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

Etude thermodynamique et structurale du film pur de tétrachlorure de carbone et des films mixtes (krypton-tétrachlorure de carbone) et (méthane-tétrachlorure de carbone) physisorbés sur graphite

Non disponible / Not availableLa caractérisation thermodynamique et structurale du film tétrachlorure de carbone sur les plans de base du graphite a été mesurée par volumétrie d'adsorption entre 205 et 260 kelvins et par diffraction de rayons X entre 45 et 240 kelvins. Elle a permis de proposer un diagramme de phases avec apparition de la deuxième couche adsorbée à 217 kelvins et fusion continue du film en première couche. Les températures critiques de condensation des première et deuxième couches sont respectivement 233 et 239 kelvins. L'étude thermodynamique et structurale (par diffraction de rayons X et diffraction de neutrons) des couches mixtes krypton-tétrachlorure de carbone et méthane-tétrachlorure de carbone met en évidence le déplacement partiel du film pré-déposé par l'adsorbat le moins condensable. La miscibilité du tétrachlorure de carbone avec le krypton ou le méthane dans la couche adsorbée est très faible sinon inexistante

Green rusts and their relationship to iron corrosion; a key role in microbially influenced corrosion

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Bioreduction of Pb-substituted ferrihydrite: impact on the nature of the biogenic minerals formed, the speciation and bioavailability of Pb

International audienceLevels of metals in terrestrial environments are an increasing concern, due to their threat to human health and ecosystem quality (Panagos et al., 2013). While metals risk assessment studies focused on their total concentration, research are currently oriented toward the evaluation of their speciation and bioavailability. Ferrihydrites (Fh), due to their large surface area and reactive surface properties, are important carrier phases in soils on which metals can be adsorbed or coprecipitated with (Tiberg, 2016). However, anaerobic transformation of such oxides in presence of dissimilatory iron reducing (DIR) bacteria like Shewanella oneidensis sp., may result in metals redistribution between the soil solution and the new (bio)formed Fe minerals (Frierdich et al., 2011). Further, the presence of metals in Fh may influence the nature of the (bio)formed minerals. To further our understanding, pure and Pb-substituted Fh (Pb/(Pb+FeIII) molar ratios of 2 and 5 %) were synthesized by coprecipitation (Schwertmann and Cornell, 2000). These Fh were incubated separately in anaerobic conditions with Shewanella oneidensis MR-1 cells in an appropriate liquid medium, for: i) 21 days (prolonged bioreduction), and ii) two 7-day periods separated by a 7-day aerobic oxidation (successive redox cycles). The nature of the (bio)formed minerals was assessed using XRD and Mössbauer spectroscopy. The bioreduction extent was measured thanks to the ferrozine method and UV-visible spectroscopy, and the partitioning of Pb between the liquid and solid phases was assessed using AAS. Finally, Pb bioavailable content in solution was determined using whole cell biosensors. Magnetite (M) was the main mineral obtained after the prolonged bioreduction (97 %), and increasing proportions of goethite (Gh) formed with Pb substitution (22 and 35 % for systems made with Pb/(Pb+FeIII) molar ratios of 2 and 5 % respectively). Gh and lepidocrocite were found to form in shorter bioreduction periods (1st anaerobic period of the successive redox cycles). The aerobic oxidation converts all the (bio)formed minerals to a poorly crystallized phase except in the highest Pb substituted system. Following the 2nd anaerobic period, M and Gh formed, while no change occurred in the highest Pb substituted system. Only minor amounts of the Pb introduced in the systems within the Fh used were found in the liquid phase and were not bioavailable. Most of the Pb introduced was associated to the (bio)formed minerals, whatever the nature of those minerals. Our results show the complex succession of (bio)formed minerals during bioreduction, the impact of a Pb substitution within ferrihydrite on the nature of the (bio)formed minerals and how these minerals act as efficient carrier phases of Pb

Biogenic Mineral Precipitation during Antimony bearing Ferrihydrite bioreduction

International audienceFe(III) oxide such as ferrihydrite are ubiquitous in sediments and soils and due to their large surface area and reactive surface properties, they can be important sorbents of metal and metalloid such as antimony (Sb). Sorption and co-precipitation are considered to be the predominant processes by which most of the metals are scavenged by iron oxides, although co-precipitation appears to be more efficient for the removal of metals from solution. However, co-precipitated metals can be released to the surrounding environment as a direct or indirect consequence of dissimilatory iron reduction (DIR), which is a microbial reduction process of geochemical importance in natural systems. Even if DIR is often implicated in the remobilization of metals, the subsequent bio-mineralization processes can lead to their sequestration into secondary mineral products. Therefore, the aim of our study was to investigate Sb behavior during DIR. Sb-bearing ferrihydrites, with variable Sb/(Fe+Sb) molar ratios, were synthezised by coprecipitation and incubated with an iron reducing bacteria, Shewanella oneidensis MR1. Chemical analysis were undertaken to monitor the rate and the extent of the bioreduction and the mobilisation of Sb. Mössbauer analysis were carried out to characterize the bulk cation properties of the biogenic minerals at different temperatures. The spectra were fitted to obtain degrees of oxidation of iron and therefore it's mineralogical signature. Measurements of the magnetization with respect to applied magnetic field were also carried out at room and low temperature and coercivity, saturation magnetization and remanence data obtained from hysteresis loops. The results revealed that the presence of Sb impacted the extent of reduction but no significant difference was measured in the rate of Fe(III) reduction. Although, the precipitaion of biogenic magnetite was evidenced independently of the intial Sb/(Fe+Sb) molar ratios, the biogenic magnetites displayed variable structural and magnetic properties implying an incorporation of Sb in their crystallographic structure

Evidence for the Fe(II)-Fe(III) Green Rust "Fougérite" mineral occurrence in a hydromorphic soil and its transformation with depth

International audienceMössbauer spectroscopy is used to characterize a Green Rust as a natural mineral for the first time. Samples are taken from a hydromorphic soil under the forest at Fougères (Brittany, France) during spring season. Spectra are compared with those of synthetic Green Rusts (GRs), i.e. hydroxy-chloride, -sulphate, -carbonate and display one ferric and one or two ferrous sites. Fe(II)/Fe(III) abundances ratio cannot be attributed definitely to one of those stoichiometric compounds. Therefore, the counter-anion species cannot be specified even though hyperfine parameters perfectly match values of synthetic samples. The Fe(II)/Fe(III) ratio obtained from the Mössbauer spectra decreases with sampling depth. The "fougerite" originates likely from the reduction of deeper Fe(III)-mineral species by anoxic waterlogging

Hydroxy-nitrite green rust: a new type of green rust formed as an intermediate reaction product

International audienceThe presence of high nitrite concentrations due to anthropogenic activities is an important water quality concern as nitrite is highly toxic to human and fauna. Nitrite toxicity is related to its transformation into carcinogenic N-nitroso compounds that are suspected to be responsible for some gastric cancers, and to its ability to convert the hemoglobin to methaemoglobin what is then unable to fix oxygen and to transport it to the tissues, resulting in hypoxia and the blue-baby syndrome [1]. To reduce the adverse effect of nitrite on human health, any process enhancing the transformation of nitrite ions to nitrogen gas is of interest for the remediation processes. This purpose can be achieved by using green rusts (GR) that are mixed iron(II-III) layered double hydroxides, commonly found in anoxic zones of natural environments. They play an important role in the geochemical redox cycling of iron and nitrogen, and can affect the speciation and mobility of many (in)organic contaminants. Here we investigate nitrite reduction by biogenic iron(II-III) hydroxycarbonate green rusts under anoxic conditions. Results reveal that biogenic GR are capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite to nitrogen gaseous species. Moreover, the study provides evidence for the first time of the formation of a hydroxy-nitrite green rust as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides

As(V) and As(III) sequestration by starch functionalized magnetite nanoparticles: influence of the synthesis route onto the trapping efficiency

We report the effect of the synthesis route of starch-functionalized magnetite nanoparticles (NPs) on their adsorption properties of As(V) and As(III) from aqueous solutions. NP synthesis was achieved by two different routes implying the alkaline precipitation of either a mixed Fe2+/Fe3+ salt solution (MC samples) or a Fe2+ salt solution in oxidative conditions (MOP samples). Syntheses were carried out with starch to Fe mass ratio (R) ranging from 0 to 10. The crystallites of starch-free MC NPs (14 nm) are smaller than the corresponding MOP (67 nm), which leads to higher As(V) sorption capacity of 0.3 mmol gFe−1 to compare with respect to 0.1 mmol gFe−1 for MOP at pH = 6. MC and MOP starch-functionalized NPs exhibit higher sorption capacities than a pristine one and the difference in sorption capacities between MOP and MC samples decreases with increasing R values. Functionalization tends to reduce the size of the magnetite crystallites and to prevent their agglomeration. Size reduction is more pronounced for MOP samples (67 nm (R0) to 12 nm (R10)) than for MC samples (14 nm (R0) to 9 nm (R10)). Therefore, due to close crystallite size, both MC and MOP samples, when prepared at R = 10, display similar As(V) (respectively, As(III)) sorption capacities close to 1.3 mmol gFe−1 (respectively, 1.0 mmol gFe−1). Additionally, according to the effect of pH on arsenic trapping, the electrostatic interactions appear as a major factor controlling As(V) adsorption while surface complexation may control As(III) adsorption