Search

The novel Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variant, Omicron (PANGO lineage B.1.1.529) is being reported from all around the world. The WHO has categorized Omicron as a Variant of Concern (VOC) considering its higher transmissibility and infectivity, vaccine breakthrough cases. As of January 6, 2022, Omicron has been reported in at least 149 countries. Therefore, this study was planned to investigate the transmission dynamics and mutational prevalence of the novel SARS‐CoV‐2 Omicron variant. The transmission dynamics and Omicron SARS‐CoV‐2 divergence was studied using GISAID and Nextstrain which provides information about the genetic sequences, epidemiological, geographical, and species‐specific data of human, avian, and animal viruses. Further, the mutation prevalence in spike glycoprotein of Omicron was studied, and the frequency of the crucial mutations was compared with the other prevalent VOCs. The transmission dynamics suggest that the Omicron was first identified in South Africa and then it was reported in the United Kingdom followed by the United States and Australia. Further, our phylogenetic analysis suggests that Omicron (BA.1) was clustered distinctly from the other VOCs. In the Spike glycoprotein, the Omicron (B.1.1.529) demonstrates critical 32 amino acid changes. This study may help us to understand mutational hotspots, transmission dynamics, phylogenetic divergence, effect on testing and immunity, which shall promote the progress of the clinical application and basic research. Highlights: First report showing the transmissibility of the novel sSevere acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) Omicron (B.1.1.529) Variant of Concern.Transmission dynamics analysis suggests that Omicron is more transmissible than other Variant of Concerns (VOCs).Omicron (BA.1) is clustered distinctly from the other VOCs in a monophyletic clade.The K417N, N440K, and G446S are the less prevalent mutations identified in the RBD of the Omicron SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 is a novel coronavirus, spread among humans, and to date, more than 100 million of laboratory-confirmed cases have been reported worldwide. The virus demonstrates 96% similarity to a coronavirus from a horseshoe bat and most probably emerged from a spill over from bats or wild animal(s) to humans. Currently, two variants are circulating in the UK and South Africa and spread to many countries around the world. The impact of mutations on virus replication, virulence and transmissibility should be monitored carefully. Current data suggest recurrent infection with SARS-CoV-2 correlated to the level of neutralising antibodies and with sustained memory responses following infection. Recently, remdesivir was FDA approved for treatment of COVID-19, however many potential antivirals are currently in different clinical trials. Clinical data and experimental studies indicated that licenced vaccines are helpful in controlling the disease. However, the current vaccines should be evaluated against the emerging variants of SARS-CoV-2. • SARS-CoV-2 is the first coronavirus pandemic that constitutes a major public health concern. • The virus evolved from a multiple recombination events and spill over from animal host (s). • Two variants of concern were recently emerged with critical changes in the spike protein. • Remdesivir is the current FDA approved drug while many potential antivirals may also play a role. • Currently five vaccines were released for this emerging pathogen, however several challenges do exist. [ABSTRACT FROM AUTHOR]

Background: The pediatric resuscitation and trauma outcome (PRESTO) model was developed to aid comparisons of risk-adjusted mortality after injury in low- and middle-income countries (LMICs). We sought to validate PRESTO using data from a middle-income country (MIC) trauma registry and compare its performance to the Pediatric Trauma Score (PTS), Revised Trauma Score, and pediatric age-adjusted shock index (SIPA). Methods: We included children (age < 15 years) admitted to a single trauma center in South Africa from December 2012 to January 2019. We excluded patients missing variables necessary for the PRESTO model—age, systolic blood pressure, pulse, oxygen saturation, neurologic status, and airway support. Trauma scores were assigned retrospectively. PRESTO's previously high-income country (HIC)-validated optimal threshold was compared to MIC-validated threshold using area under the receiver operating characteristic curves (AUROC). Prediction of in-hospital death using trauma scoring systems was compared using ROC analysis. Results: Of 1160 injured children, 988 (85%) had complete data for calculation of PRESTO. Median age was 7 (IQR: 4, 11), and 67% were male. Mortality was 2% (n = 23). Mean predicted mortality was 0.5% (range 0–25.7%, AUROC 0.93). Using the HIC-validated threshold, PRESTO had a sensitivity of 26.1% and a specificity of 99.7%. The MIC threshold showed a sensitivity of 82.6% and specificity of 89.4%. The MIC threshold yielded superior discrimination (AUROC 0.86 [CI 0.78, 0.94]) compared to the previously established HIC threshold (0.63 [CI 0.54, 0.72], p < 0.0001). PRESTO showed superior prediction of in-hospital death compared to PTS and SIPA (all p < 0.01). Conclusion: PRESTO can be applied in MIC settings and discriminates between children at risk for in-hospital death following trauma. Further research should clarify optimal decision thresholds for quality improvement and benchmarking in LMIC settings. [ABSTRACT FROM AUTHOR]

Eleven specimens of dendrochirotid holothuroids, dredged from fairly deep waters (84-120 m) at several localities off the KwaZulu-Natal coast in South Africa, are here described as Stolus pseudoalbescens n.sp. with another three specimens of perhaps the same species referred to as S. cf. pseudoalbescens since they lack the tubercles of the new species and differ in some details of the calcareous ring and podial spicules. In addition, another new species based on a single minute specimen collected at 78 m, also from the KwaZulu-Natal coast, is described as S. dentatus n.sp. The description of these two species increases to four the number of Stolus spp. now known from South Africa: S. buccalis (Stimpson, 1856); S. kilberti (Rajpal & Thandar, 1999), S. pseudoalbescens n.sp. and S. dentatus n.sp. [ABSTRACT FROM AUTHOR]

Two new genera, Trachycucumis and Trachasina, in the holothurian family Cucumariidae, are described. The former is erected to accommodate a new southern African cucumariid, here described as T. plettenbergi, from the southeast coast of South Africa, and the Trachythyone sp. Thandar (1991) from the northeast coast. Trachasina is currently monotypic and is erected to accommodate Trachythyone crucifera (Semper, 1869) which has remained erroneously in Trachythyone for so long, despite several reservations. Trachycucumis differs from Trachythyone in being a warm-water genus with body wall spicules in the form of spinous cross-shaped rods and multilocular plates with one end often prolonged as a spinous handle. The new species, T. plettenbergi differs from Thandar's Trachythyone sp. in the absence of rosette-shaped deposits and the simplicity of the plates. Trachasina, on the other hand, is unique in having 10 equal tentacles and sparsely distributed spicules in the form of spinous crosses, unlike those of Trachycucumis, and simple, thick, smooth, oval plates with few perforations and without any prolongations. [ABSTRACT FROM AUTHOR]

Presents a study regarding the description of Dendrochirotid holothuroid, genus of the Neocucumis kilburni, from the waters of South Africa. Species of the Neocucumis; Distribution of the Neocucumis kilburni; Comparison between other species of Neocucumis.

Background: The university-based low vision clinic is one of the few low vision clinics in South Africa. Aim: To describe demographic and clinical profiles of patients who attended this clinic from 2010 to 2017. Setting: The university low vision clinic, South Africa. Methods: The record cards of all patients seen at the low vision clinic over 8 years were examined and the following information was extracted: age, gender, presenting visual acuity (VA), VA following low vision assessment, cause of visual impairment and types of low vision devices recommended. Results: A total of 621 patients were examined, comprising 45.1% males and 55.9% females aged 36.0 ± 18.2 years (range: 4–93 years). Many of these patients (33.7%) had presenting VA worse than 1.3 logarithm of the Minimum Angle of Resolution (logMAR) (> 6/120) at 4 m in the better eye, and 196 (31.6%) had presenting VA of worse than 1.3 logMAR at near distance. Following optical low vision assessment, 62.4% had distance VA of 0.9 LogMAR (6/48) to −0.2 logMAR (6/3.8) and 58.4% had near VA of 0.9 logMAR (6/48) to −0.2 logMAR (6/3.8). Albinism (22.7%), unknown causes (18.2%), cataract (15.5%) and macular diseases (12.2%) were the most common causes of low vision. Amblyopia (80.7%) was the most common cause of low vision in patients aged 20 years and younger, followed by albinism (68.1%) and corneal diseases (41%). Cataract (78.1%), macular diseases (64.4%) and glaucoma (55.9%) were the most common causes of low vision in patients aged more than 60 years. Telescopes (33.8%) were the most commonly recommended form of intervention, followed by magnifiers (29.6%) and protective measures (24.5%). Conclusion: Albinism, cataract and macular diseases are the predominant causes of low vision in patients attending this low vision clinic. There was a significant improvement in VA after low-vision assessment, particularly for patients with presenting VA of better than 1.3 logMAR (6/120). [ABSTRACT FROM AUTHOR]

Background: Antimicrobial misuse is common in low-income and middle-income countries (LMICs), and this practice is a driver of antibiotic resistance. We compared community-based antibiotic access and use practices across communities in LMICs to identify contextually specific targets for interventions to improve antibiotic use practices., Methods: We did quantitative and qualitative assessments of antibiotic access and use in six LMICs across Africa (Mozambique, Ghana, and South Africa) and Asia (Bangladesh, Vietnam, and Thailand) over a 2·5-year study period (July 1, 2016-Dec 31, 2018). We did quantitative assessments of community antibiotic access and use through supplier mapping, customer exit interviews, and household surveys. These quantitative assessments were triangulated with qualitative drug supplier and consumer interviews and discussions., Findings: Vietnam and Bangladesh had the largest proportions of non-licensed antibiotic dispensing points. For mild illness, drug stores were the most common point of contact when seeking antibiotics in most countries, except South Africa and Mozambique, where public facilities were most common. Self-medication with antibiotics was found to be widespread in Vietnam (55·2% of antibiotics dispensed without prescription), Bangladesh (45·7%), and Ghana (36·1%), but less so in Mozambique (8·0%), South Africa (1·2%), and Thailand (3·9%). Self-medication was considered to be less time consuming, cheaper, and overall, more convenient than accessing them through health-care facilities. Factors determining where treatment was sought often involved relevant policies, trust in the supplier and the drug, disease severity, and whether the antibiotic was intended for a child. Confusion regarding how to identify oral antibiotics was revealed in both Africa and Asia., Interpretation: Contextual complexities and differences between countries with different incomes, policy frameworks, and cultural norms were revealed. These contextual differences render a single strategy inadequate and instead necessitate context-tailored, integrated intervention packages to improve antibiotic use in LMICs as part of global efforts to combat antibiotic resistance., Funding: Wellcome Trust and Volkswagen Foundation., (Copyright © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Purpose: We studied the clinical presentation and microbiology of patients with deep neck space infection in a developing nation to aid in determining the relevant, appropriate, and effective empirical antimicrobial treatment. We have also described the demographic data of pediatric versus adult patients and the predominant age-related subtypes of deep neck space infections., Patients and Methods: A retrospective review of the data from patients with deep neck space infections during a 5.5-year period was conducted at the academic teaching hospitals in Johannesburg, South Africa. The diagnosis of deep neck space infection was determined from the clinical, radiographic, and laboratory findings. All the patients had undergone abscess drainage via needle aspiration or surgical drainage using a sterile technique. Aerobic and anaerobic bacterial cultures and cultures for Mycobacterium tuberculosis were performed. The results were recorded, and statistical analysis was performed., Results: A total of 107 children and 52 adults with deep neck space infections were included in the present study, with 121 and 70 pus specimens retrieved. The male/female ratio was 1.14:1 for the pediatric group (57 boys [53%] and 50 girls [47%]). The adult group included 33 men (63%) and 19 women (37%). The male/female ratio for the adult group was 1.74:1. In the pediatric group, the mean age was 5.8 years (range, 2 months to 15 years). The age distribution was subcategorized into younger than 2, 2 to 10, and older than 10 years. Of the 107 children, 51 were younger than 2, 50 were aged 2 to 10, and 6 were older than 10 years. The age of the adult patients ranged from 19 to 77 years (mean, 40.9 ± 15.5). Multispace involvement of the deep neck infection was present in 8 pediatric cases (7.5%) and 31 adult cases (59.6%). The submandibular space was the most commonly affected site (73.9%) in both groups., Conclusions: Deep neck space infections differ in clinical presentation and microbiology between adults and children. The specimens from the pediatric group predominantly cultured Staphylococcus aureus. In contrast, the specimens from the adult group were mainly polymicrobial. The adult population had poorer patient outcomes, with a greater number of intensive care unit admissions, operating theater visits, and prolonged hospital stays., (Copyright © 2019 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.)

Files of 8 patients with primary angiosarcomas treated in the Department of Radiation Oncology at the University of the Witwatersrand from 1982 to 1995 were identified. None of these patients had received prior radiotherapy or chemotherapy which would have predisposed them to the formation of an angiosarcoma. Slides of 6 patients were reviewed. Five of the 6 were confirmed as having angiosarcomas, while 1 patient was found to have a peripheral neuro-epithelial tumour. Four patients had angiosarcomas of the breast, while there was 1 patient each with angiosarcoma of the skin, intestine and brain. Complete excision was the primary modality of management whenever possible. Postoperative radiotherapy was given in cases of incomplete excision, patient refusal of radical surgery or gross tumour. Four patients died within 4 months of diagnosis. Three patients are alive (2 with no evidence of disease) 22-96 months after diagnosis. In 1 patient follow-up details were not available as he did not return for treatment. Angiosarcomas are aggressive malignant tumours arising from the endothelial cells. Complete surgical excision is the treatment of choice in the management of this aggressive disease, which has a poor prognosis.