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The Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (COG-UK) was launched in March, 2020, with £20 million support from UK Research and Innovation, the UK Department of Health and Social Care, and Wellcome Trust. The goal of this consortium is to sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for up to 230 000 patients, health-care workers, and other essential workers in the UK with COVID-19, which will help to enable the tracking of SARS-CoV-2 transmission, identify viral mutations, and integrate with health data to assess how the viral genome interacts with cofactors and consequences of COVID-19.

MSc (Astrophysical Sciences), North-West University, Potchefstroom Campus Marsh et al. (2016) detected radio and optical pulsations from the binary system AR Scorpii (AR Sco). This system, with an orbital period of 3.55 h, is composed of a cool, low-mass M-dwarf and a white dwarf with a spin period of 1.95 min. Buckley et al. (2017) found that the emission from the white dwarf is strongly linearly polarised (up to 40%) with periodically changing intensities. This periodic non-thermal emission is thought to be synchrotron emission (Buckley et al., 2017; Takata et al., 2017) that is powered by the highly magnetised \begin{equation} <> alpha=\left(86.6_{-2.8}^{+3.0}\right)^{\circ} \end{equation} Using these observations, I was able to do rst-order spectral calculations to constrain some of the parameters for the system. Lastly, using phase-resolved optical observations, I was able to obtain and at the di erent orbital phases. Masters

MBA, North-West University, Potchefstroom Campus Platinum mines in South Africa are still very labour-intensive due to conventional mining methods being used. Having employees working in tough environments might cause them to lose motivation, leading to a decrease in productivity. Financial incentives are most commonly used to motivate employees to increase their productivity. The literature study focused on employee productivity, incentives and employee motivation. The factors that influence productivity, the types of incentives used and how employees are motivated were the main focus points. Previous studies with similar objectives were compared to determine whether the results of this study are supported by previous research. A questionnaire was developed based on the literature study to determine which rewards motivate the most and whether production bonuses can be used to motivate employees. The questionnaire also measured the respondents’ opinions regarding rewards and their influence on their productivity. The target population was a platinum mine in the North West province of South Africa. A total of 275 questionnaires were retrieved and used for statistical analysis. Descriptive statistical analysis was done to determine whether the sample was representative of the target population and to describe the sample. Exploratory factor analysis was done to determine the number of constructs identified in this study. These factors were then used together with the frequency data to determine the differences between wage categories. Effect sizes were used to determine the size of the differences between the wage categories. The factors that were identified were productivity, motivation, willingness to do work, section productivity, demotivation and clear targets. The results indicated that rewards had a large positive effect on productivity and motivation and a large negative effect on demotivation. It was also concluded that production bonuses can be used to motivate employees to increase their productivity. Rewards were also a large contributor to employee happiness. The study further concluded that there is a difference in how employees in different wage categories are influenced by production bonuses. Based on the conclusions, recommendations are made to management on how they can use these results to assist in the planning and revising of production bonuses and reward systems. The study was evaluated based on the achievement of the primary and secondary objectives and whether the research question was answered. The study had some limitations, which are discussed before recommendations are made for future studies. Masters

São Paulo (SP), a densely populated state in southeast Brazil that contains one of the world’s largest urban regions, has experienced its largest yellow fever virus (YFV) outbreak in decades. Surveillance in non-human primates (NHP) is important in order to detect YFV early during an epidemic or epizootic, to quantify the magnitude of the outbreak in NHP, and to evaluate the risk of YFV spillover infection in human populations. To better understand the genetic diversity and spatial distribution of YFV during the current outbreak in southeast Brazil, we generated 46 new virus genomes from YFV positive cases identified in 18 different municipalities in SP, mostly sampled from non-human primates between April 2017 and February 2018. Our data show that most NHP cases in São Paulo state were likely caused by the introduction of a single YFV lineage from Minas Gerais to São Paulo. Phylogenetic and phylogeographic analyses of these data indicate that YFV spread southwards from Minas Gerais into São Paulo state at a typical rate of

While HIV-1 subtype B has caused a large epidemic in the Western world, its transmission in Ukraine remains poorly understood. We assessed the genetic diversity of HIV-1 subtype B viruses circulating in Ukraine, characterized the transmission group structure, and estimated key evolutionary and epidemiological parameters. We analyzed 120 HIV-1 subtype B pol sequences (including 46 newly generated) sampled from patients residing in 11 regions of Ukraine between 2002 and 2017. Phylogenies were estimated using maximum likelihood and Bayesian phylogenetic methods. A Bayesian molecular clock coalescent analysis was used to estimate effective population size dynamics and date the most recent common ancestors of identified clades. A phylodynamic birth–death model was used to estimate the effective reproductive number (Re) of these clades. We identified two phylogenetically distinct predominantly Ukrainian (≥75%) clades of HIV-1 subtype B. We found no significant transmission group structure for either clade, suggesting frequent mixing among transmission groups. The estimated dates of origin of both subtype B clades were around early 1970s, similar to the introduction of HIV-1 subtype A into Ukraine. Re was estimated to be 1.42 [95% highest posterior density (HPD) 1.26–1.56] for Clade 1 and 1.69 (95% HPD 1.49–1.84) for Clade 2. Evidently, the subtype B epidemic in the country is no longer concentrated in specific geographical regions or transmission groups. The study results highlight the necessity for strengthening preventive and monitoring efforts to reduce the further spread of HIV-1 subtype B., Aids Research and Human Retroviruses, 35 (2), ISSN:0889-2229, ISSN:1931-8405

MSc (Biochemistry), North-West University, Potchefstroom Campus Chronic fatigue syndrome (CFS) is classified by the World Health Organisation (WHO) as a non-communicable disease. Fatigue is a symptom commonly experienced by many individuals and is also a symptom associated with a wide variety of diseases, but once this fatigue becomes long lasting, persistent and debilitating, a case of CFS is considered. Research of CFS dates back to the nineteen hundreds, but unfortunately, no definite underlying cause or one single positive treatment has been identified. Diagnosis also poses a difficult task due to different criteria available, but also because of the lack in confidence of diagnosing doctors in making a positive diagnosis, because this disease is still poorly understood. Recent studies and research found promising evidence that mitochondrial dysfunction may be considered as a possible underlying cause of CFS. Because mitochondria are responsible for the release of energy in cells, the connection between mitochondrial dysfunction and the underlying energy deficiency in CFS patients may indicate a good starting point for further investigation. L-carnitine plays an important role in energy metabolism and could possibly be used as potential biomarkers for energy related diseases such as CFS. The first part of the study focused on method development and validation. A pre-existing high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method coupled with electrospray ionisation (ESI) was further developed and validated to simultaneously quantify carnitine and acylcarnitines in human urine samples. The second part of the study included application of the developed and validated method to urine samples of controls and possible CFS patients. All carnitines of interest could be detected and identified with this method, although the longer chain aclylcarnitines posed some difficulty. The aim of this study was to identify altered acylcarnitine profiles associated with possible CFS patients compared to control samples. At the end, principal component analysis (PCA) statistical analysis could not differentiate between the two groups, but two acylcarnitines were identified by the Mann Whitney test to have significant p-values, namely octanoylcarnitine (C8) and decanoylcarnitine (C10). Masters

Background Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. Methods Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. Results We identified 5 subtype B Portuguese clades (26–79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998–2000) and 2000 (95% BCI, 1998–2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73–2.09) to 0.62 (95% BCI,.52–.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39–1.59) to 0.72 (95% BCI, .63–.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. Conclusions The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations., The Journal of Infectious Diseases, 220 (2), ISSN:0022-1899, ISSN:1537-6613

International audience; The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures. Thézé et al. examine the genomic epidemiology of Zika virus in Central America and Mexico. Following its likely introduction to Honduras in 2014, the virus spread undetected in the region. Genetic and epidemiological data indicate that biannual transmission peaks occurred, and could potentially be explained by local variation in mosquito abundance.

BACKGROUND. Age-specific health promotion messages appear in the Road-to-Health booklet (RtHB), an assessment and monitoring tool for child health in South Africa. Healthcare workers should communicate health promotion messages to caregivers at each clinic visit. This investigation was part of a larger RtHB survey. OBJECTIVE. To assess the implementation of health promotion messages and identify barriers to its successful implementation. METHODS. A cross-sectional descriptive study with analytical components was conducted in the Western Cape Province. Knowledge and practices of caregivers and healthcare workers were assessed at 143 randomly selected primary healthcare facilities. Information was obtained through questionnaires, direct observation of consultations and recording of health promotion material in facilities. RESULTS. In total, 2 442 children (0 - 36 months; mean (standard deviation) age 5.10 (6.24) months), 2 481 caregivers and 270 healthcare workers were included. Caregivers' educational level varied, with only 24.3% having completed Grade 12. Healthcare workers had a median of 5 (range 0.5 - 37.0) years' work experience in primary healthcare. All healthcare workers indicated that health promotion messages were important, however, messages were only conveyed in 51% of observed consultations. When it was communicated, health promotion messages were age-appropriate in 97% of cases. Barriers to the implementation of health promotion messages hinged on time and staff constraints, workload and language barriers. Various forms of health promotion material were available in facilities. CONCLUSIONS. Suboptimal implementation of the health promotion messages in the RtHB are apparent despite healthcare workers realising the importance of health promotion. Barriers to optimal implementation must be urgently addressed by the National Department of Health and healthcare workers in partnership with caregivers and with support from society to promote child health and care.

MSc (Pharmaceutical Chemistry), North-West University, Potchefstroom Campus The possible treatment and prevention of Alzheimer’s disease (AD) is one of many clinical applications of methylene blue (MB) that has recently attracted much interest. Due to its ability to interact with various targets, MB exhibits multiple mechanisms by which the progression of neurodegenerative diseases may be decreased. Recently, it has been reported that azure B (AB), the major metabolite of MB, possesses superior effects at various pharmacological targets compared to MB. This finding raises the question that much of the documented pharmacological effects of MB observed in previous studies may in fact be due to the actions of AB. The structural similarities between MB and its metabolites have made the analysis of these compounds very challenging. The published analytical methods for MB and its metabolites have significant disadvantages such as low sensitivity, uneconomically high costs, the need of professionally trained personnel and very expensive, high technology apparatus. These disadvantages delays and limits the research into MB as a drug for the treatment of AD and other neurodegenerative disorders, and also hampers investigations into the pharmacology of MB. In this study, simple and cost effective analytical methods were developed to analyse and separate MB and its metabolites. An accurate, sensitive and reliable high performance liquid chromatography (HPLC) method with which MB and its metabolites were successfully separated, was developed and fully validated. A Synergi Polar-RP column (150 x 4.6 mm, 4 μ, 80 Å) and a mobile phase composed of two parts: ammoniumacetate that is dissolved in a mixture of water and methanol (part A) and a mixture of acetonitrile and methanol (part B). The analysis were done on a Hitachi Chromaster chromatographic system. Also, successful normal phase and reverse phase thin layer chromatography (TLC) methods were developed as a crude method for accessing the purity of MB. Masters

Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas. They have a simple and direct life cycle with one host, and partially castrate the founding queens greatly reducing their fitness. Here, we report the nuclear genome sequences of one clone of each species, extracted from a field-collected infection. Using a combination of Roche 454 FLX Titanium, Pacific Biosciences PacBio RS, and Illumina GA2 instruments for C. bombi, and PacBio for C. expoeki, we could produce high-quality and well resolved sequences. We find that these genomes are around 32 and 34 MB, with 7,808 and 7,851 annotated genes for C. bombi and C. expoeki, respectively—which is somewhat less than reported from other trypanosomatids, with few introns, and organized in polycistronic units. A large fraction of genes received plausible functional support in comparison primarily with Leishmania and Trypanosoma. Comparing the annotated genes of the two species with those of six other trypanosomatids (C. fasciculata, L. pyrrhocoris, L. seymouri, B. ayalai, L. major, and T. brucei) shows similar gene repertoires and many orthologs. Similar to other trypanosomatids, we also find signs of concerted evolution in genes putatively involved in the interaction with the host, a high degree of synteny between C. bombi and C. expoeki, and considerable overlap with several other species in the set. A total of 86 orthologous gene groups show signatures of positive selection in the branch leading to the two Crithidia under study, mostly of unknown function. As an example, we examined the initiating glycosylation pathway of surface components in C. bombi, finding it deviates from most other eukaryotes and also from other kinetoplastids, which may indicate rapid evolution in the extracellular matrix that is involved in interactions with the host. Bumble bees are important pollinators and Crithidia-infections are suspected to cause substantial selection pressure on their host populations. These newly sequenced genomes provide tools that should help better understand host-parasite interactions in these pollinator pathogens., PLoS ONE, 13 (1), ISSN:1932-6203

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Background. Optimal nutrition during the first 1 000 days of life can reap lasting benefits throughout life.Objectives. To assess infant and young child-feeding (IYCF) practices and mother/caregiver-child anthropometry in two vulnerable Breede Valley communities, Western Cape.Methods. Mothers of children aged 0 - 23 months (N=322) were interviewed to assess IYCF practices. Anthropometric measurements of mothers/caregivers and children were performed according to standard procedures.Results. Mothers reported early breastfeeding (BF) initiation in 75.2% (242/322) of cases. Of infants

Introduction Supporting individuals as they disclose their HIV serostatus may lead to a variety of individual and public health benefits. However, many women living with HIV are hesitant to disclose their HIV status due to fear of negative outcomes such as violence, abandonment, relationship dissolution and stigma. Methods We conducted a systematic review of studies evaluating interventions to facilitate safer disclosure of HIV status for women living with HIV who experience or fear violence. Articles, conference abstracts and programme reports were included if they reported post-intervention evaluation results and were published before 1 April 2015. Searching was conducted through electronic databases for peer-reviewed articles and conference abstracts, reviewing websites of relevant organizations for grey literature, hand searching reference lists of included studies and contacting experts. Systematic methods were used for screening and data abstraction, which was conducted in duplicate. Study quality (rigor) was assessed with the Cochrane risk of bias tool. Results Two interventions met the inclusion criteria: the Safe Homes and Respect for Everyone cluster-randomized trial of combination HIV and intimate partner violence (IPV) services in Rakai, Uganda, and the South Africa HIV/AIDS Antenatal Post-Test Support study individual randomized trial of an enhanced counselling intervention for pregnant women undergoing HIV testing and counselling. Both programmes integrated screening for IPV into HIV testing services and trained counsellors to facilitate discussions about disclosure based on a woman's risk of violence. However, both were implemented as part of multiple-component interventions, making it impossible to isolate the impact of the safer disclosure components. Conclusions The existing evidence base for interventions to facilitate safe HIV serostatus disclosure for women who experience or fear violence is limited. Development and implementation of new approaches and rigorous evaluation of safe disclosure outcomes is needed to guide programme planners and policy makers.

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There are a number of reasons why tourists visit a specific attraction centre; these reasons are called travel motivations. Travel motivations refer to the force(s) behind an individual‘s behaviour. Investigating tourists‘ travel motives will assist the management of attractions to better cater for the needs of the tourists and will also help them to improve the development of their products. The purpose of this study was to identify the travel motives of tourists to the National Zoological Gardens of South Africa (NZG). The NZG is situated in Pretoria, South Africa, and is classified as an urban attraction. The primary purposes of the zoo are conservation and education. It is therefore of critical importance to establish whether tourists visit this zoo for these reasons. In order to determine the answer(s) to this question, a questionnaire was used as a research instrument. The questionnaire was distributed at the research site. A total of 273 completed responses were received and were included in the statistical analysis. Seven motives were identified. Among these, Enhancements of relationships, Education and learning and Nature experience seekers were rated as most important by the respondents.Keywords: Travel motivation, National Zoological Gardens of South Africa, factor analysis, urban attraction.

Determination of plasma tenofovir (TFV) concentrations in small plasma volumes and in a short time period is most desirable in a clinical setting. The HPLC-MS/MS method was developed and validated for the determination of TFV. Plasma sample volumes of 10 μL were extracted by protein precipitation. Cimetidine, used as internal standard (ISTD) and TFV were separated on a C18 (Phenomenex Kinetex TM 30 mm × 2.1 mm, 2.6 μm) reversed phase column with a pre-column. The gradient mobile phase consisted of 10 mmol/L ammonium acetate in water and acetonitrile/methanol (50:50, v/v). TFV and ISTD retentiontimes were 0.27 and 0.90 minutes, respectively, with a run time of 2 minutes. Transition of the parent to the product ion of TFV (m/z 288.072→176.038) and ISTD (m/z 253.13→158.987) were monitored in positive ionization mode. Calibration curves were linear (average r2, 0.9958) over a TFV concentration range of 12.5-600 ng/mL. The mean recovery was 96.9%. Accuracy, inter and intra-assay of three quality controls and lower limit of quantification (12.5 ng/mL) were within the acceptable limit of