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 de 118 variétés de cotonnier (Gossypium hirsutum) en condition de déficit hydrique au Togo: Characterization of 118 cotton varieties (Gossypium hirsutum) under water deficit conditions in Togo

Le déficit hydrique est le principal facteur abiotique qui limite la productivité des cultures dans les conditions de l'agriculture pluviale. L’objectif de cette étude a été d’identifier les variétés de cotonnier (Gossypium. hirsutum) tolérantes au déficit hydrique au Togo. Pour cela, 117 accessions et une variété témoin de G. hirsutum ont été caractérisées sous les régimes hydriques optimal et déficitaire. Le dispositif expérimental a été un Alpha lattice avec 120 objets en trois répétitions. Onze caractéristiques agromorphologiques ont été mesurées. Les indices de sensibilité (DSI) et de tolérance (STI) au déficit ont été calculés. Les résultats ont révélé une grande variabilité au déficit hydrique au sein des accessions testées. Le déficit hydrique a entrainé une réduction du rendement en coton graine de 85%. Par ailleurs, nous avons noté qu’en condition de déficit, le rendement a été corrélé négativement avec le DSI et positivement avec les indices STI et GMP. Quatre groupes de variétés ont été distingués. Il s’agit des variétés tolérantes à haut ou faible potentiel de production et des variétés sensibles à haut ou faible potentiel de production. Les variétés tolérantes à haut potentiel de production constituent une source importante de géniteurs, pour l’amélioration de la résistance au déficit hydrique des variétés vulgarisées au Togo. Drought is the major abiotic factor limiting crop productivity in rainfed agriculture conditions. This study aimed to identify cotton varieties (Gossypium hirsutum) tolerant to water deficit in Togo. For this purpose, 117 accessions of G. hirsutum and one check variety were characterized under optimal and deficit water conditions. The check variety was repeated three times to have 120 objects. The experiment was arranged in Alpha lattice design with 120 objects and three replications. Eleven agromorphological traits were measured. The water deficit susceptibility index (DSI) and tolerance index (STI) were calculated. The results revealed a high variability within the tested accessions to water deficit. The water deficit resulted in a 85% reduction in seed cotton yield due to a decrease in the number of capsules per plant and average capsular weight. The results also showed that, under deficit conditions, yield was negatively correlated with DSI and positively correlated with STI. Four groups of varieties were distinguished. These were tolerant varieties with high or low production potential; susceptible varieties with high or low production potential. The tolerant varieties with high production potential constitute an important source of genes for the improvement of the resistance to water deficit of the cotton cultivars of Togo