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

In vivo toxicity, anti-hyperlipidaemic, antioxidant and anti-atherogenic activities of ‘LIPO A’ A traditional herbal product in rodents

Hyperlipidemia accounts for about 17 million deaths worldwide each year. High cost and side effects have limited the use of conventional anti-lipidaemic agents in some cases, majority of whom resort to traditional medicine. The current research focused on validating the safety and efficacy of a herbal product, ‘LIPO A’ used in the management of hyperlipidaemia. Induction of hyperlipidaemia was achieved by oral administration of 3 mL of cholesterol in coconut oil for 4 weeks in male Sprague Dawley rats with water available as 40 % sucrose. Subsequently, the animals were treated with 100, 200 and 400 mg/kg of the product ‘LIPO A’ for 4 additional weeks with atorvastatin as reference drug (at 2 mg/kg body weight). Blood samples were taken for serum biochemistry and atherogenic ratios were then calculated. 2,2-Diphenyl-1-Picrylhydrazyl (DPPH) scavenging assay, total antioxidant capacity, physicochemical and phytochemical analysis were also carried out using standard methods. Treatment resulted in a dose-dependent reduction in total cholesterol with maximum reduction of 46.01 % at 400 mg/kg compared to atorvastatin with 49.30 %. There were significant changes in the low-density lipoprotein cholesterol and high-density lipoprotein cholesterol (LDL-c/HDL-c) and Total Cholesterol (TC/HDL-c) ratios which measures the atherogenic and coronary risk indices respectively. Acute and subacute toxicity studies did not reveal any signs of toxicity. High Performance Liquid Chromatography (HPLC) fingerprint revealed six well resolved peaks with two prominent compounds with retention times 24.88 and 23.95 min, which could serve as quality control markers for the product. The herbal product showed considerable antihyperlipidemic and antioxidant actions in rodent models and lend credence to its use in traditional medicine for hyperlipidaemia