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

Habitat mosaic as a driver of the resilience of native species: The case of the assemblage of small mammals from the city of Franceville, Gabon

International audienceRodents (Rodentia) are the most abundant and diverse order of mammals, present in all habitats, including urban areas. The traffic linked to globalisation has favoured their involvement in biological invasions that have an impact on local biodiversity, the economy and human health. In Franceville, Gabon, little is known about the rodent community. We therefore studied the composition and distribution of rodents along a gradient highlighting the heterogeneity of the city's landscape. The three habitat types studied showed no difference in small mammal abundance, while the diversity index was higher in the vegetated habitat (SDI = 0.73) compared to the outdoor (SDI = 0.71) and indoor (SDI = 0.45) habitats. Our work shows the importance of vegetal remnants in the city for the maintenance of native species. It also highlights the impact of introduced species on small mammal assemblages and the need for management to reduce the factors of their proliferation

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-légumineuses 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 cœur 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 d’adoption à l’échelle des filières (notamment pour les collecteurs) ont été aussi mis en évidence et quantifiés

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

Survival, morbidity, growth and developmental delay for babies born preterm in low and middle income countries - a systematic review of outcomes measured.

BackgroundPremature birth is the leading cause of neonatal death and second leading in children under 5. Information on outcomes of preterm babies surviving the early neonatal period is sparse although it is considered a major determinant of immediate and long-term morbidity.MethodsSystematic review of studies reporting outcomes for preterm babies in low and middle income settings was conducted using electronic databases, citation tracking, expert recommendations and "grey literature". Reviewers screened titles, abstracts and articles. Data was extracted using inclusion and exclusion criteria, study site and facilities, assessment methods and outcomes of mortality, morbidity, growth and development. The Child Health Epidemiology Reference Group criteria (CHERG) were used to assess quality.FindingsOf 197 eligible publications, few (10.7%) were high quality (CHERG). The majority (83.3%) report on the outcome of a sample of preterm babies at time of birth or admission. Only 16.0% studies report population-based data using standardised mortality definitions. In 50.5% of studies, gestational age assessment method was unclear. Only 15.8% followed-up infants for 2 years or more. Growth was reported using standardised definitions but recommended morbidity definitions were rarely used. The criteria for assessment of neurodevelopmental outcomes was variable with few standardised tools - Bayley II was used in approximately 33% of studies, few studies undertook sensory assessments.ConclusionsTo determine the relative contribution of preterm birth to the burden of disease in children and to inform the planning of healthcare interventions to address this burden, a renewed understanding of the assessment and documentation of outcomes for babies born preterm is needed. More studies assessing outcomes for preterm babies who survive the immediate newborn period are needed. More consistent use of data is vital with clear and aligned definitions of health outcomes in newborn (preterm or term) and intervention packages aimed to save lives and improve health