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

Development of Porosity and Copper(II) Ion Adsorption Capacity by Activated Nano-Carbon Xerogels in Relation to Treatment Schemes

In this study, activated nano-carbon xerogels were obtained by different activation schemes of a resorcinol–formaldehyde xerogel (RFX) with a resorcinol/catalyst (R/C) ratio of 50. For the precursor (RFX), activation was carried out under physical (steam) and chemical (H 3 PO 4 , KOH or NaOH) treatment in a one-stage process. Carbon xerogels were derived by simple pyrolysis at 500 °C or 700 °C for comparative purposes. The samples were characterized by different techniques including CHO elemental analysis, transmission electron microscopy (TEM) and nitrogen adsorption studies at 77 K, with the data obtained in the latter case being analyzed using the BET equation and the α S -method, as well as the fractal dimension approach. The porosities of the obtained carbons were considerably enhanced by chemical activation (mostly within the micropore range), while steam activation promoted the porosities to a lesser extent. Single-bottle removal of copper(II) ions was found to be appreciable in the case of the carbon xerogels (Q ads = 32–52 mg/g) and excellent with the activated carbon xerogels (Q ads = 76–198 mg/g). Application of the pseudo-second-order relationship gave the best fit to the kinetic uptake curves for selected samples. Activated carbon xerogels proved to be potential cation-exchange carbons whose performance appeared to be governed by the total surface area, slurry pH and the abundance of oxygen functional groups per unit surface area of the sorbent

Specific Antimicrobial Activities Revealed by Comparative Evaluation of Selected Gemmotherapy Extracts

Nowadays, unprecedented health challenges are urging novel solutions to address antimicrobial resistance as multidrug-resistant strains of bacteria, yeasts and moulds are emerging. Such microorganisms can cause food and feed spoilage, food poisoning and even more severe diseases, resulting in human death. In order to overcome this phenomenon, it is essential to identify novel antimicrobials that are naturally occurring, biologically effective and increasingly safe for human use. The development of gemmotherapy extracts (GTEs) using plant parts such as buds and young shoots has emerged as a novel approach to treat/prevent human conditions due to their associated antidiabetic, anti-inflammatory and/or antimicrobial properties that all require careful evaluations. Seven GTEs obtained from plant species like the olive (Olea europaea L.), almond (Prunus amygdalus L.), black mulberry (Morus nigra L.), walnut (Juglans regia L.), blackberry (Rubus fruticosus L.), blackcurrant (Ribes nigrum L.) and bilberry (Vaccinium myrtillus L.) were tested for their antimicrobial efficiency via agar diffusion and microbroth dilution methods. The antimicrobial activity was assessed for eight bacterial (Bacillus cereus, Staphylococcus aureus, Salmonella enterica subsp. enterica, Proteus vulgaris, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa and Listeria monocytogenes), five moulds (Aspergillus flavus, Aspergillus niger, Aspergillus ochraceus, Penicillium citrinum, Penicillium expansum) and one yeast strain (Saccharomyces cerevisiae). The agar diffusion method revealed the blackberry GTE as the most effective since it inhibited the growth of three bacterial, four moulds and one yeast species, having considered the total number of affected microorganism species. Next to the blackberry, the olive GTE appeared to be the second most efficient, suppressing five bacterial strains but no moulds or yeasts. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were then determined for each GTE and the microorganisms tested. Noticeably, the olive GTE appeared to feature the strongest bacteriostatic and bactericidal outcome, displaying specificity for S. aureus, E. faecalis and L. monocytogenes. The other GTEs, such as blueberry, walnut, black mulberry and almond (the list indicates relative strength), were more effective at suppressing microbial growth than inducing microbial death. However, some species specificities were also evident, while the blackcurrant GTE had no significant antimicrobial activity. Having seen the antimicrobial properties of the analysed GTEs, especially the olive and black mulberry GTEs, these could be envisioned as potential antimicrobials that might enhance antibiotic therapies efficiency, while the blackberry GTE would act as an antifungal agent. Some of the GTE mixtures analysed have shown interesting antimicrobial synergies, and all the antimicrobial effects observed argue for extending these studies to include pathological microorganisms

A Comprehensive View on the Quercetin Impact on Colorectal Cancer

Colorectal cancer (CRC) represents the third type of cancer in incidence and second in mortality worldwide, with the newly diagnosed case number on the rise. Among the diagnosed patients, approximately 70% have no hereditary germ-line mutations or family history of pathology, thus being termed sporadic CRC. Diet and environmental factors are to date considered solely responsible for the development of sporadic CRC; therefore; attention should be directed towards the discovery of preventative actions to combat the CRC initiation, promotion, and progression. Quercetin is a polyphenolic flavonoid plant secondary metabolite with a well-characterized antioxidant activity. It has been extensively reported as an anti-carcinogenic agent in the scientific literature, and the modulated targets of quercetin have been also characterized in the context of CRC, mainly in original research publications. In this fairly comprehensive review, we summarize the molecular targets of quercetin reported to date in in vivo and in vitro CRC models, while also giving background information about the signal transduction pathways that it up- and downregulates. Among the most relevant modulated pathways, the Wnt/β-catenin, PI3K/AKT, MAPK/Erk, JNK, or p38, p53, and NF-κB have been described. With this work, we hope to encourage further quests in the elucidation of quercetin anti-carcinogenic activity as single agent, as dietary component, or as pharmaconutrient delivered in the form of plant extracts