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

Mapping of ecosystem services flow in Mida Creek, Kenya

The concept of ecosystem services (ES) and its application in natural resources management decision making is a new conservation paradigm. A better understanding of ES in resource-rich developing countries can contribute to poverty alleviation and sustainable development, while at the same time conserving natural resources. This study assessed the flow of ES in Mida Creek, a marine reserve in Kenya, with the aim of characterizing land use/land cover (LULC) classes, spatially mapping distribution of ES, identifying important ES, and establishing the opinions of experts on ES flow. A qualitative and quantitative assessment was carried out coupling expert scores and LULC maps in a matrix structure. A participatory approach was used to engage and raise awareness with the community groups who actively participate in conservation activities in the creek, together with researchers/academics/managers who also are involved with the management of the reserve. The study was carried out between July and October 2015 and a total of 65 participants were involved. Datasets were collected using questionnaires in which ecosystem service flow was scored based on expert estimates per LULC class against the selected ES. Data were assessed using statistical and spatial analysis techniques. Results for the flow of provisioning services showed that, while palm trees were the main source of firewood (68%), other vegetation types were also an important source for wood products, including charcoal (46%), construction poles (54%) and fishing gear (68%). There was also a high flow of provisioning services (sea food and bait organisms) from water bodies (82%) and mangroves (80%). Flow for regulating services was mainly from mangroves, and for cultural services from beaches, mangroves and water bodies. Saline bare areas and sand flats scored least for all the ES. There were statistically significant differences in the scoring of the LULC against the different categories of provisioning, regulating and cultural services between the local communities and the other stakeholders. The method shows both the location of the resources utilized by the communities and, also, facilitates communication between these communities and the decision makers, thereby providing an example of a Management strategy at the local scale for other coastal regions of Kenya and elsewhere. (C) 2017 Elsevier Ltd. All rights reserved.European UnionWorld Wildlife Fund Russell E. Train Education for Nature ProgramMurray Foundationinfo:eu-repo/semantics/publishedVersio

Carbon stable isotopes suggest that hippopotamus‐vectored nutrients subsidize aquatic consumers in an East African river

© 2015 McCauley et al. The common hippopotamus, Hippopotamus amphibius, transports millions of tons of organic matter annually from its terrestrial feeding grounds into aquatic habitats. We evaluated whether carbon stable isotopes (δ13C) can be used as tracers for determining whether H. amphibius-vectored allochthonous material is utilized by aquatic consumers. Two approaches were employed to make this determination: (1) lab-based feeding trials where omnivorous river fish were fed a H. amphibius dung diet and (2) field sampling of fish and aquatic insects in pools with and without H. amphibius. Lab trials revealed that fish fed exclusively H. amphibius dung exhibited significantly more positive δ13C values than fish not fed dung. Fish and aquatic insects sampled in a river pool used for decades by H. amphibius also exhibited more positive δ13C values at the end of the dry season than fish and insects sampled from an upstream H. amphibius-free reference pool. Fish sampled in these same pools at the end of the wet season (high flow) showed no significant differences in δ13C values, suggesting that higher flows reduced retention and use of H. amphibius subsidies. These data provide preliminary evidence that δ13C values may be useful, in certain contexts, for quantifying the importance H. amphibius organic matter

Carbon stable isotopes suggest that hippopotamus‐vectored nutrients subsidize aquatic consumers in an East African river

© 2015 McCauley et al. The common hippopotamus, Hippopotamus amphibius, transports millions of tons of organic matter annually from its terrestrial feeding grounds into aquatic habitats. We evaluated whether carbon stable isotopes (δ13C) can be used as tracers for determining whether H. amphibius-vectored allochthonous material is utilized by aquatic consumers. Two approaches were employed to make this determination: (1) lab-based feeding trials where omnivorous river fish were fed a H. amphibius dung diet and (2) field sampling of fish and aquatic insects in pools with and without H. amphibius. Lab trials revealed that fish fed exclusively H. amphibius dung exhibited significantly more positive δ13C values than fish not fed dung. Fish and aquatic insects sampled in a river pool used for decades by H. amphibius also exhibited more positive δ13C values at the end of the dry season than fish and insects sampled from an upstream H. amphibius-free reference pool. Fish sampled in these same pools at the end of the wet season (high flow) showed no significant differences in δ13C values, suggesting that higher flows reduced retention and use of H. amphibius subsidies. These data provide preliminary evidence that δ13C values may be useful, in certain contexts, for quantifying the importance H. amphibius organic matter