Faculty of Science (Research Outputs)

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    Analysis of urban sprawl dynamics using machine learning, CA-Markov chain, and the Shannon entropy model: a case study in Mbombela City, South Africa
    (SpringerOpen, 2024) Mhangara, Paidamwoyo; Gidey, Eskinder; Rabia Manjoo
    Over half of the world’s population resides in urban areas. We anticipate that this pattern will become more evident, notably in South Africa. Therefore, research on urban spirals, both past and projected, is necessary for efficient urban land use planning and management. This study aims to assess the spatio-temporal urban sprawl dynamics from 2003 to 2033 in Mbombela, South Africa. We employed robust approaches such as machine learning, the cellular automata-Markov chain, and the Shannon entropy model to look at how urban sprawl changes over time using both the Landsat 4–5 Thematic Mapper and the 8 Operational Land Imagers. We conducted this study to bridge the gaps in existing research, which primarily focuses on past and current urban growth trends rather than future trends. The findings indicated that the coverage of built-up areas and vegetation has expanded by 1.98 km2 and 13.23 km2 between the years 2003 and 2023. On the other hand, the amount of land continues to decrease by -12.56 km2 and − 2.65 km2 annually, respectively. We anticipate an increase in the built-up area and vegetation to a total of 7.60 km2 and 0.57 km2, respectively, by the year 2033. We anticipate a total annual decline of -7.78 km2 and − 0.39 km2 in water bodies and open land coverage, respectively. This work has the potential to assist planners and policymakers in improving sustainable urban land-use planning.
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    A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
    (Public Library of Science, 2018-03) Geldenhuys, M.; Mortlock, M.; Weyer, J.; Bezuidt, O.; Seamark, E.C.J.; Kearney, T.
    Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.