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

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Seasonal variability of phytoplankton composition inside and outside the Marine Protected Areas of Joal-Fadiouth and Bamboung in Senegal (West Africa) [résumé]

ICAWA : International Conference AWA, Dakar, SEN, 13-/12/2016 - 15/12/2016Marine Protected Areas (MPAs) are considered tools for biodiversity and resource restoration and resilience. However, their role in improving the flow of matter through better productivity remains to be demonstrated. The present study aims to analyze the phytoplankton composition inside and outside two contrasted MPAs; Joal-Fadiouth (coastal) and Bamboung (estuary) at dry cold and wet hot seasons. Data were collected with plankton net of 20 ?m net mesh in April and September 2016. In the laboratory, by optical microscopy, the phytoplankton species were identified at the lowest possible taxonomic level by comparison of our data with those of taxonomy works. A total of 101 species belonging to 30 families were identified in the Bamboung MPA, compared with 98 species of 28 families in the Joal-Fadiouth MPA. In the latter MPA, the number of species was higher (40 species of 19 families) inside than outside (30 species of 18 families) the MPA in April i.e. the cold season. In September, i.e. the hot season, the number of species was higher (62 species of 16 families) outside than inside (50 species of 14 families). As for the Bamboung MPA, whatever the season (cold and hot), the number of species was respectively higher inside (58 species of 28 families and 61 species of 20 families) than outside (30 species of 18 families and 58 species of 20 families). However, even if both MPAs present similitude for the taxonomical composition, characteristic species of each environment have been encountered: Eucampia sp and Stephanopyxis pelagica in estuarine Bamboung MPA and Plagiogramma sp, Podocystis sp, Melosira sp and Rhabdonemma sp only encountered in Joal-Fadiouth (marine environment). Three species and / or groups of harmful algae blooms (HABs), Pseudonitzschia serieta in Joal-Fadiouth, Prorocentrium lima in Bamboung and Pseudonitzschia sp in both MPAs, were also encountered

Seasonal variability of phytoplankton composition inside and outside the Marine Protected Areas of Joal-Fadiouth and Bamboung in Senegal (West Africa) [résumé]

ICAWA : International Conference AWA, Dakar, SEN, 13-/12/2016 - 15/12/2016Marine Protected Areas (MPAs) are considered tools for biodiversity and resource restoration and resilience. However, their role in improving the flow of matter through better productivity remains to be demonstrated. The present study aims to analyze the phytoplankton composition inside and outside two contrasted MPAs; Joal-Fadiouth (coastal) and Bamboung (estuary) at dry cold and wet hot seasons. Data were collected with plankton net of 20 ?m net mesh in April and September 2016. In the laboratory, by optical microscopy, the phytoplankton species were identified at the lowest possible taxonomic level by comparison of our data with those of taxonomy works. A total of 101 species belonging to 30 families were identified in the Bamboung MPA, compared with 98 species of 28 families in the Joal-Fadiouth MPA. In the latter MPA, the number of species was higher (40 species of 19 families) inside than outside (30 species of 18 families) the MPA in April i.e. the cold season. In September, i.e. the hot season, the number of species was higher (62 species of 16 families) outside than inside (50 species of 14 families). As for the Bamboung MPA, whatever the season (cold and hot), the number of species was respectively higher inside (58 species of 28 families and 61 species of 20 families) than outside (30 species of 18 families and 58 species of 20 families). However, even if both MPAs present similitude for the taxonomical composition, characteristic species of each environment have been encountered: Eucampia sp and Stephanopyxis pelagica in estuarine Bamboung MPA and Plagiogramma sp, Podocystis sp, Melosira sp and Rhabdonemma sp only encountered in Joal-Fadiouth (marine environment). Three species and / or groups of harmful algae blooms (HABs), Pseudonitzschia serieta in Joal-Fadiouth, Prorocentrium lima in Bamboung and Pseudonitzschia sp in both MPAs, were also encountered

Caractérisation de la flore phytoplanctonique dans l'Aire Marine Protégée (AMP) de Bamboung et de deux sites environnants (Sénégal)

Au Sénégal, peu d'études sur le plan planctonique ont été réalisées pour l'évaluation de l'efficacité des Aires Marines Protégées. Dans cette perspective, la caractérisation de la flore phytoplanctonique et sa distribution spatio-temporelle à l'intérieur et à l'extérieur de l'AMP de Bamboung a été réalisée en avril et en septembre 2016. Des prélèvements d'échantillons d'eau à l'aide d'un filet à plancton de 20 µm de mailles ainsi que des mesures de paramètres physico-chimiques ont été faits dans chaque station. L'analyse des données environnementales a montré l'existence d'uneffet intersaison avec des valeurs plus élevées en avril excepté la température. Par ailleurs, un effet d'inter-sites a été observé uniquement en septembre pour la température, la salinité, la conductivité et l'oxygène dissout.En termes de diversité phytoplanctonique, en avril, 49 espèces réparties dans5 classes ont été identifiées dans l'AMP contre 47espèces et 5 classes identifiées à Diomboss et 42 espèces et 5 classes à Sangako. En septembre, 57espèces réparties dans 5 classes ont été répertoriées dans l'AMP contre 54 espèces et 4 classes à Diomboss, et 51 espèces réparties dans 4 classes identifiées à Sangako. Les résultats seuls de la richesse spécifique du phytoplancton ne permettent pas d'apporter une contribution sur l'évaluation de l'efficacité de l'AMP de Bamboung