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

Level-Crossing ADC Design and Evaluation Methodology for Normal and Pathological Electrocardiogram Signals Measurement

International audienceIn this paper, the level-crossing analog-to-digital converter (LC-ADC) is employed for electrocardiogram signals measurement. A biosignal-dependent design methodology for the LC-ADC is proposed to avoid distortion, caused by slope changes, leading to an 8-bit LC-ADC topology with a 10-kHz and 12-bit time counter. To evaluate the proposed design, the LC-ADC is modeled then evaluated regarding systematic time-quantization error and analog components’ non-idealities. A total number of 75 real electrocardiogram records from Physionet database with different waveforms and pathologies are used. LC-ADC evaluation results for time-quantization error show that 100% of the reconstructed signals have a signal-to-distortion ratio higher than 21 dB, which is the value of good quality. The evaluation of comparators’ offset voltage impact is analyzed with different ranges of the signal-to-distortion ratio showing the robustness of the proposed design methodology. Internal digital-to-analog converters (DACs) non-linearity impacts are evaluated showing only 1-dB degradation for signal distortion

First Report of Extended-Spectrum β-Lactamase ( bla CTX-M1 ) and Colistin Resistance Gene mcr-1 in E. coli of Lineage ST648 from Cockroaches in Tunisia

International audienceMultidrug resistance in Enterobacteriaceae has become a major concern worldwide that is increasingly observed in human, animals, and also cockroaches. In our study, we found that cockroaches may play an important role as a potential vector of multidrug-resistant Enterobacteriaceae in the hospital environment and collective catering

Towards Time-Quantized Pseudo-Random Sampling for Green Communication

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First Report of Extended-Spectrum β-Lactamase ( bla CTX-M1 ) and Colistin Resistance Gene mcr-1 in E. coli of Lineage ST648 from Cockroaches in Tunisia

International audienceMultidrug resistance in Enterobacteriaceae has become a major concern worldwide that is increasingly observed in human, animals, and also cockroaches. In our study, we found that cockroaches may play an important role as a potential vector of multidrug-resistant Enterobacteriaceae in the hospital environment and collective catering

Seasonal patterns of viral, microbial and planktonic communities in Sidi Salem: a freshwater reservoir (North of Tunisia)

International audienceWe investigated the distribution and dynamics of viruses, prokaryotes and small eukaryotic phytoplankton in Sidi Salem freshwater reservoir (Northern Tunisia). Samples were collected from the deepest station at different depths throughout the water column for 2 years (February 2009 to January 2011). The reservoir was characterized by seasonal alternations of thermal stratification and homothermy. Among the different microbial communities counted using flow cytometry (FCM), picocyanobacteria constituted an important autotrophic component since they were always present and their highest concentration reached 3.02 and 2.65 x 10(5) cells.mL(-1) in March 2009 and June 2010, respectively. The heterotrophic prokaryotic communities (represented mainly by bacteria) were characterized by a clear separation between two subgroups referred to as high-DNA and low-DNA content populations, and the highest concentrations of heterotrophic bacteria (i.e., 3.8 x 10(7) cells.mL(-1)) were recorded in spring 2009. Several viral groups referred to as virus-like particles (VLP) groups 1, 2 and 3 could also be discriminated using FCM. VLP1 and VLP2 displayed a significant correlation with the heterotrophic bacteria (r = 0.80 and 0.78, P < 0.001) but seem to be independent from picocyanobacteria and/or chlorophyll a, suggesting these VLPs were mainly bacteriophages. At last, the virus to prokaryotic ratio could be high, especially in summer (mean = 22, max = 487), suggesting a strong coupling between bacteria and viruses, at least at certain periods of the year

Adapting waterpipe-specific pictorial health warning labels to the Tunisian context using a mixed method approach.

BackgroundWaterpipe (WP) use is rapidly increasing among young people worldwide due to the widespread misperception that it is safer than cigarette smoking. Health warning labels (HWLs) can effectively communicate tobacco-related health risks but have yet to be developed for WP. This study aimed to optimize and adapt a set of 16 pictorial WP-specific HWLs, developed by an international Delphi study, to the Tunisian context. HWLs were grouped into four themes: WP health risks, WP harm to others, WP-specific harms, and WP harm compared to cigarettes.MethodsUsing a mixed method approach, we conducted ten focus groups combined with a survey among young WP users and nonusers (N = 63; age 18-34 years). In the survey, participants rated the HWLs on several communication outcomes (e.g., reaction, harm perception, effectiveness) and were then instructed to view all HWLs in each theme and rank them in the order of overall perceived effectiveness, from the most to the least effective. Afterward, participants provided in-depth feedback on HWLs and avenues for improvement. Mean effectiveness rating scores and percentages of participants' top-ranked HWLs were calculated. Discussions were audio-taped, transcribed verbatim, and analyzed thematically.ResultsThe top-ranked HWLs were those showing oral cancers, orally transmitted diseases, and a sick child. Focus group discussion illustrated that these selections were based on participants' reactions to the direct impact of WP on a person's physical appearance and evoking guilt over children's exposure to WP smoke. Suggestions for improvement highlighted the need to use the local dialect and more affirmative statements (e.g., avoiding "may" or "can").ConclusionsThis study is the first in North Africa to attempt to advance HWLs policy as the World Health Organization recommended. The results of this study can be used as a basis for implementing WP-specific health messages in the Eastern Mediterranean Region

Optimization of extraction with salicylic acid, rheological behavior and antiproliferative activity of pectin from Citrus sinensis peels

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Painful bruising syndrome: A case report

Painful bruising syndrome or Gardner-Diamond syndrome is characterized by an auto erythrocyte sensitization syndrome. We report, here a new case of painful bruising syndrome in a woman with no psychiatric disorders. A 29-year-old female patient presented with complaints of painful bruising over the lower extremities of three years duration. She had a personal history of a severe rheumatoid arthritis. Dermatological examination revealed multiple erythematous, nonedematous and ecchymotic macules over the legs. A psychiatric examination was normal. Complete blood count, prothrombin time and liver function tests were normal. Intracutaneous sensitivity test confirmed Painful bruising syndrome

Metabolic Syndrome according to Three Definitions in Hammam-Sousse Sahloul Heart Study: A City Based Tunisian Study

Objectives. Metabolic syndrome (MetS) is a major risk factor of CVD. The aim of the present study is to determine the prevalence of the MetS, its components, and its different profiles according to NCEP-ATP III 2001, IDF 2005, and JIS 2009 definitions in Hammam-Sousse Sahloul Heart Study (HSHS). Study Design. The study involved 1121 participants (364 men and 757 women; sex-ratio  =  0.48; mean age  =  47.49 ± 16.24 years) living in Hammam Sousse city, located in the east of Tunisia. Methods. Anthropometric parameters, blood pressure, lipids levels, glycemia, insulinemia, and body mass index were measured. Statistical analyses were performed by SPSS16.0. Results. The percentage of participants who had MetS defined according to NCEP ATP III, IDF 2005, and JIS 2009 definitions was respectively, 29.5%, 38.4%, and 39.6%. With regard to gender, the prevalence of MetS is higher in men than in women according to IDF 2005 definition (38.5% men versus 38.3% women, P=0.961) and according to JIS 2009 definition (41.8% men versus 38.6% women, P=0.307), whereas, according to NCEP ATP III definition, the prevalence of MetS is higher in women than in men (30% versus 28.6%, P=0.627). The prevalence of MetS increased with increasing age according to the three definitions (P<0.001) and peaked in the oldest age group (≥70 years) according to IDF 2005 and JIS 2009. Furthermore, a significant difference in the prevalence of MetS components according to gender was observed. Indeed, the abdominal obesity is the most frequent MetS compound in women group, but hypertension and low HDL-C are the most frequent in men. In addition, according to the three definitions, the most frequent MetS profile in our study is “higher waist circumference, hypertension, and low HDL-C.” Conclusion. The high prevalence of MetS is a serious public health problem in Hammam-Sousse Sahloul community. Higher waist circumference, hypertension, and low HDL-C were the most frequent profile in our study