rayon de bulle critique qui dépend de la hauteur d'impact, de la pression extérieure et des caractéristiques du piston. Les bulles dont le rayon initial est supérieur à la valeur critique implosent au moment de l'impact, tandis que les petites bulles ne sont activées qu'après (sous tension). Des évolutions de pression différentes sont observées après l'impact en fonction de la présence/absence de grandes bulles. Nous étudions enfin l'oxydation du phénol en montrant que l'impact sur l'eau pure est incapable de générer des espèces radicalaires responsables de la dégradation. En ajoutant du peroxyde d'hydrogène comme oxydant, la molécule est décomposée sous certaines conditions. En général, la quantité d'oxydant requise pour déclencher une oxydation significative diminue lors de l'augmentation de l'intensité de l'impact sur lequel dépend le taux de dégradation

Investigation of the collapse of bubbles after the impact of a piston on a liquid free surface

International audienceA novel technique based on the impact of a piston on a liquid confined in a vessel is described. Pressure measurements reveal that strong pressure variations (up to 100 atmospheres) with a rich content of frequencies are efficiently transmitted to the liquid. High-speed camera visualizations show that pre-existing millimetric bubbles always collapse during the first instants of the impact whereas the behavior of submillimetric bubbles depends on the features of the pressure evolution in the system. In addition to the impact velocity, the amount of gas/vapor trapped between the piston and the liquid's surface plays an important role on how pressure evolves. Only when negative pressure occurs tiny bubbles grow significantly and collapse. The violent collapse of bubbles promote turbulence and mixing at very small length-scales which renders this technique interesting to intensify processes limited by heat and mass diffusion

Influence of acid–base properties of Mg-based catalysts on transesterification: role of magnesium silicate hydrate formation

International audienceThe transesterification reaction assisted through heterogeneous basic catalysis was thoroughly studied because of its importance in transforming biomass, as for biodiesel production or lactone opening. As catalysts with the strongest basic properties are not always the most efficient ones, a series of magnesium-based materials, exhibiting a large range of acido–basic properties, was investigated. Moreover, in order to compare gas and liquid phases operating conditions, a model reaction (transesterification of ethyl acetate with methanol) was chosen. It appears that gas phase transesterification (at 393 K) requires strong basic sites, whereas magnesium silicate, exhibiting moderate basicity together with acidic properties, is a very reactive catalyst in the liquid phase (at 333 K) depending on its preparation method. The set of experimental data (XRD, XPS, DRIFTS, MEB, 29Si and 25Mg NMR) demonstrated that a magnesium silicate hydrate structure (MSH) is formed at the surface of the most active silicates. It is thus concluded that different mechanisms operate under gas and liquid conditions, and that among the magnesium silicate materials, the MSH phase exhibits specific acido–basic properties beneficial to this kind of reaction