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

Seismic hazard assessment of Western Coastal Province of Saudi Arabia: deterministic approach

Abstract Seismic hazard assessment is carried out by utilizing deterministic approach to evaluate the maximum expected earthquake ground motions along the Western Coastal Province of Saudi Arabia. The analysis is accomplished by incorporating seismotectonic source model, determination of earthquake magnitude (M max), set of appropriate ground motion predictive equations (GMPE), and logic tree sequence. The logic tree sequence is built up to assign weight to ground motion scaling relationships. Contour maps of ground acceleration are generated at different spectral periods. These maps show that the largest ground motion values are emerged in northern and southern regions of the western coastal province in Saudi Arabia in comparison with the central region

A Deep Learning Model for Earthquake parameters Observation in IoT System-based Earthquake Early Warning

International audienc

Response in Physiological Traits and Antioxidant Capacity of Two Cotton Cultivars under Water Limitations

Deficit irrigation water (DW) is one of the main stress factors that negatively affect cotton cultivation. Hence, the identification of cotton cultivars tolerant to DW and sandy soil conditions is particularly needed. Understanding the response of cultivars to DW is essential for estimating water needs. Besides, by understanding the physiological and antioxidant status, reflecting distinct growth, yield, and fiber quality traits under DW, the cultivar tolerant to DW can be identified in the early stage of plant growth. Therefore, two cotton cultivars (Giza 86 and Giza 92, selected for their suitability to the climatic conditions of the study area) were evaluated in this study under two DW regimes (80% or 60% of crop evapotranspiration; ETc) vs. complete irrigation water (CW; 100% of ETc as a control). These regimes amounted to 1228 or 922 vs. 1536 mm season−1, respectively, for field trials conducted during the 2019 and 2020 summer seasons. DW (80% or 60% of ETc) significantly decreased relative water content, membrane stability index, chlorophyll content, plant height, yield components, and fiber quality traits. Otherwise, phenolic compounds, proline contents, as well as antioxidant enzyme activities increased in concomitance with an increase in electrolyte leakage and malondialdehyde content. The harmful effects of the higher DW (60% of ETc) were more pronounced in both cultivars. However, compared to Giza 86, Giza 92 showed higher performance under both CW and DW regimes, accounting for higher values for all studied traits in the blooming stage. The correlation coefficient showed that most of the physiological traits and antioxidants under study were effective criteria in identifying a high-yielding cultivar under DW in the cotton blooming stage and therefore can be used to select the cotton cultivar more suitable for the conditions of the study area. Biplot analysis was used to study the relationship between DW and all evaluated traits, as it was found that the most prominent traits were elongation (%) with Giza 92 + 100% ETc, yellowness degree with Giza 86 + 100% ETc, and SOD with Giza 92 + 60% ETc

Response in Physiological Traits and Antioxidant Capacity of Two Cotton Cultivars under Water Limitations

Deficit irrigation water (DW) is one of the main stress factors that negatively affect cotton cultivation. Hence, the identification of cotton cultivars tolerant to DW and sandy soil conditions is particularly needed. Understanding the response of cultivars to DW is essential for estimating water needs. Besides, by understanding the physiological and antioxidant status, reflecting distinct growth, yield, and fiber quality traits under DW, the cultivar tolerant to DW can be identified in the early stage of plant growth. Therefore, two cotton cultivars (Giza 86 and Giza 92, selected for their suitability to the climatic conditions of the study area) were evaluated in this study under two DW regimes (80% or 60% of crop evapotranspiration; ETc) vs. complete irrigation water (CW; 100% of ETc as a control). These regimes amounted to 1228 or 922 vs. 1536 mm season−1, respectively, for field trials conducted during the 2019 and 2020 summer seasons. DW (80% or 60% of ETc) significantly decreased relative water content, membrane stability index, chlorophyll content, plant height, yield components, and fiber quality traits. Otherwise, phenolic compounds, proline contents, as well as antioxidant enzyme activities increased in concomitance with an increase in electrolyte leakage and malondialdehyde content. The harmful effects of the higher DW (60% of ETc) were more pronounced in both cultivars. However, compared to Giza 86, Giza 92 showed higher performance under both CW and DW regimes, accounting for higher values for all studied traits in the blooming stage. The correlation coefficient showed that most of the physiological traits and antioxidants under study were effective criteria in identifying a high-yielding cultivar under DW in the cotton blooming stage and therefore can be used to select the cotton cultivar more suitable for the conditions of the study area. Biplot analysis was used to study the relationship between DW and all evaluated traits, as it was found that the most prominent traits were elongation (%) with Giza 92 + 100% ETc, yellowness degree with Giza 86 + 100% ETc, and SOD with Giza 92 + 60% ETc