Application of semi-automated settlement detection for an integrated topographic map information system update in South Africa

Complete, accurate and up-to-date topographic data is of vast importance as it is widely required by different government agencies, non-governmental organisations, the private sector as well as the general public for urban mapping, rural development and environmental management, to mention but a few applications. Efficient semi-automatic methods for detecting settlements as change area indicators are required in order to achieve a sustainable up-to-date topographic database. This study reviewed the capability of geographic object based image analysis (GEOBIA) as a semi-automated method for settlement detection using 2012 SPOT 5imagery in the KwaZulu-Natal Province, South Africa.The application of GEOBIA provide the ability to segment imagery into areas resembling features of interest. For this study GEOBIA settlement detection provided 70.7% overall accuracy while the existing semi-automated South African global human settlement layer (SA_GHSL) had 60% overall accuracy. These results presents an opportunity to apply GEOBIA semi-automated method to target areas of new settlement development more efficiently and with consistent repeatable manner. Thus assisting topographic update analyst to be drawn to more areas of new settlement development at an enhanced efficient rate. However the spectral variability of roof tops which are prominent identifiable feature by remote sensing for settlement areas prove to be the most challenging obstacle towards semi-automated settlement detection

ESTABLISHING A PLATFORM FOR SPRAY DRYING INHALABLE VACCINES IN SOUTH AFRICA

Mycobacterium bovis BCG is the current vaccine for tuberculosis (TB). However, BCG as it is currently administered shows highly variable efficacy in protecting adults against TB. The natural route of infection of TB is via inhalation of bacilli-containing aerosols and it is postulated that immunization by the natural route of infection may lead to a greater immunity given the fact that the lungs are the primary target of infection. By eliciting both local and systemic immune responses, it is anticipated that an inhaled form of BCG will offer greater protection against pulmonary TB. Current commercial BCG vaccine preparations are filled as bacterial suspensions in vials, dried through lyophilization and stabilized through refrigeration with a one year shelf life. However, freeze-dried BCG does not exhibit a particle form conducive for delivery via the aerosol route and must be injected. Spray drying studies by Harvard University and Medicine in Need (MEND) scientists have demonstrated that BCG could be spray dried into a viable aerosol with up to 1 year of stability under refrigerated conditions, with the potential for room temperature stability. To support the further preclinical development of the BCG aerosol for application in the developing world, MEND established a state-of-the-art Biosafety level 3 spray drying facility with local expertise in South Africa, where the vaccine will be produced for an IND-enabling toxicology study meeting OECD Good Laboratory Practice (GLP) requirements. Frozen BCG bulk is spray dried and the resulting dry powder is characterized in terms of viability and aerosol properties. The dried BCG aerosol is then aseptically filled into capsules using a semi-automatic filling device for delivery using a low-cost hand-held inhaler. In conclusion, the spray drying technology was successfully transferred from Harvard University to the MEND facility in Pretoria. MEND is developing local expertise and infrastructure to support further preclinical and clinical development of BCG for inhalation

Adolescents at risk of self-harm in Ghana: a qualitative interview study exploring the views and experiences of key adult informants

Background In Ghana, rates of self-harm in young people are as high as they are in high income countries. Self-reported interpersonal, familial and societal stressors form the most important background, and self-harm is seen by young people as a way of responding to that stress. In the present study, we obtained the views of key adult informants about self-harm among adolescents in Ghana – what they thought as possible reasons for self-harm in young people and what actions might be needed at an individual or population level to respond to the problem. Methods We interviewed face-to-face 11 adults, using a semi-structured interview guide. We used an experiential thematic analysis technique to analyse the transcribed interviews. Results The analysis identified five themes: “underestimating the prevalence of self-harm in adolescents”, “life on the streets makes self-harm less likely”, “self-harm in adolescents is socially and psychologically understandable”, “ambivalence about responding to adolescent self-harm”, and “few immediate opportunities for self-harm prevention in Ghana”. Adolescent self-harm was acknowledged but its scale was underestimated. The participants offered explanations for adolescent self-harm in social and psychological terms that are recognisable from accounts in high income countries. Low rates among street-connected young people were explained by their overarching orientation for survival. Participants agreed that identification was important, but they expressed a sense of inadequacy in identifying and supporting adolescents at risk of self-harm. Again, the participants agreed that self-harm in adolescents should be prevented, but they recognised that relevant policies were not in place or if there were policies they were not implemented – mental health and self-harm were not high on public or political priorities. Conclusions The adults we interviewed about young people who self-harm see themselves as having a role in identifying adolescents at risk of self-harm and see the organisations in which they work as having a role in responding to individual young people in need. These are encouraging findings that point to at least one strand of a policy in Ghana for addressing the problem of self-harm in young people

Adolescent self-harm in Ghana: a qualitative interview-based study of first-hand accounts

Background: Recent prevalence studies suggest that self-harm among adolescents in sub-Saharan Africa is as common as it is in high income countries. However, very few qualitative studies exploring first-person accounts of adolescent self-harm are available from sub-Saharan Africa. We sought to explore the experiences and first-person perspectives of Ghanaian adolescents reporting self-harm - for deeper reflections on the interpretive repertoires available in their cultural context for making sense of self-harm in adolescents. Methods: Guided by a semi-structured interview protocol, we interviewed one-to-one 36 adolescents (24 in-school adolescents and 12 street-connected adolescents) on their experiences of self-harm. We applied experiential thematic analysis to the data. Results: Adolescents’ description of the background to their self-harm identified powerlessness in the family context and unwanted adultification in the family as key factors leading up to self-harm among both in-school and street-connected adolescents. Adolescents’ explanatory accounts identified the contradictory role of adultification as a protective factor against self-harm among street-connected adolescents. Self-harm among in-school adolescents was identified as a means of “enactment of tabooed emotions and contestations”, as a “selfish act and social injury”, as “religious transgression”, while it was also seen as improving social relations. Conclusions: The first-person accounts of adolescents in this study implicate familial relational problems and interpersonal difficulties as proximally leading to self-harm in adolescents. Self-harm in adolescents is interpreted as an understandable response, and as a strong communicative signal in response to powerlessness and family relationship difficulties. These findings need to be taken into consideration in the planning of services in Ghana and are likely to be generalisable to many other countries in sub-Saharan Africa

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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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

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