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

Chemical, sensory qualities and microbial load of standardized Digitaria exilis (Acha) based dishes commonly consumed in Niger State, Nigeria

Background: The role of indigenous or traditional food crops in the improvement of food security in Nigeria cannot be over emphasized. The availability of these local foods in their socially acceptable forms, and at affordable prices seems to be the key to overcoming the major constrains towards consumer utilization of locally available foods.Objective: The study investigated the chemical content, sensory and microbial qualities of standardized acha based dishes commonly consumed in Niger state, Nigeria.Materials and Methods: Five acha based dishes (acha jollof, tuwo acha, acha porridge, acha kunun and steamed acha) commonly consumed in Niger state were selected fromfive zones and the recipes standardized in accordance with the standardization procedures. The dishes were assessed for consumer acceptability. Proximate, mineral, and nutrient inhibitor composition were analysed using standard methods. The dishes were also evaluated for microbiological quality using Aerobic Plate Count (APC).Results: The values of proximate, mineral, nutrient-inhibitor composition and sensory evaluation of the dishes were significantly different at p<0.05. The mean crude protein values of the dishes ranged from 0.75 to 6.03% while the carbohydrate contents varied from 13.4 to 24.50%.The mineral contents ranged from 3.40 to 33.00mg, 2.20 to 10.16mg 10.04 to 35.00mg, 15.90 to 70.43mg, 0.00 to 24.25mg and 4.50 to 37.20mg for phosphorus, potassium, sodium, zinc, iron and calcium, respectively. The values of the nutrient-inhibitor of the dishes ranged from 89.05 to 147.50mg, 0.00 to 0.09 mg and 1.10 to 8.60mgfor phytate, tannin and oxalate, respectively. The values of the of the sensory attributes of the dishes ranged from 2.25 to 4.20, 3.00 to 4.33, 2.50 to 3.92, 2.75 to 4.08 and 3.00 to 4.50 for taste, flavour, colour, consistency and overall acceptability, respectively. The microbial load of the dishes within the 24 hours fell within the acceptable levels.Conclusion: The study showed that acha-based dishes had low nutrient inhibitors.Keywords: Acha dishes, standardized, nutrient, sensory qualities, microbial loa

The ASOS Surgical Risk Calculator: development and validation of a tool for identifying African surgical patients at risk of severe postoperative complications

Background: The African Surgical Outcomes Study (ASOS) showed that surgical patients in Africa have a mortality twice the global average. Existing risk assessment tools are not valid for use in this population because the pattern of risk for poor outcomes differs from high-income countries. The objective of this study was to derive and validate a simple, preoperative risk stratification tool to identify African surgical patients at risk for in-hospital postoperative mortality and severe complications. Methods: ASOS was a 7-day prospective cohort study of adult patients undergoing surgery in Africa. The ASOS Surgical Risk Calculator was constructed with a multivariable logistic regression model for the outcome of in-hospital mortality and severe postoperative complications. The following preoperative risk factors were entered into the model; age, sex, smoking status, ASA physical status, preoperative chronic comorbid conditions, indication for surgery, urgency, severity, and type of surgery. Results: The model was derived from 8799 patients from 168 African hospitals. The composite outcome of severe postoperative complications and death occurred in 423/8799 (4.8%) patients. The ASOS Surgical Risk Calculator includes the following risk factors: age, ASA physical status, indication for surgery, urgency, severity, and type of surgery. The model showed good discrimination with an area under the receiver operating characteristic curve of 0.805 and good calibration with c-statistic corrected for optimism of 0.784. Conclusions: This simple preoperative risk calculator could be used to identify high-risk surgical patients in African hospitals and facilitate increased postoperative surveillance. © 2018 British Journal of Anaesthesia. Published by Elsevier Ltd. All rights reserved.Medical Research Council of South Africa gran