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

Intrathecal donor lymphocyte infusion for the treatment of suspected refractory lymphomatous meningitis: a case report.

A 43-year-old female with large T-cell non-Hodgkin's lymphoma and central nervous system (CNS) involvement underwent HLA-identical-sibling peripheral blood stem cell transplantation (SCT) during her third complete remission. She presented a possible refractory CNS relapse 5 months after the transplant. She was then treated with intrathecal (IT) donor lymphocyte infusions (DLI). No side effects were observed after three DLI injections. The patient died 13 months later from infectious complications with no evidence of progressive disease. To our knowledge, this is the first case report of IT DLI for possible refractory lymphomatous meningitis.Case ReportsJournal ArticleSCOPUS: ar.jFLWINinfo:eu-repo/semantics/publishe

Reduced intensity conditioning haematopoietic stem cell transplantation with mesenchymal stromal cells infusion for the treatment of metachromatic leukodystrophy: a case report.

We report the case of a 23-year-old woman who presented with an adult form of metachromatic leukodystrophy (MLD) evolving over one year with a progressive neurological deterioration. A non-myeloablative matched related haematopoietic stem cell transplantation (HSCT) with concomitant mesenchymal stromal cells (MSCs) infusion was performed. Engraftment occurred rapidly with no significant toxicity or side effects following the MSC infusion. At a follow up of 40 months, the patient had a stabilisation of all neurological manifestations of her disease. This case report suggests the feasibility and the potential efficacy of reduced intensity conditioning (RIC) allogeneic HSCT combined with MSC infusion for patients with the adult form of MLD.Case ReportsJournal Articleinfo:eu-repo/semantics/publishe

Long-term follow-up of autologous peripheral blood stem cell transplantation in the treatment of a patient with acute panmyelosis with myelofibrosis.

Case ReportsJournal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

The Infantilization of the Colonized: Medical and Psychiatric Descriptions of Drinking Habits in the Colonial Maghreb

French doctors and psychiatrists traveling through or working in the colonial Maghreb during the nineteenth and twentieth centuries commonly reported in their publications that the colonized they encountered reminded them of children. They also described practically every aspect of the behavior of the colonized as childlike in some respect. While this equation of the colonized with children was by no means restricted to the medico-psychiatric source material and can be found in a variety of different colonial publications, this chapter will focus on publications by doctors and psychiatrists, as their status as widely accepted experts and as alleged pillars of science and modernity made their statements, in the eyes of their French readership, more authoritative than those of other authors. Though this is usually not stated explicitly, the children imagined in these comparisons were presumably European, which accords with a long tradition of European medical and psychiatric experts comparing the colonized to an imaginary European normality. Yet comparisons of the colonized with children in the publications of French doctors and psychiatrists were more than just colorful and anecdotal descriptions of life in the colonies; they were part of an implicit, ongoing process of diagnosing the behavior of the colonized as intrinsically different from French behavior. These comparisons implicitly suggested that colonized adults and European children were roughly on the same developmental level, and concluded that both groups had a similar relationship to French adults: that is, receiving education from them, following their lead, and letting them make important decisions on their behalf. The framing of the colonized as children highlights the colonial understanding of there being a clear power imbalance in the colonies—with France as the undisputed paterfamilias, so to speak, and with the colonized unable to reach French levels of reason and modernity on their own