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

Prévalence de la précarité et caractéristiques associées à l'obésité morbide chez des patients candidats à la chirurgie bariatrique

PARIS6-Bibl. St Antoine CHU (751122104) / SudocSudocFranceF

Bio contamination of surfaces and medical devices in controlled environment areas at a hospital in Morocco

The hospital environment, especially medical devices and surfaces, represents a secondary reservoir for pathogens. This work aims to evaluate the microbiological quality of surfaces and medical equipment of controlled environment services (burn unit, operating room, and sterilization service) at a hospital in Meknes (center of Morocco). This study was carried out for three months (September-December of 2017). A total of 63 samples were taken by swabbing technique from different surfaces and medical equipment after bio-cleaning. Identification was performed according to conventional bacteriological methods and by microscopic observation for fungi. The study showed that 68% of the surface was contaminated. The operating room recorded a rate of 93% of contamination (p-value <0.01), 83% for sterilization service, and 47% for burn unit. A percentage of 67% of the isolates were identified as Gram-positive bacteria against 32% Gram-negative bacteria (p-value <0.05). Bacterial identification showed Coagulase-negative Staphylococci (45%), Enterobacter cloacae (14%), Micrococcus sp (10%), Klebsiella pneumoniae, peptostreptococcus sp and Pseudomonas fluorescens (7% for each one), Escherichia coli, and Methicillin-resistant Staphylococcus aureus (5% for each one). These results require corrective action represented by rigorous cleaning and disinfection procedures

Infectious Risk of the Hospital Environment in the Center of Morocco: A Case of Care Unit Surfaces

Background. Equipment and hospital surfaces constitute a microbial reservoir that can contaminate hospital users and thus create an infectious risk. The aim of this work, which was carried out for the first time at a hospital in Meknes (regional hospital in the center of Morocco), is to evaluate the microbiological quality of surfaces and equipment in three potential risk areas (burn unit, operating room, and sterilization service). Methods. This study was carried out over a period of 4 months (February–May 2017). A total of 60 samples were taken by swabbing according to the standard (ISO/DIS 14698-1 (2004)) in an environment of dry area and equipment after biocleaning. Isolation and identification were performed according to conventional bacteriological methods and by microscopic observation for fungi. Results. The study showed that 40% of surface samples were contaminated after biocleaning. The burn unit recorded a percentage of 70% contamination (p value <0.001), 13% for the sterilization service, and 7% for the operating room. 89% of the isolates were identified as Gram-positive bacteria against 11% for fungi (p value <0.001). Bacterial identification showed coagulase-negative staphylococci (32%), Bacillus spp. (16%), Corynebacterium (8%), and oxidase-negative Gram-positive bacillus (40%) while fungal identification showed Aspergillus niger (n = 2) and Aspergillus nidulans (n = 1). Conclusion. To control the infectious risk related to equipment and hospital surfaces, it would be necessary to evaluate the disinfection protocol applied in these units

Susceptibility patterns of bacteria isolated from the hospital environment towards disinfectants commonly used for surfaces and medical devices

This study aimed to evaluate the bactericidal activity of common disinfectants used for surfaces and medical devices. Sodium hypochlorite (D1), disinfectant (D2) composed of N-(3-aminopropyl)-N-dodecylpropane-1,3-diamine, chloride de didecyldimethylammonium, and disinfectant (D3) composed of Didecyldimethylammonium chloride and Polyhexamethylene biguanide hydrochloride, were tested against 15 strains isolated from the hospital environment and four reference bacteria. The microdilution method was performed to assess antimicrobial activity. The susceptibility was evaluated by comparing the minimum inhibitory dilution with the dilution of disinfectant recommended by the manufacture. D1 and D2 were active against Staphylococcus epidermidis, Staphylococcus saprophyticus, Enterobacter cloacae, Escherichia coli, Pseudomonas fluorescens, Methicillin-resistant Staphylococcus aureus, Bacillus spp, Corynebacterium spp, Gram-positive bacillus, Escherichia coli ATCC 25922, Bacillus subtilis ATCC 3366, and Pseudomonas aeruginosa ATCC 27853 strains but not active against Micrococcus spp, and Staphylococcus aureus ATCC 29213. D3 was ineffective against Micrococcus spp, Bacillus Gram Positive, Staphylococcus epidermidis, and Escherichia coli ATCC 25922. Therefore, D1 and D2 can eliminate most pathogenic bacteria in hospitals, in comparison to D3. It is necessary to monitor the antibacterial activity of disinfectants against reference strains but also against those usually present on surfaces. The obtained results could have promising applications in controlling the emergence of nosocomial infections