First fungal genome sequence from Africa : a preliminary analysis

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.We thank the National Research Foundation (NRF) of South Africa, members of the Tree Protection Co-operative Programme, the THRIP initiative of the Department of Trade and Industry and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology and the Oppenheimer Foundation for funding.http://www.sajs.co.zanf201

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

Link between structural and mechanical stablility of fcc- and bcc-based ordered Mg-Li alloys

The first principles pseudopotential calculations based on the Perdew-Burke-Ernzerhof (PBE) form of generalized gradient approximation (GGA) within density functional theory (DFT) have been utilized to investigate the structural and elastic properties of cubic-based Mg-Li alloys. The heats of formation and elastic moduli were used in predicting structural stability profile, and their results are consistent with each other. In terms of phase stability, an interesting correlation between the calculated tetragonal shear modulus (C) and formation energy of corresponding bcc and fcc ordered compounds relative to hcp Mg and Li lattices is drawn. The predicted stability trend due to structural energy difference was further confirmed by electronic structure calculations based on Jones-type analysis

Reducing the Risk of Being a Victim of Crime in South Africa: You can tell and be Heard!

People who use AAC know that silence is not always golden. Persons with disability, and in particular those with complex communication needs, have a heightened risk of becoming the victim of crime, abuse and neglect. In order to address one of the several problems associated with this, the present study looked at vocabulary needed to disclose or report crime or abuse in South Africa. Furthermore, it also focussed on the development of communication boards in four of the 11 official South African languages (Afrikaans, English, Sepedi and isiZulu). Thirty-six participants were involved in 4 language-based focus groups (English, Afrikaans, Sepedi and isiZulu). Participants were asked to generate a list of possible words they deemed important when wanting to disclose a crime, abuse or neglect. Participants then prioritized the top 55 words. When the lists from the four language groups were compared, a total of 56 words appeared on two or more of the lists. An electronic mail survey indicated that Picture Communication Symbols (PCS™) were the most frequently used symbol set in South Africa, and hence the board was developed using PCS™. A discrepancy analysis revealed that these 56 words could be represented by a staggering 219 symbols, of which 2 words (swear, threaten) did not have any existing PCS™ symbols. Consequently, they were developed. It is hoped that the process of developing the communication boards described in this paper might also be useful to the AAC community in other countries. Futhmore, the communicaton boards developed in this study can serve as a template for other languages.http://www.tandf.co.uk/journals/titles/07434618.as