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

Unveiling the Potential of Novel Macrophytes for the Treatment of Tannery Effluent in Vertical Flow Pilot Constructed Wetlands

The phytoremediation potential of macrophytic species has made them an inevitable component of constructed wetlands (CWs) for the treatment of industrial effluents. The macrophytes must have tolerance for the harsh conditions imposed by effluents for an effective establishment of the CW system. In this context, the basic purpose of this work was to investigate the efficacy of five indigenous emergent macrophytes (Brachiaria mutica, Canna indica, Cyperus laevigatus, Leptochloa fusca, and Typha domingensis) for the remediation of tannery effluent in vertical subsurface flow CWs. The ability of each macrophytic species to tolerate pollution load and to remove pollutants from the effluent was assessed. The effect of tannery effluent on the survival and growth of macrophytes was also studied. The treated tannery effluent samples were analyzed for electrical conductivity (EC), pH, biochemical oxygen demand (BOD5), chemical oxygen demand (COD), total dissolved solids (TDS), total suspended solids (TSS), chlorides (Cl−), sulphates (SO42−), oil and grease, and Cr levels. All of the studied macrophytes significantly decreased the pollution load of tannery effluent, and the higher nutrient content of effluent stimulated their growth without any signs of negative health effects. Leptochloa fusca and T. domingensis performed better in removing pollutants and showed higher growth rates and biomass than other tested macrophytes and can be considered preferred species for use in CWs treating tannery effluent. Brachiaria mutica showed morphologically better results than C. indica and C. laevigatus

Exploring Optimal Tillage Improved Soil Characteristics and Productivity of Wheat Irrigated with Different Water Qualities

Irrigation with low water quality can adversely affect soil characteristics, optimal moisture for tillage, and crop productivity, particularly in arid and semi-arid regions. We determined the optimal moisture for tillage processing and the effects of optimal and wet tillage on physical and chemical soil characteristics and wheat productivity after irrigation with different water qualities (waste, saline, and highly saline water). We used the Atterberg limit to determine the suitable moisture content for tillage. Tillage at optimal moisture content improved soil characteristics by reducing soil salinity, sodicity, bulk density, shear strength, compaction, and increasing hydraulic conductivity compared to that of wet tillage. It also enhanced growth and productivity of wheat grown with low quality of water (i.e., fresh and waste water), resulting in higher grain yield and root weight at different growth stages than that of saline and highly saline water. In conclusion, tillage at optimal moisture content alleviates the impact of salinity through improving soil physical and chemical characteristics. Optimum tillage can be applied at 20 and 24 days from the previous irrigation in saline and highly saline soils, respectively. Irrigation with waste water resulted in a higher wheat grain yield than saline and highly saline water