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

Protection Intégrée des rotations avec Colza et blé tendre : Conception et évaluation multicritères d’itinéraires techniques économes en produits phytosanitaires

Le projet PICOBLE avait pour objectif, en se plaçant à l’échelle de l’itinéraire technique, de contribuer à la recherche de solutions permettant de réduire l’usage de produits phytosanitaires dans les systèmes de culture à base de colza et de blé. Il a permis de concevoir et de tester des ITK innovants pour différentes situations. Les résultats obtenus concluent à la possibilité d’une réduction des produits phytosanitaires de 30 à 40% sans affectation de la marge de l’agriculteur sur la base des hypothèses de prix prises, mais avec une réduction du volume de production de 10% pouvant affecter l’économie des filières avales. Les connaissances acquises permettent d’envisager de nouvelles pistes de réduction à plus long terme mais elles nécessitent encore un travail considérable, il faudra en particulier aborder des échelles plus larges au niveau du système de culture ou du paysage.Integrated protection of crop rotation with winter oilseed rape (WOSR) and winter wheat: Conception and multicriteria evaluation of pesticides saver cropping practices The PICOBLE project was looking for knowledge and knowhow likely to contribute to a reduction of pesticides use in wheat and WOSR-based rotations, at the scale of annual cropping practices. New cropping techniques have been imagined, discussed and tested in the field before being assessed with a multi-criteria approach. A 30-40% reduction of the total amount of pesticides is possible, without X. Pinochet et al. 244 Innovations Agronomiques 28 (2013), 243-256 affecting the farmer economic result under given price hypothesis, but with a 10% reduction of the production, that might affect the economic competiveness of the connected industries. Results and knowledge produced during the project open new perspectives for further reductions on the longer term. Nevertheless, work is still needed and approaches have to be extended to cropping systems and landscapes scales

Associations céréale-légumineuse multi-services

Depuis plusieurs décennies, l’évolution de l’agriculture en France est, dans un certain nombre de régions de grande culture et d’élevage marquée fortement par la simplification des assolements accompagnée d’un usage accru des intrants et la standardisation des itinéraires techniques. Le challenge est maintenant de concevoir des agroécosystèmes plus diversifiés dans l’objectif d’une gestion écologique des parcelles cultivées devant se traduire par une amélioration de la productivité et la stabilité des systèmes face à divers aléas et la fourniture de différents services éco-systémiques. Ce projet a exploré l’augmentation de la diversité cultivée au sein de la parcelle via des associations céréale-légumineuse. Il a montré la diversité des services que l’on peut en attendre en agriculture biologique et en agriculture conventionnelle, en système céréalier et en système d’élevage. Ces associations permettent de répondre à la fois à des enjeux de production, de réduction des intrants, de réduction des impacts environnementaux des cultures, de stabilité face à des aléas biotiques et abiotiques. Le coeur du projet a consisté a testé différents leviers d’actions pour aider à l’orientation des performances de ces associations pour différents objectifs. Les atouts et contraintes ’adoption à l’échelle des filières (notamment pour les collecteurs) ont été aussi mis en évidence et quantifiés