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

Effects of the parasite Argulus ambloplites (Wilson, 1920) on welfare and mouthbreeding eggs capacity of Oreochromis niloticus (Linnaeus, 1758) females

Declines in the reproduction performance of Oreochromis niloicus fish have been observed for two decades in the fish farms located on the edge of the Aby lagoon. Research on the causes of these reproductive drops has led to a series of experiments with pathogens harvested from these spawners in a preliminary study in 2012 that found the parasite Argulus ambloplites in abundance. Thus, the aim of this study was to know the effects of the two forms of the parasites A. ambloplites on the welfare and mouthbrooding eggs capacity of the fish O. niloticus. As a method, fish spawners were exposed to an artificial infestation with naupli parasites as treatment one and adult parasites as treatment two in a total randomised design experiment containing three groups triplicated. Fulton’s condition factor K, mouth infestation intensity, number of mouthbrooding eggs, and the relationship between mouth infestation intensity and number of mouthbrooding eggs were biological parameters followed and determined. K values were lower in infested fish. Females of control group presented inside their mouth 601 eggs for incubating per female, against 0 egg inside the mouth of females parasitised fish. A strong nonlinear and negative correlation has been established between the absence of eggs in incubation in females and the intensity of mouth parasite infestation. The welfare and eggs mouthbrooding capacity of O. niloticus females were negatively affected by the parasite A. ambloplites infestation

Identification Des Lésions Hépatiques D’origine Parasitaire Chez Les Bovins De L’abattoir De Daloa (Centre-Ouest De La Côte d’Ivoire)

Description du sujet. Cette étude relative aux pathologies du foie de bovin a été effectuée à l’abattoir de la ville de Daloa. Elle a concerné 345 bovins de la race Zébu.Objectifs. Cette étude a pour but de contribuer à la sécurité alimentaire en fournissant des données sur les pathologies hépatiques.Méthode. Une inspection post mortem faisant appel aux capacités sensorielles, telles que la vue, l’odorat et le toucher a été réalisée. Le foie suspecté est saisi et fait l’objet d’une incision pour une inspection plus détaillée.Résultats. Nous avons procédé à la saisie des foies de 110 bovins présentant des lésions prédominantes qui sont de la plus dominante à la moins : la distomatose, l’abcès, la sclérose du foie, la cholangite sténosante, la cholangite fibrosante, l’hépatite nécrosante, la télangiectasie maculeuse, etc.Conclusion. Des règles d’hygiène strictes à l’abattoir et à l’endroit de la population bovine doivent être respectées pour limiter la propagation des germes et éviter les contaminations des manipulateurs et des consommateurs. Description of the subject. This study on pathologies of bovine liver was carried out at the slaughterhouse in the town of Daloa. It concerned 345 cattle of the Zebu Breed.Objectives. This study aims to contribute to food security by providing data on hepatic pathologies.Method. A post-mortem inspection using sensory abilities, such as sight, smell and touch was performed. The suspected liver is seized and incised for further inspection. Results. We seized the livers of 110 cattle with predominant lesions which are from the most dominant to the least: distomatosis, abscess, sclerosis of the liver, stenosant cholangitis, fibrosing cholangitis, necrotizing hepatitis, macular telangiectasia, etc.Conclusions. Strict hygiene rules at the slaughterhouse and at the location of the bovine population must be observed to limit the spread of germs and prevent contamination of handlers and consumers

A field trial to assess a blood-Stage malaria vaccine

BACKGROUND--Blood-stage malaria vaccines are intended to prevent clinical disease. The malaria vaccine FMP2.1/AS02A, a recombinant protein based on apical membrane antigen 1 (AMA1) from the 3D7 strain of Plasmodium falciparum, has previously been shown to have immunogenicity and acceptable safety in Malian adults and children. METHODS--In a double-blind, randomized trial, we immunized 400 Malian children with either the malaria vaccine or a control (rabies) vaccine and followed them for 6 months. The primary end point was clinical malaria, defined as fever and at least 2500 parasites per cubic millimeter of blood. A secondary end point was clinical malaria caused by parasites with the AMA1 DNA sequence found in the vaccine strain. RESULTS--The cumulative incidence of the primary end point was 48.4% in the malariavaccine group and 54.4% in the control group; efficacy against the primary end point was 17.4% (hazard ratio for the primary end point, 0.83; 95% confidence interval [CI], 0.63 to 1.09; P = 0.18). Efficacy against the first and subsequent episodes of clinical malaria, as defined on the basis of various parasite-density thresholds, was approximately 20%. Efficacy against clinical malaria caused by parasites with AMA1 corresponding to that of the vaccine strain was 64.3% (hazard ratio, 0.36; 95% CI, 0.08 to 0.86; P = 0.03). Local reactions and fever after vaccination were more frequent with the malaria vaccine. CONCLUSIONS--On the basis of the primary end point, the malaria vaccine did not provide significant protection against clinical malaria, but on the basis of secondary results, it may have strain-specific efficacy. If this finding is confirmed, AMA1 might be useful in a multicomponent malaria vaccine

Responding to Communicable Diseases in Internationally Mobile Populations at Points of Entry and along Porous Borders, Nigeria, Benin, and Togo

Recent multinational disease outbreaks demonstrate the risk of disease spreading globally before public health systems can respond to an event. To ensure global health security, countries need robust multisectoral systems to rapidly detect and respond to domestic or imported communicable diseases. The US Centers for Disease Control and Prevention International Border Team works with the governments of Nigeria, Togo, and Benin, along with Pro-Health International and the Abidjan-Lagos Corridor Organization, to build sustainable International Health Regulations capacities at points of entry (POEs) and along border regions. Together, we strengthen comprehensive national and regional border health systems by developing public health emergency response plans for POEs, conducting qualitative assessments of public health preparedness and response capacities at ground crossings, integrating internationally mobile populations into national health surveillance systems, and formalizing cross-border public health coordination. Achieving comprehensive national and regional border health capacity, which advances overall global health security, necessitates multisectoral dedication to the aforementioned components

MOESM1 of Phase 1 randomized controlled trial to evaluate the safety and immunogenicity of recombinant Pichia pastoris-expressed Plasmodium falciparum apical membrane antigen 1 (PfAMA1-FVO [25-545]) in healthy Malian adults in Bandiagara

Additional file 1. Raw data set of the IgG and GIA responses for the phase 1 trial of PfAMA1 FVO [25-545] in Malians adults in Bandiagara