Browsing by Author "Ngandu, Nobubelo Kwanele"

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    Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
    (American Society for Microbiology, 2013) Muhire, Brejnev Muhizi; Golden, Michael; Tanov, Emil Pavlov; Harkins, Gordon William; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Monjane, Adérito Luis; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick
    Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.
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    Uptake and predictors of early postnatal follow–up care amongst mother–baby pairs in South Africa: Results from three population–based surveys, 2010–2013
    (Edinburgh University Global Health Society, 2017) Larsen, Anna; Cheyip, Mireille; Aynalem, Getahun; Dinh, Thu–ha; Jackson, Debra; Ngandu, Nobubelo Kwanele; Chirinda, Witness; Mogashoa, Mary; Kindra, Gupreet; Lombard, Carl; Goga, Ameena
    BACKGROUND Achieving World Health Organization (WHO) recommendations for postnatal care (PNC) within the first few weeks of life is vital to eliminating early mother–to–child transmission of HIV (MTCT) and improving infant health. Almost half of the annual global deaths among children under five occur during the first six weeks of life. This study aims to identify uptake of three PNC visits within the first six weeks of life as recommended by WHO among South African mother–infant pairs, and factors associated with uptake. METHODS We analyzed data from three facility–based, nationally representative surveys (2010, 2011/12 and 2012/13) primarily designed to determine the effectiveness of the South African program to prevent MTCT. This analysis describes the proportion of infants achieving the WHO recommendation of at least 3 PNC visits. Interviews from 27 699 HIV–negative and HIV–positive mothers of infants aged 4–8 weeks receiving their six week immunization were included in analysis. Data were analyzed using STATA 13.0 and weighted for sample ascertainment and South African live births. We fitted a multivariable logistic regression model to estimate factors associated with early PNC uptake. RESULTS Over half (59.6%, 95% confidence interval (CI) = 59.0–60.3) of mother–infant pairs received the recommended three PNC visits during the first 6 weeks; uptake was 63.1% (95% CI = 61.9–64.3) amongst HIV exposed infants and 58.1% (95% CI = 57.3–58.9) amongst HIV unexposed infants. Uptake of early PNC improved significantly with each survey, but varied significantly by province. Multivariable analysis of the pooled data, controlling for survey year, demonstrated that number of antenatal visits (4+ vs <4 Adjusted odds ratio (aOR) = 1.13, 95% CI = 1.04–1.23), timing of initial antenatal visits (≤12 weeks vs >12 weeks, aOR = 1.13, 95% CI = 1.04–1.23), place of delivery (clinic vs hospital aOR = 1.5, 1.3–1.6), and infant HIV exposure (exposed vs unexposed aOR = 1.2, 95% CI = 1.1–1.2) were the key factors associated with receiving recommended PNC visits. CONCLUSIONS Approximately 40% of neonates did not receive three or more postnatal care visits in the first 6 weeks of life from 2010–2013. To improve uptake of early PNC, early antenatal booking, more frequent antenatal care attendance, and attention to HIV negative women is needed.