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

Identification de caract\ue9ristiques agronomiques pour le diagnostic et la prise de d\ue9cision de r\ue9g\ue9n\ue9ration des vergers de cacaoyers en C\uf4te d\u2019Ivoire

The rehabilitation of the old cocoa (Theobrama cacao L.) farms is one of the major challenges for a sustainable cocoa production. A study was carried out to set up a guide which could be used as a decision making tool for a quick and efficient diagnosis of the old cocoa orchards and to choose the appropriate regeneration option (rehabilitation or replanting). A sample of 90 rehabilitated cocoa farms and of 75 replanted cocoa farms was surveyed in 12 regions representing the three main cocoa producing sectors in the country. Data were collected on the key agronomic characteristics of these cacao farms. These were cocoa variety, farm size, age, yield, planting density, number of shade trees and the level of damages caused by insects and diseases. The results showed that age, planting density and yield were the discriminating criteria of these farms. The average values of these criteria were 25 to 30 years for the age, 800 to 1 000 trees ha-1 for the planting density and 250 to 400 kg ha-1 an-1 for the yield. Based on these criteria and their average values, a decision making guide was designed for the diagnosis of cocoa farms and the choice of regeneration option. According to this guide, old cocoa farms (more than 25 years), degraded and unproductive should be replanted. However, younger farms having planting density and yield higher than the average values above should be rehabilitated.La r\ue9g\ue9n\ue9ration des vieux vergers de cacaoyers (Theobrama cacao L.) est une des strat\ue9gies mises en place en C\uf4te d\u2019Ivoire pour assurer une production durable de cacao. Une \ue9tude a \ue9t\ue9 conduite en vue d\u2019\ue9laborer un guide pour r\ue9aliser un diagnostic rapide et ad\ue9quat des vergers et prendre la bonne d\ue9cision de r\ue9g\ue9n\ue9ration, en optant judicieusement pour la r\ue9habilitation ou la replantation. Un \ue9chantillon de 90 plantations de cacaoyers r\ue9habilit\ue9es et de 75 autres replant\ue9es a \ue9t\ue9 enqu\ueat\ue9 dans 12 d\ue9partements repr\ue9sentatifs des trois principales zones de production de cacao du pays. Des donn\ue9es ont \ue9t\ue9 collect\ue9es sur les caract\ue9ristiques agronomiques majeures de ces cacaoy\ue8res. Il s\u2019est agi de la vari\ue9t\ue9 de cacaoyer, la superficie de la plantation, l\u2019\ue2ge, le rendement, la densit\ue9 de plantation, le nombre d\u2019arbre d\u2019ombrage permanent et le niveau des d\ue9g\ue2ts des insectes et des maladies. Les r\ue9sultats ont montr\ue9 que les crit\ue8res discriminants des vergers r\ue9g\ue9n\ue9r\ue9s sont l\u2019\ue2ge, la densit\ue9 de plantation et le rendement. Leurs valeurs moyennes sont comprises entre 25 et 30 ans pour l\u2019\ue2ge, 800 et 1\ua0000 arbres ha-1 pour la densit\ue9 et entre 250 et 400 kg ha-1 an-1 pour la production. A partir de ces trois crit\ue8res et de leurs valeurs moyennes, un guide a \ue9t\ue9 \ue9labor\ue9 pour le diagnostic des vergers de cacaoyers et la prise de d\ue9cision. Selon ce guide, les vieilles plantations de cacaoyers (plus de 25 ans), d\ue9grad\ue9es et improductives doivent \ueatre replant\ue9s. Cependant, les cacaoy\ue8res plus jeunes ayant des densit\ue9s de plantation et des rendements plus \ue9lev\ue9s que les valeurs moyennes ci-dessus devraient \ueatre r\ue9habilit\ue9es

A catalog of gene expression in the developing kidney.

Background. Anopheles gambiae, a major vector of malaria, is widely distributed throughout sub-Saharan Africa. In an attempt to eliminate infective mosquitoes, researchers are trying to develop transgenic strains that are refractory to the Plasmodium parasite. Before any release of transgenic mosquitoes can be envisaged, we need an accurate picture of the differentiation between the two molecular forms of An. gambiae, termed M and S, which are of uncertain taxonomic status. Methodology/Principal Findings. Insertion patterns of three transposable elements (TEs) were determined in populations from Benin, Burkina Faso, Cameroon, Ghana, Ivory Coast, Madagascar, Mali, Mozambique, Niger, and Tanzania, using Transposon Display, a TE-anchored strategy based on Amplified Fragment Length Polymorphism. The results reveal a clear differentiation between the M and S forms, whatever their geographical origin, suggesting an incipient speciation process. Conclusions/Significance. Any attempt to control the transmission of malaria by An. gambiae using either conventional or novel technologies must take the M/S genetic differentiation into account. In addition, we localized three TE insertion sites that were present either in every individual or at a high frequency in the M molecular form. These sites were found to be located outside the chromosomal regions that are suspected of involvement in the speciation event between the two forms. This suggests that these chromosomal regions are either larger than previously thought, or there are additional differentiated genomic regions interspersed with undifferentiated regions

Impact de la résistance aux pyréthrinoïdes sur l'efficacité des moustiquaires imprégnées dans la prévention du paludisme : résultats des essais en cases expérimentales avec la deltaméthrine SC

Une étude sur l'impact de la résistance d'#Anopheles gambiae s.s. aux pyréthrinoïdes sur l'efficacité des moustiquaires imprégnées de deltaméthrine à la dose de 25 mg de matière active/m2 a été conduite à la station expérimentale de Yaokoffikro. Les résultats de cette étude ont été comparés à une autre expérimentation réalisée dans les cases-pièges de la vallée du M'bé où les populations d'#Anopheles gambiae s.s. sont sensibles à la deltaméthrine. La comparaison de ces deux études montre que la deltaméthrine utilisée en imprégnation des moustiquaires perd une partie de son "effet dissuasif" dans la zone où #Anopheles gambiae s.s. est résistant aux pyréthrinoïdes mais que son pouvoir létal reste le même, que les populations d'#An. gambiae s.s. soient sensibles ou résistantes à la deltaméthrine. En conséquence, dans les zones de forte résistance d'#An. gambiae$ s.s. induite par le gène kdr, l'efficacité des moustiquaires imprégnées de deltaméthrine se maintient en termes de protection personnelle. (Résumé d'auteur

Genetic characterization of oleaginous bottle gourd (Lagenaria siceraria) germplasm from Côte d'Ivoire using agromorphological and molecular markers

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the analysis of molecular variance (AMOVA), 28% of the total variation resides among accessions and 72% occurs within populations. The AMOVA computed in order to differentiate cultivars, displayed the same trends when no prior grouping of accessions was considered. The differentiation within cultivar (97%) was more than that, among cultivars (3%). Tree topologies inferred by neighbour-joining analysis reflected no clear cut off grouping

Impact de la résistance aux pyréthrinoïdes sur l'efficacité des moustiquaires imprégnées dans la prévention du paludisme : résultats des essais en cases expérimentales avec la deltaméthrine SC

Une étude sur l'impact de la résistance d'#Anopheles gambiae s.s. aux pyréthrinoïdes sur l'efficacité des moustiquaires imprégnées de deltaméthrine à la dose de 25 mg de matière active/m2 a été conduite à la station expérimentale de Yaokoffikro. Les résultats de cette étude ont été comparés à une autre expérimentation réalisée dans les cases-pièges de la vallée du M'bé où les populations d'#Anopheles gambiae s.s. sont sensibles à la deltaméthrine. La comparaison de ces deux études montre que la deltaméthrine utilisée en imprégnation des moustiquaires perd une partie de son "effet dissuasif" dans la zone où #Anopheles gambiae s.s. est résistant aux pyréthrinoïdes mais que son pouvoir létal reste le même, que les populations d'#An. gambiae s.s. soient sensibles ou résistantes à la deltaméthrine. En conséquence, dans les zones de forte résistance d'#An. gambiae$ s.s. induite par le gène kdr, l'efficacité des moustiquaires imprégnées de deltaméthrine se maintient en termes de protection personnelle. (Résumé d'auteur

Etude du spermogramme dans le couple infertile a Lome

Introduction: L’infertilité de l’homme est une découverte récente car n’était ni souvent pensée, ni souvent débattue. L’objectif de notre étude était d’identifier les données relatives au spermogramme dans le couple infertile à Lomé.Matériel et Méthode: Il s’est agi d’une étude transversale descriptive des couples admis en consultation gynécologique pour désir de maternité, du 1er Juillet 2014 au 31 Mars 2015 (9 mois). Notre étude s’est déroulée en consultation externe du service de gynécologique et obstétrique du centre hospitalier universitaire Sylvanus Olympio (CHU-SO) et dans les structures privées qui ont acceptées participer à l’étude à savoir, la Clinique Immaculée Conception (CIC) et la Clinique Etoile.Résultats : Nous avions enregistré 48 couples, sur nos 3 sites de collecte au cours de notre période d’étude. Pour les couples à hommes infectiles, une hypospermie (22,2%), une oligospermie (74,1%) et une nécrozoospermie (22,22%) ont été observées.L’asthénozoospermie a été retrouvée dans 74,1 % de couples infertiles Les résulats révélaient une tératozoospermie33,33%. L’association d’anomalies la plus retrouvée a été l’asthénonécrozoospermie (48,15%).Conclusion : Le spermogramme demeure l’examen para-clinique clé de l’infertilité masculine. La responsabilité de l’homme est aussi incriminée dans les problèmes d’infertilité du couple. Mots clés : homme, infertilité, Tog