A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Technical Quality of a Mobile SPOC

Computer based Learning Environments are mainly shaped by emerging environments such as Massive Open Online Courses (MOOCs), SPOCS (Small Private Online Courses) and Mobile learning. This variety challenges the quality of the content delivered in these various environments. In Moroccan higher education, SPOCS is a trending topic widely used in its context of blended learning. The present work focuses on an SPOC delivered as a hybrid mobile app and on factors that define its technical quality. The objective is to propose a set of technical quality factors which are defined following a study of literature, focusing on frameworks, labels, practices that are used to assess the quality of e-learning environments, MOOCs, SPOCs and mobile applications. ISO standards for the quality software and the guidelines for the most dominant Mobile Operating Systems (Android/IOS/Windows phone) are also considered when defining these criteria. The proposed criteria can be twofold used: 1) to assess the technical quality of an existing mobile SPOC; 2) constitutes guidelines to increase the technical quality of a new mobile SPOC</p

User Profiling in a SPOC: A method based on User Video Clickstream Analysis

In the present paper, we address to construct a structured user profile in a Small Private Online Course (SPOC) based on user’s video clickstream analysis. We adopt an implicit approach to infer user’s preferences and experience difficulty based on user’s video sequence viewing analysis at the click-level as Play, Pause, Move forward… the Bayesian method is used in order to infer implicitly user’s interests. Learners with similar clickstream behavior are then segmented into clusters by using the unsupervised K-Means clustering algorithm. Videos that could meet the individual learner interests and offer a best and personalized experienced learning can therefore be recommended for a learner while enrolling in a SPOC based on his videos interactions and exploiting similar learners’ profiles

User Profiling in a SPOC: A method based on User Video Clickstream Analysis

In the present paper, we address to construct a structured user profile in a Small Private Online Course (SPOC) based on user’s video clickstream analysis. We adopt an implicit approach to infer user’s preferences and experience difficulty based on user’s video sequence viewing analysis at the click-level as Play, Pause, Move forward… the Bayesian method is used in order to infer implicitly user’s interests. Learners with similar clickstream behavior are then segmented into clusters by using the unsupervised K-Means clustering algorithm. Videos that could meet the individual learner interests and offer a best and personalized experienced learning can therefore be recommended for a learner while enrolling in a SPOC based on his videos interactions and exploiting similar learners’ profiles

Cloaca in Discordant Monoamniotic Twins: Prenatal Diagnosis and Consequence for Fetal Lung Development

Objective - Describe a case of cloaca prenatally diagnosed in one of a set of monoamniotic twins. Study Design - Retrospective review of a case. Results - Cloaca is one of the most complex and severe degrees of anorectal malformations in girls. We present a discordant cloaca in monoamniotic twins. Fetal ultrasound showed a female fetus with a pelvic midline cystic mass, a phallus-like structure, a probable anorectal atresia with absence of anal dimple and a flat perineum, and renal anomalies. The diagnosis was confirmed by fetal magnetic resonance imaging postnatally. Conclusions - The rarity of the malformation in a monoamniotic pregnancy, the difficulties of prenatal diagnosis, the pathogenic assumptions, and the consequences of adequate amniotic fluid for fetal lung development are discussed

Cloaca in Discordant Monoamniotic Twins: Prenatal Diagnosis and Consequence for Fetal Lung Development

Abstract Objective Describe a case of cloaca prenatally diagnosed in one of a set of monoamniotic twins. Study Design Retrospective review of a case. Results Cloaca is one of the most complex and severe degrees of anorectal malformations in girls. We present a discordant cloaca in monoamniotic twins. Fetal ultrasound showed a female fetus with a pelvic midline cystic mass, a phallus-like structure, a probable anorectal atresia with absence of anal dimple and a flat perineum, and renal anomalies. The diagnosis was confirmed by fetal magnetic resonance imaging postnatally. Conclusions The rarity of the malformation in a monoamniotic pregnancy, the difficulties of prenatal diagnosis, the pathogenic assumptions, and the consequences of adequate amniotic fluid for fetal lung development are discussed

Severe Phenotype of Cutis Laxa Type 1B with Antenatal Signs due to a Novel Homozygous Nonsense Mutation in <b><i>EFEMP2</i></b>

Abstract: EFEMP2 mutations are known to be responsible for autosomal recessive cutis laxa type 1B (ARCL1B), a rare multisystem disease affecting skin, skeleton, and vascular structures. We report 2 additional related cases of ARCL1B of particular severity leading to termination of pregnancy. Cardinal signs of this connective tissue disease were already seen during the second trimester of pregnancy, then confirmed and clarified at autopsy. Anomalies included cutis laxa, arachnodactyly, clubfoot, wormian bones, moderate bowing of long bones with slender bone trabeculae, rib fractures, undermuscularized diaphragm, hiatal hernia, and arterial tortuosity with thick vascular walls and disorganized elastic fibers. Sequencing of the EFEMP2 gene revealed a novel homozygous nonsense mutation: c.639C>A (p.Cys213*). We performed a thorough histological analysis and discuss differential diagnoses, genotype-phenotype correlations, and the challenge of prenatal diagnosis of this disease. (c) 2018 S. Karger AG, Base