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

Effects of selected soil and water conservation technologies on nutrient losses and maize yields in the central highlands of Kenya

Mitigating nutrient loss is a prerequisite of sustainable agriculture in the tropics. We evaluated three soil and water conservation technologies (mulching, minimum tillage and tied ridging) for two cropping seasons (long rains 2011, short rains 2011) at two sites in the central highlands of Kenya. The objectives were: to determine effects of the technologies on runoff, sediment yield and nutrient loads in sediment, and to assess influence of the technologies on maize yields. Experimental design was a randomized complete block with 3 treatments replicated thrice. At the beginning of experiment, soil was sampled at 0–15 cm depth and analyzed for pH, N, P, K, C, Ca and Mg. Mulch was applied at a rate of 5 t ha−1. Runoff was sampled, sediments extracted by drying in oven at 105 °C, and analyzed for NPK and C loads. Data were subjected to analysis of variance using SAS 9.1.3 and means separated using Fishers’ LSD at 5% level of significance. Results showed reduced nutrient losses with the technologies. In Meru South, sediment yield was reduced by 41 and 7% during long rains 2011 (p = 0.03), and by 71 and 68% during short rains 2011 (p = 0.01) under mulching and minimum tillage, respectively. Runoff and maize yields were positively influenced by mulching. In Mbeere South, sediment yield was lower under soil and water conservation technologies. Runoff was reduced by 52 and 49% during long rains 2011 and by 51 and 30% during short rains 2011 under tied ridging and mulching respectively, compared with control. Total crop failure occurred during long rains 2011 due to erratic rains. During short rains 2011 tied ridging and mulching increased maize yield by 94 and 75%, respectively, compared with control. This study highlights the importance of analyzing soil and water conservation technologies within rain-fed farming systems perspective in response to declining food production and supports a focus on tied ridging and mulching