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

Investigations on (C6H9N2)2[MIIBr4] halogenometallate complexes with MII = Co, Cu and Zn: Crystal structure, thermal behavior and magnetic properties

International audienceThree complexes with the general formula (C6H9N2)2[MIIBr4] with MII = Cu (1), Co (2) and Zn (3) have been grown by the slow evaporation method at room temperature. These compounds were subjected to the following characterization techniques: single crystal X-ray diffraction, thermal analysis (ATG-TD), In situ X-ray powder diffraction and temperature dependent magnetic susceptibility measurements. The crystals of (C6H9N2)2[CuBr4] belong to the triclinic P1¯ space group, whereas (C6H9N2)2[CoBr4] and (C6H9N2)2[ZnBr4] crystallize in the orthorhombic system with the Pbcn space group. Molecular structures of the three coordination compounds consist of [MBr4]2- anions and 2-amino-6-methylpyridinium cations linked together via non-covalent interactions including hydrogen bonding, π···π stacking and halogen···halogen interactions which lead to three-dimensional supramolecular architecture. The thermal decomposition of the copper compound reveals the slow crystallization of CuBr at 130 °C. Both compounds 1 and 2 exhibit weak antiferromagnetic interactions. © 2017 Elsevier B.V

Functional outcome in traumatic brain injury in Tunisia

IntroductionTraumatic brain injury (TBI) occurs mainly in young adults in full swing. The objective of this work is to specify the functional outcome of patients with TBI sequelae.MethodsWe included adult patients who were hospitalised between January 2009 and December 2013 for the management of TBI sequelae. We excluded patients with a history of neurological or psychiatric disorders before the TBI. We contacted these patients in an attempt to clarify their current functional status. For each patient we stated: the functional independence measurement (FIM), the severity of disability based on the Glasgow Outcome Scale (GOS). The motor part of the Canadian neurological scale was used to evaluate motor impairments.Results27 patients were included. 89.3% of our patients were male. The mean age was 34.6 (range: 19 to 66 years). The TBI was severe in 19 cases and moderate in 8 patients. The average duration of post-traumatic coma was 38.7 days. Initial FIM was 66.4/126. The overall assessment of disability by the GOS found two vegetative states; 9 patients had moderate disability and 16 patients had severe disability. A motor impairment was found in all these patients. Only one patient had resumed his previous occupation; 2 had resumed a professional activity with adaptation of the workplace; and 3 others were following appropriate training.ConclusionThe socio-professional reintegration remains a difficult goal to achieve, due to neuropsychological disorders in addition to orthopaedic sequelae which often causes neuro dependency and disability. However, it should optimise the residual functional capacity whenever the possibility of a life plan is offered to the patient

Designing a smartphone exergame for children with cerebral palsy in the home environment

Children with cerebral palsy must perform daily exercise which is a tedious and energy consuming task. Exergames can make this routine more engaging, which can increase the compliance of the patient. This research explores the feasibility of an exergame device called the Squid Monster. The device is the result of a research through design process, and it is designed to be played on smartphones in the home environment. It operates on the smartphone's integrated sensors and two external squeeze sensors, making it accessible and cost-effective. We conceptualize how the design can be supported using a machine learning adaptive difficulty system, aiming to increase flow and therapeutic adherence of the device. Ultimately, guidelines are provided to designers for future work in this field

Cytogenetic and molecular responses of ammonium sulphate application for tolerance to extreme temperatures in Vicia faba L.

Effects of ammonium sulphate [(NH4)(2)SO4] on mitosis, cell cycle and chromosomes in Vicia faba L. seeds exposed to extreme temperatures were investigated using flowcytometric and cytogenetic analysis. Seeds germinated at high and low temperatures showed a significant decrease in mitotic index as compared to those of optimum temperature conditions. Application of 50 and 1000 mu M (NH4)(2)SO4 were successful in alleviating the negative effects of low and high temperature on mitotic activity, respectively. 50 mu M (NH4)(2)SO4 showed the most positive effect on cell cycle at the extreme temperatures. This concentration increased the cell division removing or decreasing the negative effects of temperature stress. Namely, the highest G2/M and S phase percentages under stress conditions were obtained with application of 50 mu M (NH4)(2)SO4. Chromosomal aberrations were not observed in cells of seeds germinated in distilled water and also at any temperatures. However, the frequency of chromosomal aberrations increased significantly by increasing (NH4)(2)SO4 concentration. The highest aberration frequency in all temperature degree tested was found at 1000 mu M (NH4)(2)SO4 concentration.Department of Scientific Research Project Management of Suleyman Demirel University (SDUBAP)Suleyman Demirel University [1636-YL-08]The authors thank the Department of Scientific Research Project Management of Suleyman Demirel University (SDUBAP) for the financial support of the project SDUBAP (1636-YL-08). Thanks also to Dr. Gulderen Yanikkaya DEMIREL and Mehtap OZDEMIR (Istanbul Centro Laboratory Flowcytometry Department, Istanbul, Turkey) for its help in flow cytometric study

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property–free knowledge base for future anticoronavirus drug discovery

International Nosocomial Infection Control Consortium report, data summary of 50 countries for 2010-2015: Device-associated module

•We report INICC device-associated module data of 50 countries from 2010-2015.•We collected prospective data from 861,284 patients in 703 ICUs for 3,506,562 days.•DA-HAI rates and bacterial resistance were higher in the INICC ICUs than in CDC-NHSN's.•Device utilization ratio in the INICC ICUs was similar to CDC-NHSN's. Background: We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2010-December 2015 in 703 intensive care units (ICUs) in Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific. Methods: During the 6-year study period, using Centers for Disease Control and Prevention National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI), we collected prospective data from 861,284 patients hospitalized in INICC hospital ICUs for an aggregate of 3,506,562 days. Results: Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the INICC medical-surgical ICUs, the pooled rate of central line-associated bloodstream infection, 4.1 per 1,000 central line-days, was nearly 5-fold higher than the 0.8 per 1,000 central line-days reported from comparable US ICUs, the overall rate of ventilator-associated pneumonia was also higher, 13.1 versus 0.9 per 1,000 ventilator-days, as was the rate of catheter-associated urinary tract infection, 5.07 versus 1.7 per 1,000 catheter-days. From blood cultures samples, frequencies of resistance of Pseudomonas isolates to amikacin (29.87% vs 10%) and to imipenem (44.3% vs 26.1%), and of Klebsiella pneumoniae isolates to ceftazidime (73.2% vs 28.8%) and to imipenem (43.27% vs 12.8%) were also higher in the INICC ICUs compared with CDC-NHSN ICUs. Conclusions: Although DA-HAIs in INICC ICU patients continue to be higher than the rates reported in CDC-NSHN ICUs representing the developed world, we have observed a significant trend toward the reduction of DA-HAI rates in INICC ICUs as shown in each international report. It is INICC's main goal to continue facilitating education, training, and basic and cost-effective tools and resources, such as standardized forms and an online platform, to tackle this problem effectively and systematically

International Nosocomial Infection Control Consortiu (INICC) report, data summary of 43 countries for 2007-2012. Device-associated module

We report the results of an International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2007-December 2012 in 503 intensive care units (ICUs) in Latin America, Asia, Africa, and Europe. During the 6-year study using the Centers for Disease Control and Prevention's (CDC) U.S. National Healthcare Safety Network (NHSN) definitions for device-associated health care–associated infection (DA-HAI), we collected prospective data from 605,310 patients hospitalized in the INICC's ICUs for an aggregate of 3,338,396 days. Although device utilization in the INICC's ICUs was similar to that reported from ICUs in the U.S. in the CDC's NHSN, rates of device-associated nosocomial infection were higher in the ICUs of the INICC hospitals: the pooled rate of central line–associated bloodstream infection in the INICC's ICUs, 4.9 per 1,000 central line days, is nearly 5-fold higher than the 0.9 per 1,000 central line days reported from comparable U.S. ICUs. The overall rate of ventilator-associated pneumonia was also higher (16.8 vs 1.1 per 1,000 ventilator days) as was the rate of catheter-associated urinary tract infection (5.5 vs 1.3 per 1,000 catheter days). Frequencies of resistance of Pseudomonas isolates to amikacin (42.8% vs 10%) and imipenem (42.4% vs 26.1%) and Klebsiella pneumoniae isolates to ceftazidime (71.2% vs 28.8%) and imipenem (19.6% vs 12.8%) were also higher in the INICC's ICUs compared with the ICUs of the CDC's NHSN