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

Ecological applications of Pseudomonas as a biopesticide to control two-spotted mite Tetranychus urticae: chitinase and HCN production

The two-spotted spider mite (Tetranychus urticae Koch) is an important pest of many horticultural crops. A study was conducted to evaluate the effect of three fluorescent Pseudomonas isolates obtained from rhizospheric soil of tomato (Solanum lycopersicon) in Agadir, Morocco: Q110B, Q036B and Q172B, as potential biological control agents for T. urticae. Both acaricide and repellent activities were assessed on homogenous adult mites. The acaricidal activity test evaluated five concentrations of bacterial suspensions: 0 (control), 102, 104, 106, 108, and 1010 cfu ⋅ ml–1, while only the 1010 cfu ∙ ml−1 concentration of each bacterium was used for the repellent bioassay. The mortality rate and repellentindex were recorded 24, 48 and 72 h after application. Results indicated that the survival rate of T. urticae was reduced (p ≤ 0.01) by all three bacterial isolates compared to control. Within the 24–72 h time period the mortality rates ranged from 8 to 87%, 16 to 99%, and 13 to 89%, for Q110B, Q036B and Q172B isolates, respectively. The isolate Q036B (LC50 = 0.598 cfu ⋅ ml–1) provided higher mortality rates than Q172B and Q110B with LC50 values of 90,846 and 169,585 cfu ⋅ ml–1, respectively. Repellent activity was also the highest with Pseudomonas Q036B having a 71% repellence index at 48 h after application. Regarding the mechanism of action, all three isolates produced hydrogen cyanide, and exhibited protease and cellulose activities, although only Q036B and Q172B had potential chitinase action. Identification analysis showed that the isolates were either Pseudomonas putida (Q172B) or P. fluorescens (Q110B and Q036B). Our results indicate that the P. fluorescens isolate Q036B is a promising candidate for biological control of T. urticae, and has potential to contribute to an integrated pest management program to control this important pest. Then the fruits produced will be qualified as safe for consumers and the environment. The present work was customized to give support for policy decision makers as an agroecological potential meeting needs of industries and ecological balance

Mapping of Hydrothermal Alteration Zones in the Kelâat M’Gouna Region Using Airborne Gamma-Ray Spectrometry and Remote Sensing Data: Mining Implications (Eastern Anti-Atlas, Morocco)

The mapping of hydrothermal alteration zones associated with mineralization is of paramount importance in searching for metal deposits. For this purpose, targeting alteration zones by analyzing airborne geophysical and satellite imagery provides accurate and reliable results. In the Kelâat M’Gouna inlier, located in the Saghro Massif of the Moroccan Anti Atlas, natural gamma-ray spectrometry and ASTER satellite data were used to map hydrothermal alteration zones. Natural gamma-ray spectrometry data were processed to produce maps of Potassium (K in %), Uranium (eU in ppm), Thorium (eTh in ppm) and ratios of K/eTh and K/eU. In addition, four-band ratios were computed, on ASTER data, to map the distribution of clay minerals, phyllitic minerals, propylitic minerals, and iron oxides. The combined results obtained from geophysical and satellite data were further exploited by fuzzy logic modelling using the Geographic Information System (GIS) to generate a mineral prospectivity map. Seven hydrothermal alteration zones likely to be favorable for mineralization have been identified. They show a spatial correlation with (i) known surface prospects and mineral occurrences, (ii) the granite-encasing contact zone, and (iii) the fault zones (Sidi Flah and Tagmout faults). This research therefore provides important information on the prospecting of mineral potential in the study area

Mineral prospectivity mapping: a potential technique for sustainable mineral exploration and mining activities – a case study using the copper deposits of the Tagmout basin, Morocco

Mineral prospectivity mapping (MPM) based on the principle of geometric mean was applied to stream sediment geochemical, fault density, and aeromagnetic data from Tagmout basin, Morocco to determine new areas for optimizing copper exploration. The application of a fuzzy operator using stream sediment data, factor analysis, and fault density map, allowed weights to be assigned to these parameters so that the MPM function can process them to indicate the most favorable zones of copper mineralization. The model's accuracy as evaluated using a normalized density index (Nd with value 1.22) shows the reliability of the method. The potential copper concentration areas represent 8.22% of the entire basin of which 30% are concentrated in the western portion of the basin and other significant areas are in the southwest and northeast portions. The results indicate that MPM is a powerful technique for planning exploration programs that aim for sustainable mining activities

Litho-structural interpretation of aeromagnetic anomalies reveals potential for mineral exploration in Tizi n'Test Region, Western High Atlas, Morocco

Abstract This study interprets aeromagnetic data from the Tizi n'Test area in the High Atlas massif of Morocco, aiming to gain insights into its litho-structural architecture and implications for mineral exploration and mining. We employed six different analytical techniques to the residual magnetic field data, including reduction to the pole (RTP), upward continuation, total horizontal derivative, Tilt angle, Centre for Exploration Targeting (CET) analysis, and Euler deconvolution. Our analyses differentiated the study area into three magnetic domains: the eastern Ouzellarh block, characterized by positive anomalies, a central domain characterized by a negative magnetic signature demarcating the transitional zone between the Anti-Atlas and the High Atlas separated by the Ouchden fault: and the western domain, represented by the Tichka massif. The application of total horizontal derivative, tilt angle, and a combination of filters in ternary image formats (Tilt angle, upward continuation 1000 + Tilt angle and upward continuation 3000 + Tilt angle) revealed both known and previously unidentified geological lineaments, mapping structural complexity across various orientations (NE–SW, NNE–SSE, E–W, NW–SE, and N–S). The CET grid analysis method unveiled the structural complexity, highlighting the geodynamic evolution of the region. Particularly, the Ouchden fault delineates a magnetic domain divide between the ancient High Atlas and the Ouzellarh block (Anti-Atlas). Furthermore, Euler deconvolution indicated magnetic source depths ranging from 52 m in the western domain of the Tichka massif to 6560 m in the Ouzellarh block. A comprehensive structural scheme, classified by C-A fractal analysis, identified zones favourable for exploration and mining, particularly along the Ouchden fault, Tizi n'Test, NE-SW trending lineaments in the northwestern domain, as well as along the Tichka granite’s margin