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

The effect of dietary Crataegus Sinaica on the growth performance, immune responses, hemato-biochemical and oxidative stress indices, tissues architecture, and resistance to Aeromonas sobria infection of acrylamide-exposed Clarias gariepinus

This study investigated the effect of using a natural dietary supplement of Crataegus Sinaica (CS) to mitigate the negative impacts of waterborne acrylamide (ACR) on the health and performance of freshwater fish, African catfish (Clarias gariepinus). For this aim, 270 fish were divided into six groups (45 fish/group). Three groups were kept in non-contaminated water and fed a non-fortified basal diet, 1% CS, and 2% CS. The other three groups were exposed to ACR (26.6 mg/L water) and fed a basal diet, 1% CS, and 2% CS. After 60 days, the growth performance, liver and kidney function, stress indicators, oxidative stress indices, immunological response, vital tissue architecture, and resistance to Aeromonas sobria have been evaluated. Results indicated that CS dietary supplementation (1% and 2% CS) significantly counteracted ACR-induced reduced growth and survival. Furthermore, both CS dietary supplementation significantly balanced the ACR-induced leukopenia, anemia, hypoalbuminemia, hypoglobulinemia, and hypoproteinemia. Likewise, 1% and 2% CS addition to the ACR-exposed fish diets significantly reduced the ACR-induced increase in serum enzymes, bilirubin, renal damage products, hyperglycemia, and cortisol. Instead, the ACR-evoked depletion of antioxidant (glutathione peroxidase, superoxide dismutase, catalase, and reduced glutathione) and innate immune (lysozyme, complement3, and nitric oxide) components were significantly restored by both CS dietary supplementation. Besides, the ACR-induced pathological alterations in hepatic, renal, and splenic tissues were considerably lessened by CS. Besides, the reduced disease resistance of ACR-exposed fish was restored when challenged with A.sobria in a fish-fed 1% and 2% CS-fortified diet. Noteworthy, the inclusion of 2% CS produced better results than 1%. Overall, feeding C. gariepinus a diet supplemented with 2% CS significantly improved the fish's overall health, growth, and disease resistance, despite the ACR water pollution that consequently would sustain aquaculture

Immunosuppression, growth retardation, and transcriptomic profile alterations induced by chronic copper toxicity in Clarias gariepinus: The ameliorative effect of zinc oxide nanoparticles

This study was designated to look into the toxicological effects of long-term exposure of African catfish (Clarias gariepinus) to a heavy metal (copper) on the growth, hematology, immune-antioxidant functions and their regulating genes, and resistance to Aeromonas sobria. Furthermore, the efficiency of dietary zinc oxide nanoparticles (ZNPs) to ameliorate copper toxicity was assessed. Fish (n=300: average body weight: 90.56±0.20 g) were equally allocated into six groups in five replicates (10 fish/replicate; 50 fish/ group) for 60 days at a water temperature of 25 ± 1.2 ◦C. Three diets were formulated with varying ZNPs levels: control (0 mg kg−1), ZNPs20 (20 mg kg−1), and ZNPs30 (30 mg kg−1), with actual zinc concentrations of 45, 65, and 75 mg kg−1, respectively. The experimental groups were named, control, ZNPs20, and ZNPs30 groups which were fed on the control, ZNPs20, and ZNPs30 diets, respectively without copper exposure. Additionally, the CuCL2, CuCL2+ZNPs20, and CuCL2+ZNPs30 groups were received the same feeding regime as the control, ZNPs20, and ZNPs30 groups, respectively and exposed to copper chloride, CuCL2 (10 mg L−1). At the end of the exposure trial (60 days), all experimental groups were challenged with 0.2 mL of A. sobria (1×108 CFU mL−1) and the mortalities were recorded daily for additional 7 days. The results displayed that copper exposure resulted in lower growth metrics and survivability. The final body weight, weight gain, feed intake, and survivability were reduced in the CuCL2 group by 39.29%, 23.79%, 63.37%, and 20%, respectively with increasing the feed conversion ratio by 52.13% compared to the control group. In addition, reduced hematological (red blood cells (58.40%), hemoglobin (48.11%), packed cell volume (40.59%), white blood cells (46.85%), total proteins (43.12%), albumin (41.98%), and globulin (44.23%)), immune (lysozymes (59.74%), complement 3 (41.89%), nitric oxide (57.14%), and phagocytic activity (38.75%)), and antioxidant parameters (glutathione peroxidase (82.95%), catalase (74.08%), and superoxide dismutase (48.59%)), as well as higher oxidative (malondialdehyde) (200.30%) indicator were observed in the CuCL2 group compared to the control group. A down-regulation of the antioxidant (glutathione peroxidase-1) and immune (lysozyme-G, lysozyme-C, transforming growth factor-beta, and myeloperoxidase) genes with up-regulation of the inflammatory cytokines (interleukin-1ß, interleukin-8, tumor necrosis factor-alpha, nuclear factor kappa β, and Toll-like receptor 5) was noticed in the CuCL2 group. In addition, the survivability of the CuCL2 group during A. sobria challenge was reduced (25%) compared to the control group. Noticeably, ZNPs diets modulated the growth, survival, and antioxidant/immune functions and their associated genes of the copper-exposed fish. In addition, ZNPs increased the resistance of the copper-exposed fish to A. sobria challenge. ZNPs diets especially at 30 mg kg−1 level proposed a promising feed additive for mitigating the stress consequences of copper exposure in African catfish