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

Irvingia gabonensis leaf extract scavenges nitric oxide and hydrogen peroxide in vitro and modulates arsenic-induced hepatic oxidative stress in wistar rats

Abstract Background Arsenic is a carcinogenic heavy metal that contaminates the environment, predisposing the exposed populace to its detrimental health effects. This study investigated the liver protective effect of ethanol leaf extract of Irvingia gabonensis (ELEIG) in sodium arsenite (SA)-exposed Wistar rats and its nitric oxide (NO.) and hydrogen peroxide (H2O2)-scavenging properties in vitro. Methods Eleven experimental groups made up of five (5) rats each (weight range 100 - 161 g) were used in this study. Group 1 (normal control) had normal rat chow and water. Group 2 received 4.1 mg/kg body weight (kgbw) of SA. Groups 3–8 received SA and graded doses of ELEIG and groups 9-11 had varied doses of ELEIG. Treatment, which spanned 14 days, was by oral gavage. Concentrations of catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), malondialdehyde (MDA) as well as activities of liver enzymes (AST, ALT, ALP, and GGT) and concentrations of total bilirubin (TBIL) and direct bilirubin (DBIL) were determined using standard procedures. Standard methods were also used to determine the in vitro NO. and H2O2-scavenging properties of the extract. Results Exposure to SA orchestrated significant (p ˂ 0.05) increases in CAT, MDA, AST, ALT, ALP and GGT and significant (p ˂ 0.05) decreases in SOD and GPx, relative to control. There were insignificant (p ˃ 0.05) differences in TBIL and DBIL concentrations, compared with control. Simultaneous and post-treatment with ELEIG at graded doses, alleviated the noxious effects of SA. In addition, ELEIG scavenged NO. and H2O2 in concentration-dependent manner. Conclusion The results suggest that ELEIG possesses potent antioxidant property and combats SA-induced hepatic oxidative stress/toxicity in Wistar rats

Evaluation of the Antioxidant Properties of Carvacrol as a Prospective Replacement for Crude Essential Oils and Synthetic Antioxidants in Food Storage

The phenolic structural analogues of synthetic antioxidants such as butylated hydroxytoluene (BHT) in essential oils have been reported to exhibit antioxidant properties. Additionally, their lipophilicity makes them suitable for use in lipid-rich foods. This study evaluated the antioxidant capacity of carvacrol, a monoterpenoid antioxidant compound in the Monodora myristica (Gaertn.) seed essential oil, compared to the seed essential oil and BHT. In vitro studies (ferric reducing antioxidant power (FRAP), metal chelating activity (MCA), and nitric oxide scavenging activity (NOSA)) were conducted to ascertain if the antioxidant capacity of carvacrol was comparable to that of the seed essential oil. The potential binding affinity and molecular interactions between carvacrol and lipoxygenase (LOX) and its homologous model were investigated in silico. The molecular docking was performed using Autodock Vina, and the best poses were subjected to molecular dynamics simulation. The IC50 for MCA and NOSA were: carvacrol 50.29 µL/mL, seed essential oil (SEO) 71.06 µL/mL; and carvacrol 127.61 µL/mL, SEO 165.18 µL/mL, respectively. The LOX model was Ramachandran favoured (97.75%) and the overall quality factor in the ERRAT plot was 95.392. The results of the molecular docking and molecular dynamics simulations revealed that lipoxygenase has a higher affinity (−22.79 kcal/mol) for carvacrol compared to BHT. In the LOX–BHT and LOX–carvacrol complexes, the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and the radius of gyration (RoG) were not significantly different, indicating similar molecular interactions. The results obtained from this study suggest that carvacrol exhibits an antioxidant capacity that may be explored as an alternative for crude essential oils and synthetic compounds during the storage of lipid-rich foods