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

A patient-driven strategy to unravel new PCSK9 functions in dyslipidemia and human induced pluripotent stem cells differentiation

PCSK9 est un régulateur clé du métabolisme du cholestérol par le foie à travers la dégradation lysosomiale du récepteur aux LDL (low-density lipoprotein). Alors que les mutations gain de fonction (GOF) de PCSK9 induisent une hypercholestérolémie autosomique dominante, les mutations pertes de fonctions (LOF) entraînent un taux spontanément bas de LDL-cholestérol, ainsi qu’un protection cardiovasculaire. Du fait des limitations inhérentes aux modèles d’études, tels que les lignées cellulaires transfectées ou des animaux transgéniques, les fonctions de PCSK9 restent encore mal connues. Ainsi, nous avons utiliser des cellules souches pluripotentes induites (hiPSC) spécifiques de patients pour les différencier en hépatocytes et modéliser la physiopathologie liée aux mutations de PCSK9 GOF-S127R et LOF-R104C/V114A. Nous avons démontré que les hépatocytes obtenus récapitulaient la physiopathologie liés aux mutations de PCSK9. De plus, les cellules portant la mutation S127R ont montré une importante réponse au traitement par les statines, qui est corrélée à la réponse clinique des patients portant cette même mutation. Enfin, notre étude nous a permis de mettre à jour une fonction inattendue de PCSK9 dans les hiPSC et pendant leur différenciation. Elle montre que PCSK9 affecterait la prolifération des hiPSC ainsi qu’une voie de signalisation clé du développement régulée par NODAL. Cette régulation se ferait à travers une interaction directe entre PCSK9 et DACT2, un régulateur intracellulaire de la voie de signalisation de NODAL. En conclusion, les hiPSC s’avèrent être un modèle cellulaire translationnel pertinent pour mettre à jour de nouvelles fonctions hépatiques de PCSK9.PCSK9 has been identified as a key regulator of cholesterol metabolism by the liver through inducing lysosomal degradation of the low-density lipoprotein receptor (LDLR). While PCSK9 gain-of-function (GOF) mutations induced autosomal dominant hypercholesterolemia and increased cardiovascular risk, loss-of-function (LOF) mutations are associated with low LDL-cholesterol levels and cardiovascular protection. Due to limitations inherent to current models including animal and human cells lines transfected with DNA constructs or transgenic animal models, PCSK9 functions are not fully understood. Therefore, we took advantage of patient related somatic cells reprogramming intoinduced pluripotent stem cells (hiPSC) to generate hepatocyte-like cells (HLC) and model the pathophysiology of PCSK9 mutations in dyslipidemia through focusing on two intracellular mutation forms; GOF (S127R) and LOF (R104C/V114A). We showed that HLC could recapitulate the key pathophysiological features of PCSK9 mutations. Moreover, HLC with the S127R mutation displayed an increased uptake of LDL upon statin treatment, which was correlated with the original patient clinical response. In parallel, this model enabled us to unravel a new unexpected role of PCSK9 in hiPSC and during differentiation. PCSK9 was found to affect the proliferation of hiPSC and regulate a key developmental signaling pathway mediated by NODAL. This regulation might occur by a direct interaction between PCSK9 and DACT2, an intracellular attenuator of NODAL signaling pathway. In conclusion, hiPSC provide a pertinent translational model to decipher PCSK9 hepatic functions and a novel cellular environment to highlight new functions

From Human-Induced Pluripotent Stem Cells to Liver Disease Modeling: A Focus on Dyslipidemia

International audienceSince the reprogramming of human somatic cells into induced pluripotent stem cells (hiPSCs) became a reality, numerous advances have been made for the reprogramming process itself, cell differentiation and disease modeling. While differentiation procedures of hiPSCs into hepatocyte-like cells are under continuous investigations in order to generate fully mature and functional hepatocytes, current models already showed great promises in terms of modeling liver pathologies including metabolic diseases. This review provides an overview of the reprogramming, hepatic differentiation, and application aspects of patient-derived hepatocyte-like cells, with a more focused attention on the modeling of cholesterol metabolism defects

Urine-sample-derived human induced pluripotent stem cells as a model to study PCSK9-mediated autosomal dominant hypercholesterolemia

International audienceProprotein convertase subtilisin kexin type 9 (PCSK9) is a critical modulator of cholesterol homeostasis. Whereas PCSK9 gain-of-function (GOF) mutations are associated with autosomal dominant hypercholesterolemia (ADH) and premature atherosclerosis, PCSK9 loss-of-function (LOF) mutations have a cardio-protective effect and in some cases can lead to familial hypobetalipoproteinemia (FHBL). However, limitations of the currently available cellular models preclude deciphering the consequences of PCSK9 mutation further. We aimed to validate urine-sample-derived human induced pluripotent stem cells (UhiPSCs) as an appropriate tool to model PCSK9-mediated ADH and FHBL. To achieve our goal, urine-sample-derived somatic cells were reprogrammed into hiPSCs by using episomal vectors. UhiPSC were efficiently differentiated into hepatocyte-like cells (HLCs). Compared to control cells, cells originally derived from an individual with ADH (HLC-S127R) secreted less PCSK9 in the media (−38.5%; P=0.038) and had a 71% decrease (P<0.001) of low-density lipoprotein (LDL) uptake, whereas cells originally derived from an individual with FHBL (HLC-R104C/V114A) displayed a strong decrease in PCSK9 secretion (−89.7%; P<0.001) and had a 106% increase (P=0.0104) of LDL uptake. Pravastatin treatment significantly enhanced LDL receptor (LDLR) and PCSK9 mRNA gene expression, as well as PCSK9 secretion and LDL uptake in both control and S127R HLCs. Pravastatin treatment of multiple clones led to an average increase of LDL uptake of 2.19±0.77-fold in HLC-S127R compared to 1.38±0.49 fold in control HLCs (P<0.01), in line with the good response to statin treatment of individuals carrying the S127R mutation (mean LDL cholesterol reduction=60.4%, n=5). In conclusion, urine samples provide an attractive and convenient source of somatic cells for reprogramming and hepatocyte differentiation, but also a powerful tool to further decipher PCSK9 mutations and function

PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs

International audienceProprotein convertase subtilisin kexin type 9 (PCSK9) is a key regulator of low-density lipoprotein (LDL) cholesterol metabolism and the target of lipid-lowering drugs. PCSK9 is mainly expressed in hepatocytes. Here, we show that PCSK9 is highly expressed in undifferentiated human induced pluripotent stem cells (hiPSCs). PCSK9 inhibition in hiPSCs with the use of short hairpin RNA (shRNA), CRISPR/cas9-mediated knockout, or endogenous PCSK9 loss-of-function mutation R104C/V114A unveiled its new role as a potential cell cycle regulator through the NODAL signaling pathway. In fact, PCSK9 inhibition leads to a decrease of SMAD2 phosphorylation and hiPSCs proliferation. Conversely, PCSK9 overexpression stimulates hiPSCs proliferation. PCSK9 can interfere with the NODAL pathway by regulating the expression of its endogenous inhibitor DACT2, which is involved in transforming growth factor (TGF) β-R1 lysosomal degradation. Using different PCSK9 constructs, we show that PCSK9 interacts with DACT2 through its Cys-His-rich domain (CHRD) domain. Altogether these data highlight a new role of PCSK9 in cellular proliferation and development

Characterization of genetic variants in the EGLN1/PHD2 gene identified in a European collection of patients with erythrocytosis

: Hereditary erythrocytosis (HE) is a rare hematological disorder characterized by an excess of red blood cell production. Here we describe a European collaborative study involving a collection of 2160 patients with erythrocytosis sequenced in 10 different laboratories. We focused our study on the EGLN1 gene and identified 39 germline missense variants including one gene deletion in 47 probands. EGLN1 encodes the PHD2 prolyl 4-hydroxylase, a major inhibitor of the Hypoxia-Inducible Factor. We performed a comprehensive study to evaluate the causal role of the identified PHD2 variants: in silico study of localization, conservation, and deleterious effects; analysis of hematological parameters of carriers identified in the UK Biobank; functional studies of the protein activity and stability; and comprehensive study of PHD2 splicing. Altogether, this study allowed the classification of 16 pathogenic or likely pathogenic mutants in a total of 48 patients and relatives. The in silico studies extented to the variants described in the literature showed that a minority of PHD2 variants can be classified as pathogenic (36/96), without any differences with the variants of unknown significance regarding the severity of the developed disease (hematological parameters and complications). Here, we demonstrated the great value of federating laboratories working on such rare pathology to implement the criteria required for genetic classification, a strategy that should be extended to all hereditary hematological diseases