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

Caractérisation physicochimique des eaux de la nappe phréatique de la vallée de Boghol, commune de Dabaga/Agadez (Niger)

La vallée de Boghol est située dans la région d’Agadez au nord du Niger. Elle constitue un bassin de production où l’agriculture irriguée est la principale activité. Cette dernière occupe la grande majorité de la population et se pratique durant toute l’année avec l’eau souterraine comme l’unique source d’eau d’irrigation. Malgré la méconnaissance de la qualité de ces eaux, l’irrigation connait une intensification susceptible d’impacter la nappe phréatique. L’objectif de ce travail est de contribuer à caractériser les eaux de ladite vallée. L’approche méthodologique s’est basée sur le prélèvement des échantillons d’eau au niveau des puits maraichers sur la base d’un transect permettant de couvrir toute la vallée. Ces eaux ont fait l’objet de mesures physiques sur le terrain et d’analyses chimiques au laboratoire par titrimétrie, puis photométrie. Outre l’analyse en composante principale, le traitement des résultats a été fait en utilisant le diagramme de Piper et celui de Schoeller-Berkaloff. Aussi, les méthodes du taux d’absorption du sodium (SAR), Wilcox et de carbonate de sodium résiduel (RSC) ont été utilisées. Les résultats de l’étude montrent que les eaux sont de bonne qualité organoleptique. Quant au pH, les valeurs sont presque neutres dans tous les ouvrages. La conductivité électrique varie de 220,50 à 606,3 μs/cm et présente le plus grand nombre de corrélation avec les autres paramètres physicochimiques. Tous les échantillons ont un faciès chimique bicarbonaté calcique et ont une bonne aptitude à l’irrigation. Cependant, il est constaté une augmentation spatiotemporelle du taux de minéralisation et celui du nitrate. D’où la nécessité de préserver cette qualité en adoptant des bonnes pratiques d’irrigation. The Boghol Valley is located in the Agadez region in northern Niger. It is a production basin where irrigated agriculture is the main activity. The latter occupies the vast majority of the population and is practiced all the year with groundwater as the only source of irrigation water. Despite the lack of knowledge about the quality of these waters, irrigation is being intensified and is likely to impact the water table. The objective of this work is to help characterize the waters of this valley. The methodological approach was based on the collection of water samples from vegetable wells/market garden wells based on a transect covering the whole valley. These waters were the subject of physical measurements in the field and chemical analyses in the laboratory by titrimetry, then photometry. In addition to the main component analysis, the results were processed using the Piper and Schoeller-Berkaloff diagrams. Also, the methods of sodium absorption rate (SAR), Wilcox, and residual sodium carbonate (RSC) were used. The results of the study show that the water is of good organoleptic quality. As for pH, the values are almost neutral in all works. Electrical conductivity ranges from 220.50 to 606.3 μs/cm and i