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

Numerical Simulation for the Fractional SIRC Model and Influenza A

Abstract: In this paper, A Chebyshev spectral method is presented to study the deals with the fractional SIRC model associated with the evolution of influenza A disease in human population. The properties of the Chebyshev polynomials are used to derive an approximate formula of the Caputo fractional derivative. This formula reduces the SIRC model to the solution of a system of algebraic equations which is solved using Newton iteration method. The convergence analysis and an upper bound of the error of the derived formula are given. We compared our numerical solutions with those numerical solutions using fourth-order Runge-Kutta method. The obtained results of the SIRC model show the simplicity and the efficiency of the proposed method. Also, illustration for propagation of influenza A virus and the relation between the four cases of it along the time at the fractional derivative are given

Effect of Dietary Moringa oleifera Leaves Nanoparticles on Growth Performance, Physiological, Immunological Responses, and Liver Antioxidant Biomarkers in Nile tilapia (Oreochromis niloticus) against Zinc Oxide Nanoparticles Toxicity

The current study addresses the influence of Moringa oleifera leaves nanoparticles (MO-NPs) on growth, biochemical, immunological, and hepatic antioxidant alterations induced by zinc oxide nanoparticles toxicity in Nile tilapia (O. niloticus). Fish (N = 180) were divided into four groups with replicates. The first one was set as a control group and the second group was fed an MO-NPs-enriched diet (2.5 g/kg diet). The third group was exposed to 8 mg/L ZnO-NPs, while the forth group was exposed to 8 mg/L ZnO-NPs and fed on MO-NPs (2.5 g/kg diet) for 2 months. Exposure of O. niloticus to 8 mg/L ZnO-NPs induced the following consequences: a sharp decrease in the growth parameters; a marked increment in the biochemical biomarkers (glucose, cortisol, and liver enzymes (ALT, AST, ALP); a significant increase in serum renal products, urea and creatinine, cholesterol, and LDH levels. Nonetheless, the dietary MO-NPs supplementation for 2 months significantly alleviated the ZnO-NPs toxicity and significantly enhanced the growth indices, plus normalizing the physio-biochemical levels in the exposed group to ZnO-NPs toxicity to reach the levels of the control group. The MO-NPs markedly improved hepatic antioxidant biomarkers, MDA, and TAC, while, decreasing SOD, CAT, and GSH levels to be near the control values. Moreover, supplemented fish in MO-NPs (2.5 g/kg diet) and exposed to ZnO-NPs provided a remarkable increase in the immune profile (respiratory burst (RB) activity, lysozyme, and total immunoglobulins (IgM)) compared to the ZnO-NPs-intoxicated group. Based on the findings of the study, the exposed O. niloticus to ZnO-NPs were immune-antioxidant-depressed, besides showing growth retardation, and physio-biochemical alterations. On the other hand, a supplemented diet with MO-NPs is a novel approach to ameliorate ZnO-NPs toxicity for sustaining aquaculture and correspondingly protecting human health

Effect of Dietary <i>Moringa oleifera</i> Leaves Nanoparticles on Growth Performance, Physiological, Immunological Responses, and Liver Antioxidant Biomarkers in Nile tilapia (<i>Oreochromis niloticus</i>) against Zinc Oxide Nanoparticles Toxicity

The current study addresses the influence of Moringa oleifera leaves nanoparticles (MO-NPs) on growth, biochemical, immunological, and hepatic antioxidant alterations induced by zinc oxide nanoparticles toxicity in Nile tilapia (O. niloticus). Fish (N = 180) were divided into four groups with replicates. The first one was set as a control group and the second group was fed an MO-NPs-enriched diet (2.5 g/kg diet). The third group was exposed to 8 mg/L ZnO-NPs, while the forth group was exposed to 8 mg/L ZnO-NPs and fed on MO-NPs (2.5 g/kg diet) for 2 months. Exposure of O. niloticus to 8 mg/L ZnO-NPs induced the following consequences: a sharp decrease in the growth parameters; a marked increment in the biochemical biomarkers (glucose, cortisol, and liver enzymes (ALT, AST, ALP); a significant increase in serum renal products, urea and creatinine, cholesterol, and LDH levels. Nonetheless, the dietary MO-NPs supplementation for 2 months significantly alleviated the ZnO-NPs toxicity and significantly enhanced the growth indices, plus normalizing the physio-biochemical levels in the exposed group to ZnO-NPs toxicity to reach the levels of the control group. The MO-NPs markedly improved hepatic antioxidant biomarkers, MDA, and TAC, while, decreasing SOD, CAT, and GSH levels to be near the control values. Moreover, supplemented fish in MO-NPs (2.5 g/kg diet) and exposed to ZnO-NPs provided a remarkable increase in the immune profile (respiratory burst (RB) activity, lysozyme, and total immunoglobulins (IgM)) compared to the ZnO-NPs-intoxicated group. Based on the findings of the study, the exposed O. niloticus to ZnO-NPs were immune-antioxidant-depressed, besides showing growth retardation, and physio-biochemical alterations. On the other hand, a supplemented diet with MO-NPs is a novel approach to ameliorate ZnO-NPs toxicity for sustaining aquaculture and correspondingly protecting human health