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

Etude d'un modèle de neuropaludisme chez le rat et évaluation des effets pharmacologiques d'un candidat-médicament

Le neuropaludisme (NP) est la forme la plus mortelle du paludisme. C'est une complication neurologique observée uniquement dans les cas d'infection par Plasmodium falciparum, principalement chez les enfants de moins de 5 ans vivant en Afrique Sub-saharienne, et les adultes non-immuns, notamment les femmes enceintes et les touristes visitant les zones d'endémie. Les signes cliniques sont à présent bien décrits (prostration, convulsions répétées, difficultés respiratoires, coma,...), mais les mécanismes physiopathologiques conduisant au NP sont encore mal définis. Leur élucidation est rendue difficile par la localisation cérébrale de la pathologie du vivant des patients et la faible disponibilité des données nécropsiques. Bien que l'accès aux tissus humains soit limité en nombre, les résultats d'autopsie ont permis d'établir que le NP résulte d'une séquestration des globules parasités au niveau de l'endothélium intra-vasculaire, associée à une forte réaction immunitaire. La stratégie de prise en charge du NP combine un traitement étiologique à base de dérivés d'artémisinine, ou de quinine et un traitement adjuvant symptomatique destiné à pallier à la défaillance multiorganique qui est à l'origine de l'issue fatale souvent observée. Le modèle de NP expérimental actuellement le plus utilisé est le modèle souris infecté par P. berghei ANKA. La pertinence de ce modèle est toutefois remise en cause en raison notamment des différences histo-pathologiques observées par rapport à la forme humaine. En effet, les souris manifestant les symptômes du NP ne présentent que très rarement le phénomène de séquestration, caractéristique majeure du NP chez l'Homme. Par ailleurs, comparativement à la réponse immunitaire de la souris, le modèle rat s'est également révélé plus proche de la réaction de l'Homme, dans le cas d'une autre parasitose, la schistosomose. L'objectif de la première partie du projet thèse a donc été la mise en place et l'évaluation d'un modèle alternatif de NP chez le rat. Ainsi un modèle de NP chez le rat Sprague Dawley infecté par la souche murine P. berghei K173 a été caractérisé sur les plans clinique, biologique (paramètres hématologiques et biochimiques),histopathologique et du profil cytokinique (cytokines cérébrales et sériques). La forte similarité des symptômes et des lésions associées au NP du rat Sprague Dawley infecté par P. berghei K173 par rapport au NP humain permet de valider la pertinence de ce modèle pour l'étude de la physiopathologie du NP. L'objectif de la deuxième partie de mon projet de thèse a été d'évaluer les effets pharmacologiques d'un candidat-médicament, l'isoflurane, pour le traitement adjuvant du NP. Ce composé présente l'avantage d'être déjà utilisé chez l'Homme à d'autres fins thérapeutiques et dispose donc d'une autorisation de mise sur le marché. Les résultats obtenus montrent une efficacité nette de l'isoflurane avec une rémission totale des signes de paralysie pour 47.8% des rats traités ainsi qu'un gain de survie des rats NP traités de 2 à 10 jours par rapport aux rats NP non traités. Ce gain de survie des animaux traités pourrait permettre un allongement de la fenêtre du temps de traitement étiologique, améliorant ainsi sensiblement le pronostic du NP. L'isoflurane, dont le mécanisme d'action semble être la réversion de la séquestration des globules parasités, limite les complications neurologiques souvent responsables de séquelles liées au NP. Des études ultérieures permettront d'optimiser ce nouveau protocole de traitement adjuvant du NP.Cerebral malaria (CM) is the most deadly form of malaria. It is a neurological complication observed only in cases of infection with Plasmodium falciparum that affects mainly children under five years living in Sub-Saharan Africa and non-immune adults including pregnant women and tourists visiting endemic areas. Although clinical signs are well described (prostration, respiratory distress convulsions, coma), the pathophysiological mechanisms leading to CM are still unclear. Their elucidation in vivo is made difficult by the cerebral location and the low availability of autopsy data. Instead of limited access to human tissues, autopsy results have shown that CM results from a strong immune response linked to sequestration of infected red blood cells in the intravascular endothelium. Cerebral malaria management combines an etiological treatment with artemisinin derivatives or quinine and adjunct treatment of the multi-visceral failures, responsible of fatal outcome. P. berghei ANKA-infected mouse is widely used as experimental murine model of CM. However the relevance of this model is still questioned because of the histopathologic differences from the human form. Indeed, CM mice rarely exhibit the red blood cell sequestration that is a major feature of human CM. Furthermore, compared to mouse, the rat displays a closer immune response to human in Schistosoma infection. This PhD research project first aimed to implement and assess an alternative rat model of CM. The clinical, biological, histo-pathological features as well as the cytokine profiling of an experimental model of CM were characterized in Sprague Dawley rats infected with P. berghei strain K173. The strong similarity of the symptoms and lesions observed in this model with those reported in human CM confirms its high relevance. The second objective of this thesis project was to assess the pharmacological effects of a drug-candidate in adjunct treatment of CM. Results demonstrated a strong efficacy of the molecule tested with 47.8% of the treated CM rats showing total remission. Moreover we observed a 2- to 10-day survival gain in the treated CM rats group compared to the non-treated CM rat group. Preliminary data suggest that this drug-candidate may reverse the endothelial sequestration of parasitized red blood cells and so limit the neurological sequels related to CM. It is anticipated that the gain in survival associated with this drug-candidate use will extend the window of the etiological treatment time, thus significantly improving the global prognosis of CM. Further studies are needed to optimize this adjunct CM treatment protocol

Study of a cerebral malaria model in rats and pharmacological effects assessment of a drug-candidate

Le neuropaludisme (NP) est la forme la plus mortelle du paludisme. C'est une complication neurologique observée uniquement dans les cas d'infection par Plasmodium falciparum, principalement chez les enfants de moins de 5 ans vivant en Afrique Sub-saharienne, et les adultes non-immuns, notamment les femmes enceintes et les touristes visitant les zones d'endémie. Les signes cliniques sont à présent bien décrits (prostration, convulsions répétées, difficultés respiratoires, coma,...), mais les mécanismes physiopathologiques conduisant au NP sont encore mal définis. Leur élucidation est rendue difficile par la localisation cérébrale de la pathologie du vivant des patients et la faible disponibilité des données nécropsiques. Bien que l'accès aux tissus humains soit limité en nombre, les résultats d'autopsie ont permis d'établir que le NP résulte d'une séquestration des globules parasités au niveau de l'endothélium intra-vasculaire, associée à une forte réaction immunitaire. La stratégie de prise en charge du NP combine un traitement étiologique à base de dérivés d'artémisinine, ou de quinine et un traitement adjuvant symptomatique destiné à pallier à la défaillance multiorganique qui est à l'origine de l'issue fatale souvent observée. Le modèle de NP expérimental actuellement le plus utilisé est le modèle souris infecté par P. berghei ANKA. La pertinence de ce modèle est toutefois remise en cause en raison notamment des différences histo-pathologiques observées par rapport à la forme humaine. En effet, les souris manifestant les symptômes du NP ne présentent que très rarement le phénomène de séquestration, caractéristique majeure du NP chez l'Homme. Par ailleurs, comparativement à la réponse immunitaire de la souris, le modèle rat s'est également révélé plus proche de la réaction de l'Homme, dans le cas d'une autre parasitose, la schistosomose. L'objectif de la première partie du projet thèse a donc été la mise en place et l'évaluation d'un modèle alternatif de NP chez le rat. Ainsi un modèle de NP chez le rat Sprague Dawley infecté par la souche murine P. berghei K173 a été caractérisé sur les plans clinique, biologique (paramètres hématologiques et biochimiques),histopathologique et du profil cytokinique (cytokines cérébrales et sériques). La forte similarité des symptômes et des lésions associées au NP du rat Sprague Dawley infecté par P. berghei K173 par rapport au NP humain permet de valider la pertinence de ce modèle pour l'étude de la physiopathologie du NP. L'objectif de la deuxième partie de mon projet de thèse a été d'évaluer les effets pharmacologiques d'un candidat-médicament, l'isoflurane, pour le traitement adjuvant du NP. Ce composé présente l'avantage d'être déjà utilisé chez l'Homme à d'autres fins thérapeutiques et dispose donc d'une autorisation de mise sur le marché. Les résultats obtenus montrent une efficacité nette de l'isoflurane avec une rémission totale des signes de paralysie pour 47.8% des rats traités ainsi qu'un gain de survie des rats NP traités de 2 à 10 jours par rapport aux rats NP non traités. Ce gain de survie des animaux traités pourrait permettre un allongement de la fenêtre du temps de traitement étiologique, améliorant ainsi sensiblement le pronostic du NP. L'isoflurane, dont le mécanisme d'action semble être la réversion de la séquestration des globules parasités, limite les complications neurologiques souvent responsables de séquelles liées au NP. Des études ultérieures permettront d'optimiser ce nouveau protocole de traitement adjuvant du NP.Cerebral malaria (CM) is the most deadly form of malaria. It is a neurological complication observed only in cases of infection with Plasmodium falciparum that affects mainly children under five years living in Sub-Saharan Africa and non-immune adults including pregnant women and tourists visiting endemic areas. Although clinical signs are well described (prostration, respiratory distress convulsions, coma), the pathophysiological mechanisms leading to CM are still unclear. Their elucidation in vivo is made difficult by the cerebral location and the low availability of autopsy data. Instead of limited access to human tissues, autopsy results have shown that CM results from a strong immune response linked to sequestration of infected red blood cells in the intravascular endothelium. Cerebral malaria management combines an etiological treatment with artemisinin derivatives or quinine and adjunct treatment of the multi-visceral failures, responsible of fatal outcome. P. berghei ANKA-infected mouse is widely used as experimental murine model of CM. However the relevance of this model is still questioned because of the histopathologic differences from the human form. Indeed, CM mice rarely exhibit the red blood cell sequestration that is a major feature of human CM. Furthermore, compared to mouse, the rat displays a closer immune response to human in Schistosoma infection. This PhD research project first aimed to implement and assess an alternative rat model of CM. The clinical, biological, histo-pathological features as well as the cytokine profiling of an experimental model of CM were characterized in Sprague Dawley rats infected with P. berghei strain K173. The strong similarity of the symptoms and lesions observed in this model with those reported in human CM confirms its high relevance. The second objective of this thesis project was to assess the pharmacological effects of a drug-candidate in adjunct treatment of CM. Results demonstrated a strong efficacy of the molecule tested with 47.8% of the treated CM rats showing total remission. Moreover we observed a 2- to 10-day survival gain in the treated CM rats group compared to the non-treated CM rat group. Preliminary data suggest that this drug-candidate may reverse the endothelial sequestration of parasitized red blood cells and so limit the neurological sequels related to CM. It is anticipated that the gain in survival associated with this drug-candidate use will extend the window of the etiological treatment time, thus significantly improving the global prognosis of CM. Further studies are needed to optimize this adjunct CM treatment protocol

Refined Immunochemical Characterization in Healthy Dog Skin of the Epidermal Cornification Proteins, Filaggrin, and Corneodesmosin

International audienceFilaggrin (FLG) and corneodesmosin (CDSN) are two key proteins of the human epidermis. FLG loss-of-function mutations are the strongest genetic risk factors for human atopic dermatitis. Studies of the epidermal distribution of canine FLG and CDSN are limited. Our aim was to better characterize the distribution of FLG and CDSN in canine skin. Using immunohistochemistry on beagle skin, we screened a series of monoclonal antibodies (mAbs) specific for human FLG and CDSN. The cross-reactive mAbs were further used using immunoelectron microscopy and Western blotting. The structure of canine CDSN and FLG was determined using publicly available databases. In the epidermis, four anti-FLG mAbs stained keratohyalin granules in the granular keratinocytes and corneocyte matrix of the lower cornified layer. In urea-extracts of dog epidermis, several bands corresponding to proFLG and FLG monomers were detected. One anti-CDSN mAb stained the cytoplasm of granular keratinocytes and cells of both the inner root sheath and medulla of hair follicles. Dog CDSN was located in lamellar bodies, in the extracellular parts of desmosomes and in corneodesmosomes. A protein of 52 kDa was immunodetected. Genomic DNA analysis revealed that the amino acid sequence and structure of canine and human CDSN were highly similar

Young Sprague Dawley rats infected by Plasmodium berghei: A relevant experimental model to study cerebral malaria.

Cerebral malaria (CM) is the most severe manifestation of human malaria yet is still poorly understood. Mouse models have been developed to address the subject. However, their relevance to mimic human pathogenesis is largely debated. Here we study an alternative cerebral malaria model with an experimental Plasmodium berghei Keyberg 173 (K173) infection in Sprague Dawley rats. As in Human, not all infected subjects showed cerebral malaria, with 45% of the rats exhibiting Experimental Cerebral Malaria (ECM) symptoms while the majority (55%) of the remaining rats developed severe anemia and hyperparasitemia (NoECM). These results allow, within the same population, a comparison of the noxious effects of the infection between ECM and severe malaria without ECM. Among the ECM rats, 77.8% died between day 5 and day 12 post-infection, while the remaining rats were spontaneously cured of neurological signs within 24-48 hours. The clinical ECM signs observed were paresis quickly evolving to limb paralysis, global paralysis associated with respiratory distress, and coma. The red blood cell (RBC) count remained normal but a drastic decrease of platelet count and an increase of white blood cell numbers were noted. ECM rats also showed a decrease of glucose and total CO2 levels and an increase of creatinine levels compared to control rats or rats with no ECM. Assessment of the blood-brain barrier revealed loss of integrity, and interestingly histopathological analysis highlighted cyto-adherence and sequestration of infected RBCs in brain vessels from ECM rats only. Overall, this ECM rat model showed numerous clinical and histopathological features similar to Human CM and appears to be a promising model to achieve further understanding the CM pathophysiology in Humans and to evaluate the activity of specific antimalarial drugs in avoiding/limiting cerebral damages from malaria

Filaggrin expression and processing deficiencies impair corneocyte surface texture and stiffness in mice

Abundant corneocyte surface protrusions, observed in patients with atopic dermatitis with filaggrin loss-of-function mutations, are inversely associated with levels of natural moisturizing factors (NMFs) in the stratum corneum. To dissect the etiological role of NMFs and filaggrin deficiency in surface texture alterations, we examined mouse models with genetic deficiencies in the synthesis or degradation of filaggrin monomers for NMFs, cell stiffness (elastic modulus) and corneocyte surface protrusion density (dermal texture index). Five neonatal and adult mouse models carrying inactivating mutations of SASPase (Sasp−/−), filaggrin (Flgft/ft and Flg−/−), filaggrin-hornerin (FlgHrnr−/−), and bleomycin hydrolase (Blmh−/−) were investigated. Sasp−/− and Flg−/− were on the hairless mouse background. Atomic force microscopy was used to determine elastic modulus and dermal texture index. Corneocytes of each neonatal as well as hairless adult knockout mouse exhibited an increased number of protrusions and decreased elastic modulus. In these mice, NMFs were reduced except for Sasp−/−. Dermal texture index was inversely correlated with NMFs and elastic modulus. Our findings demonstrate that any filaggrin-NMF axis deficiency can affect corneocyte mechanical properties in mice and likely in humans. Differences in NMFs and corneocyte surface texture between neonatal and adult as well as hairless and hairy mice emphasize the need for carefully selecting the most appropriate animal models for studies

Histological illustrations of cerebral lesions in ECM K173 infected SD rats.

<p>(<b>A</b>) Acute perivascular neuropilar hemorrhage with severe extension (circle). Diffuse intracerebral hemorrhages (<b>B</b> and <b>C</b>) with presence of numerous parasites (<b>D</b>). ECM brains were collected from rats without systemic lavage. Histological slices of ECM brains stained using hematoxylin-eosin.</p

Hematological parameters in the course of infection in ECM (n = 17), NoECM (n = 22) and control (n = 13) groups.

<p>Mean Corpuscular Volume (MCV) (<b>A</b>) and Mean Corpuscular Hemoglobin Concentration (MCHC) (<b>B</b>) kinetics. The hematological parameters are aligned from and on the basis of the day (D) when parasitemia was estimated at 5% (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181300#pone.0181300.s001" target="_blank">S1B Fig</a>). All data are represented by mean ±standard error of the mean (SEM).</p

Dorsal view of brains from K173 infected SD rats after systemic lavage.

<p>(<b>A</b>) Healthy brain of a Control (Ctrl) rat. (<b>B</b>) ECM brain shows petechial hemorrhages especially on cerebellum and edema with disappearance of cerebral longitudinal fissure. (<b>C</b>) NoECM brain presents no macroscopic lesion.</p

Localization of parasites in cerebral vessels in ECM K173 infected SD rats.

<p>(<b>A</b>) Thrombosis. (<b>B</b>) Parasites were localized in peripheries of cerebral vessels in direct contact with the endothelium. <b>(C</b> and <b>D)</b> Extravascular hemorrhage with parasites (arrows) localized in peripheries. ECM brains were collected from rats without systemic lavage. Histological slices of ECM brains stained using hematoxylin-eosin.</p