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

Tracheal Aspirate Cultures in Intubated Neonates: A Descriptive Epidemiological Cohort Study

BACKGROUND: Considerable variability in antibiotic prescribing practices in neonatal intensive care units (NICUs) and increasing knowledge about the adverse consequences of antibiotic exposure in neonates highlights the need for a better understanding of antibiotic prescribing practices. Antibiotic prescribing practices related to positive tracheal aspirate culture results, which could represent either colonization or invasive infection, is unknown. METHODS: We conducted a retrospective cohort study of intubated neonates admitted to Children’s National Health System (CNHS) who had one or more tracheal aspirate cultures sent May to December 2016. Data collected through chart review included changes in vital signs, secretion characteristics, ventilator settings, oxygen requirement, white blood cell count, C-reactive protein (CRP), and chest x-ray results in the 48 hours preceding tracheal aspirate culture order. Outcome measures collected include duration of antibiotic therapy, hospital and NICU length of stay, ventilator days, discharge on respiratory support, recurrence of respiratory infection, bronchopulmonary dysplasia, colonization with multidrug-resistant organism (MDRO), and mortality. Clinical factors present in those with an identified pathogen were compared with those without, using chi squared for dichotomous and t-test for continuous variables. RESULTS: We identified 51 intubated neonates who met inclusion criteria; 43 (84%) were preterm with median gestation 28 weeks (IQR 25-31). Median birth weight was 1140 g (IQR 744-2360) and 47% were female. A pathogen was identified in 37% of isolates. S. aureus (7) was the most frequently isolated pathogen, followed by K. pneumoniae (5) and Enterobacter spp (4). Hemodynamic instability and abnormal laboratory values were the common clinical factors in the 48 hours preceding cultures. Antibiotics were prescribed for 45 (88%) neonates with a median of 14 days (IQR 6-16). The most frequently prescribed antibiotics were vancomycin (67%) and gentamicin (63%). Those with respiratory culture positive for a pathogen had a higher odds of having had change in respiratory secretion characteristics (OR 14.3; 95% CI 1.3-130.9) and increase in oxygen requirement (OR 4.1; 95% CI 1.0-16.6). CONCLUSIONS: Although most neonates are treated with antibiotics, fewer than half of respiratory cultures identified a pathogen. Those with an identified pathogen were more likely to have changes in respiratory secretion characteristics and increased oxygen requirement

Association between anti-thyroid peroxidase and anti-cytokeratin 18 autoantibodies and bronchial asthma in women

Background: The mechanisms of intrinsic or non-allergic asthma remain uncertain as allergens have no obvious role in driving the inflammatory process in the airways. This study was designed to test the possible presence of an autoimmune pathogenesis of bronchial asthma and to investigate the similarities and differences between allergic and non-allergic asthma. Design: Cross-sectional prospective cohort study. Subjects and methods: 50 asthmatic women and 30 healthy control women were tested for thyroid function, anti-TPO, anti-CK18 autoantibodies, and total IgE measurements. Pulmonary function tests, skin-prick test and history of asthma risk factors were done for asthmatic women. Results: Allergic asthma were found in half of the asthmatic patients and the other half (25/50) were non-allergic according to the results of skin-brick test and serum level of IgE. The thyroid function tests were not statistically different between asthmatic and control groups as well as between non-allergic and allergic asthma groups (P > 0.05). Serum anti-TPO autoantibodies and anti-CK18 autoantibodies’ levels were significantly higher in asthmatic patients than the control group and also in non-allergic asthma patients than allergic asthma patients. In asthmatic patients serum anti-TPO autoantibodies showed negative correlation with FEV1 (pre- and post) and serum IgE. Conclusion: Positive anti-TPO autoantibodies and anti-CK18 autoantibodies in asthmatic patients and their higher level in the non-allergic asthma group may strengthen the presence of a hidden autoimmune phenomenon in non-allergic asthma

Validity of magnetic resonance image and HLA-B27 in early detection of sacroiliitis in Egyptian spondyloarthropathic patients

Objective The aim of this study was to compare the validity of MRI in the early detection of sacroiliitis with laboratory findings of human leukocyte antigen-B27 (HLA-B27), conventional radiography, and clinical assessment. Participants and methods Sixty patients with spondyloarthropathy (group II) with duration of illness less than 2 years and 20 healthy controls (group I) were included in this study. Both groups were subjected to assessment of history, clinical examination, and laboratory investigations (erythrocyte sedimentation rate, C-reactive protein titer, rheumatoid factor, HLA-B27). Conventional radiography and MRI of the sacroiliac joints were performed. Spondyloarthropathic patients were divided according to MRI as follows: group IIA, which included patients with sacroiliitis, and group IIB, which included patients without sacroiliitis. Results In our study, ankylosing spondylitis was diagnosed in 22 (36.6%) patients, followed by undifferentiated spondyloarthropathy in 12 (20%) patients, reactive arthritis in 10 (16.7%) patients, psoriatic arthropathy in 10 (16.7%) patients, and enteropathic arthropathy in six (10%) patients. Evidence of sacroiliitis was found in 66.6% (40/60) of patients by MRI, which was higher than the result obtained by plain radiography 20% (12/60). HLA-B27 positivity found in 53.3% (32/60) of patients. There was a significant difference between the two groups in HLA-B27 and radiological sacroiliitis; there was no sacroiliitis in the control group. MRI showed sacroiliitis even in patients with no inflammatory back pain. There was a highly statistically significant difference between patient subgroups in disease duration (P = 0.001) and primary complaints and clinical sacroiliitis (P = 0.001). Conclusion MRI is the preferred modality in the detection of early sacroiliitis in spondyloarthropathy and HLA-B27 positivity is a highly useful predictor of early sacroiliiti

Life cycle assessment for photovoltaic integrated shading system with different end of life phases

The aim of this study is to conduct a novel life cycle assessment (LCA) process for a window-mounted building attached photovoltaic panel that is used as a photovoltaic integrated shading (PVIS) device, using GaBi software. Also, the study takes into consideration three different scenarios of the LCA process to reach the most environmentally-friendly system. The three scenarios differ mainly in the end of life processes phase, which in response affects the inputs of the stages within the LCA process. The newly proposed end of life phases are disposing the wastes in the landfill scenario, recycling scenario and recovery scenario. The results showed that the 30 Wp PVIS is environmentally wise to apply to buildings. For the three proposed scenarios, the highest emissions are generated during the production and end of life phases. Consequently, the recycling and the recovery scenarios are more environmentally-friendly in the long run compared to the landfill scenario

Clinical diagnosis of distal diabetic polyneuropathy using neurological examination scores: correlation with nerve conduction studies

Aim The aim of this study was to diagnose diabetic sensorimotor polyneuropathy using neurological examination scores and to correlate the findings with nerve conduction studies (NCS). Patients and methods Thirty patients with type 2 diabetes were included in the study. Detection and grading of neuropathy were carried out based on the Diabetic Neuropathy Symptom (DNS) Score, modified Neuropathy Symptom Score (NSS), Diabetic Neuropathy Examination (DNE), and modified Neuropathy Disability Score (NDS). For the NCS, amplitudes, velocities, and latencies of seven nerves - that is, four motor (median, ulnar, tibial, and common peroneal) and three sensory (median, ulnar, and sural) nerves - were recorded. If the patient had two or more abnormal findings in any of these nerves, the patient was diagnosed as having peripheral sensorimotor neuropathy. Thereafter, the sensitivity, specificity, and diagnostic efficacy of each neurological score were recorded taking NCS as the gold standard. Results Diabetic sensorimotor polyneuropathy was diagnosed clinically and electrophysiologically in 17 patients (56.7%). However, there were nine cases (30%) of subclinical neuropathy. Neurological examination scores were significantly correlated with each other and with individual variables of NCS and the nerve conduction sum score. Taking the NCS as gold standard, DNS, modified NSS, DNE, and modified NDS had 65.4, 61.5, 30.8, and 61.5% sensitivity and 100, 75, 100, and 100% specificity, respectively. Their diagnostic efficacies were 70, 63.3, 40, and 66.7%, respectively. Conclusion Neurological examination scores can detect and grade neuropathy in the majority of cases. However, NCS was accurate for detection of diabetic sensorimotor polyneuropathy, especially for the subclinical neuropathies