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 Level of Compliance of Food Handlers with National Regulations on Food Hygiene and Safety Practices: A Case of Selected Fast Food Outlets in Thohoyandou, South Africa

Abstract Food safety is becoming a key public health priority because a large number of people consume their meals outside their homes. As a result, they are exposed to food borne illnesses that originate from food stalls, restaurants and other food outlets. Hence the study focused on level of compliance of food handlers with national regulations on food hygiene and safety practices. The method used to collect data was participant observational checklist where the researcher had to go round with the workers during their daily chores. Simple random sampling was used to select 122 food handlers as participants in the study. Fast food outlets were also evaluated according to codified regulations and sixty food premises were observed for compliance using a checklist and compared with standards and the requirements prescribed by in Foodstuffs, Cosmetics and Disinfectants Act of 1972, regulation Data analysis involved descriptive statistics (frequencies and percentages) and analysis was made based on the standards and the requirements prescribed by Regulation R962 of November 2012. The findings showed that food handlers observed personal hygiene by wearing clean uniforms, covering their heads with hair nets, and washed their hands, indicating that food handlers maintained accepted standards in terms of personal hygiene regulations

The role of ancient human settlements in creating nutrient hotspots in a savanna ecosystem, central Zimbabwe

Ancient human settlements play an important role in creating heterogeneous African savanna ecosystems through forming nutrient hotspots with increased biodiversity and improved forage quality. However, plant community development and herbivore utilization of these sites after abandonment remain poorly understood. We compared plant and soil parameters in ancient human settlements with off-sites locations. In addition, we set camera traps in ancient settlements and surrounding vegetation to determine their use by herbivores. Grass basal cover, height, biomass and species diversity in ancient settlements had recovered to similar levels with the surrounding landscape. Ancient settlements had small trees (in terms of height and canopy volume), lower tree density and lower species diversity than the surrounding landscape. Soil phosphorus and calcium were higher in ancient settlements than surrounding landscape, while pH, nitrogen, potassium, magnesium and sodium were similar between the two sites. Impala and greater kudu camera sightings were higher in ancient settlements than surrounding vegetation, while warthogs showed no preferential foraging between ancient settlements and surrounding vegetation. We conclude that ancient settlements created functional heterogeneity through altering the structure of savanna vegetation influencing foraging patterns of herbivores such as impala

“We Used to go Asking for the Rains”: Local Interpretations of Environmental Changes and Implications for Natural Resource Management in Hwange District, Zimbabwe

In Hwange District, Zimbabwe, people living in the vicinity of the largest protected area of the country are facing rapid climate and environmental changes. Adopting an ethnoecological perspective, we sought to understand the way changes are understood locally in an area where people have interacted with their environment for centuries. In this chapter, we examine local people’s knowledge, expertise, and interpretative diagnoses about the environmental and climate changes they perceive around them. Qualitative fieldwork, including participant observation, semi-structured interviews, and structured free-listing interviews, was carried out over a three-month period in the communal lands of the district. Among changes related to wildlife interactions and landscape transformations, people mainly mobilize knowledge of trees and birds to predict rainfall and explain climate variability (related to seasons, precipitation, and temperatures). The most important findings of this research lie in people’s descriptions of ecological changes and their interpretations and explanations for these changes, which focus on arguments that are cultural (abandonment of ritual practices, access to ancestral sites), demographic (population growth), and political (wildlife management). For example, the disturbances in precipitation patterns are understood as a manifestation of the anger of ancestral spirits. We argue that these interpretive frameworks reflect the strong marginalization of the communities of the district from the national program of community-based natural resource management, CAMPFIRE, and that these discourses allow silenced voices to express themselves about sociopolitical concerns in an authoritarian context

Studies of rhizobial competitiveness for nodulation in soybean using a non-destructive split-root system

Split-root systems (SRS) constitute an appropriate methodology for studying the relevance of both local and systemic mechanisms that participate in the control of rhizobia-legume symbioses. In fact, this kind of approach allowed to demonstrate the autoregulation of nodulation (AON) systemic response in soybean in the 1980s. In SRS, the plant main root is cut and two lateral roots that emerge from the seedlings after root-tip removal are confined into separate compartments. After several days of growth, these plants have two separate roots that can be inoculated with the same or with different bacteria, at the same or at different times. In this work, we have used a non-destructive SRS to study two different competitiveness relations between rhizobial strains in soybean roots. One of them is the competition for nodulation between two soybean-nodulating rhizobia: the slow-grower Bradyrhizobium japonicum USDA110 and the fast-grower Sinorhizobium fredii HH103. The second is the competitive blocking of S. fredii 257DH4 nodulation in the American soybean Osumi by Sinorhizobium fredii USDA257, which is unable to nodulate American soybeans. Our results showed that the competitiveness relationships studied in this work are mitigated or even avoided when the competitive strains are spatially separated in different compartments containing half-roots from the same plant, suggesting that competitive relations are more related to local plant responses. In our opinion, split-root systems are an appropriate approach to further study competitive relations among rhizobial strains