EBV latent membrane protein 1 abundance correlates with patient age but not with metastatic behavior in north African nasopharyngeal carcinomas

BACKGROUND: Undifferentiated nasopharyngeal carcinomas are rare in a majority of countries but they occur at a high incidence in South China and to a lesser extent in North Africa. They are constantly associated with the Epstein-Barr virus (EBV) regardless of patient geographic origin. In North Africa, the distribution of NPC cases according to patient age is bi-modal with a large group of patients being around 50 years old (80%) and a smaller group below 25 years old. We and others have previously shown that the juvenile form of NPC has distinct biological characteristics including a low amount of p53 and Bcl2 in the tumor tissue and a low level of anti-EBV IgG and IgA in the peripheral blood. RESULTS: To get more insight on potential oncogenic mechanisms specific of these two forms, LMP1 abundance was assessed in 82 NPC patients of both groups, using immuno-histochemistry and semi-quantitative evaluation of tissue staining. Serum levels of anti-EBV antibodies were simultaneously assessed. For LMP1 staining, we used the S12 antibody which has proven to be more sensitive than the common anti-LMP1 CS1-4 for analysis of tissue sections. In all NPC biopsies, at least a small fraction of cells was positively stained by S12. LMP1 abundance was strongly correlated to patient age, with higher amounts of the viral protein detected in specimens of the juvenile form. In contrast, LMP1 abundance was not correlated to the presence of lymph node or visceral metastases, nor to the risk of metastatic recurrence. It was also independent of the level of circulating anti-EBV antibodies. CONCLUSION: The high amount of LMP1 recorded in tumors from young patients confirms that the juvenile form of NPC has specific features regarding not only cellular but also viral gene expression

PREDICAT: a semantic service-oriented platform for data interoperability and linking in earth observation and disaster prediction

The increasing volume of data generated by earth observation programs such as Copernicus, NOAA, and NASA Earth Data, is overwhelming. Although these programs are very costly, data usage remains limited due to lack of interoperability and data linking. In fact, multi-source and heterogeneous data exploitation could be significantly improved in different domains especially in the natural disaster prediction one. To deal with this issue, we introduce the PREDICAT project that aims at providing a semantic service-oriented platform to PREDIct natural CATastrophes. The PREDICAT platform considers (1) data access based on web service technology; (2) ontology-based interoperability for the environmental monitoring domain; (3) data integration and linking via big data techniques; (4) a prediction approach based on semantic machine learning mechanisms. The focus in this paper is to provide an overview of the PREDICAT platform architecture. A scenario explaining the operation of the platform is presented based on data provided by our collaborators, including the international intergovernmental Sahara and Sahel Observatory (OSS)

Clinical characteristics and outcomes of critically ill COVID-19 patients in Sfax, Tunisia

Background Africa, like the rest of the world, has been impacted by the coronavirus disease 2019 (COVID-19) pandemic. However, only a few studies covering this subject in Africa have been published. Methods We conducted a retrospective study of critically ill adult COVID-19 patients—all of whom had a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection—admitted to the intensive care unit (ICU) of Habib Bourguiba University Hospital (Sfax, Tunisia). Results A total of 96 patients were admitted into our ICU for respiratory distress due to COVID-19 infection. Mean age was 62.4±12.8 years and median age was 64 years. Mean arterial oxygen tension (PaO2)/fractional inspired oxygen (FiO2) ratio was 105±60 and ≤300 in all cases but one. Oxygen support was required for all patients (100%) and invasive mechanical ventilation for 38 (40%). Prone positioning was applied in 67 patients (70%). Within the study period, 47 of the 96 patients died (49%). Multivariate analysis showed that the factors associated with poor outcome were the development of acute renal failure (odds ratio [OR], 6.7; 95% confidence interval [CI], 1.75–25.9), the use of mechanical ventilation (OR, 5.8; 95% CI, 1.54–22.0), and serum cholinesterase (SChE) activity lower than 5,000 UI/L (OR, 5.0; 95% CI, 1.34–19). Conclusions In this retrospective cohort study of critically ill patients admitted to the ICU in Sfax, Tunisia, for acute respiratory failure following COVID-19 infection, the mortality rate was high. The development of acute renal failure, the use of mechanical ventilation, and SChE activity lower than 5,000 UI/L were associated with a poor outcome

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.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Childhood Rubella Encephalitis

We to report clinical biological and radiologic features of rubella encephalitis in childhood and assess its prognostic impact. Our retrospective study was conducted in an intensive care unit of a university hospital in Sfax, Tunisia. Twenty-one children (age range, 1-15 years) were included. Median age was 9 years (lower and upper quartiles, 7-11 years). On admission, generalized maculopapular eruption was found in 17 cases (81%). Median Glasgow Coma Scale score was 7 (lower and upper quartiles, 7-8). Twenty patients (95.2%) experienced at least 1 episode of seizures. Sixteen patients (76.2%) developed a status epilepticus. The result for enzyme-linked immunosorbent assay detecting anti-rubella immunoglobulin (M) was positive in the serum and in the cerebrospinal fluid samples for all our patients. Magnetic resonance imaging (MRI) of the brain was performed on admission for 3 patients (14.3%) and within a median of 4 days (lower and upper quartiles, 2-6 days) for 8 patients. The test was normal in 6 cases. Two deaths were recorded (9.5%). Survivors had no neurological sequelae 6 months after intensive care unit discharge. </jats:p