Browsing by Author "Nieuwoudt, Martin"

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    Cumulative viral load as a predictor of CD4+ Tcell response to antiretroviral therapy using Bayesian statistical models
    (PLoS, 2019-11-13) Sempa, Joseph B.; Rossouw, Theresa M.; Lesaffre, Emmanuel; Nieuwoudt, Martin
    Introduction: There are Challenges in statistically modelling immune responses to longitudinal HIV viral load exposure as a function of covariates. We define Bayesian Markov Chain Monte Carlo mixed effects models to incorporate priors and examine the effect of different distributional assumptions. We prospectively fit these models to an as-yet-unpublished data from the Tshwane District Hospital HIV treatment clinic in South Africa, to determine if cumulative log viral load, an indicator of long-term viral exposure, is a valid predictor of immune response. Methods: Models are defined, to express ‘slope’, i.e. mean annual increase in CD4 counts, and ‘asymptote’, i.e. the odds of having a CD4 count ≥500 cells/μL during antiretroviral treatment, as a function of covariates and random-effects. We compare the effect of using informative versus non-informative prior distributions on model parameters. Models with cubic splines or Skew-normal distributions are also compared using the conditional Deviance Information Criterion. Results: The data of 750 patients are analyzed. Overall, models adjusting for cumulative log viral load provide a significantly better fit than those that do not. An increase in cumulative log viral load is associated with a decrease in CD4 count slope (19.6 cells/μL (95% credible interval: 28.26, 10.93)) and a reduction in the odds of achieving a CD4 counts ≥500 cells/μL (0.42 (95% CI: 0.236, 0.730)) during 5 years of therapy. Using informative priors improves the cumulative log viral load estimate, and a skew-normal distribution for the random-intercept and measurement error results is a better fit compared to using classical Gaussian distributions. Discussion: We demonstrate in an unpublished South African cohort that cumulative log viral load is a strong and significant predictor of both CD4 count slope and asymptote. We argue that Bayesian methods should be used more frequently for such data, given their flexibility to incorporate prior information and non-Gaussian distributions.
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    Observed full blood count and lymphocyte subset values in a cohort of clinically healthy South African children from a semi-informal settlement in Cape Town
    (Health & Medical Publishing Group, 2015-09) Lawrie, Denise; Payne, Helen; Nieuwoudt, Martin; Glencross, Deborah Kim
    Background. The paediatric full blood count and lymphocyte subset reference intervals used by the National Health Laboratory Service (NHLS), South Africa (SA), are taken from two international reference interval publications. Differences in reference intervals suggest that international data sets may not be appropriate for use in SA. Objective. To study immunohaematological values of a group of clinically healthy children from an informal settlement in Cape Town, SA, to assess whether international paediatric reference intervals used by the NHLS are appropriate. Methods. A cross-sectional study of 207 female and 174 male HIV-uninfected children living in an informal settlement in Cape Town was performed. Full blood counts, automated differential counts and lymphocyte subset analysis were done using internationally accepted technologies. Data were categorised by age and reference intervals compiled using medians and 95% confidence intervals (CIs). Gender comparisons were calculated by non-parametric tests. Results. Although median and 95% CI values differed slightly, physiological trends for red cell, platelet, white blood cell differential and lymphocyte subsets were similar to international reference intervals currently in use at the NHLS. Benign ethnic neutropenia was not a significant finding, and gender-specific intervals were not necessary until 12 years of age. Lower overall median values for haemoglobin and haematocrit, and higher median values for mean cell volume and red cell distribution width, were noted. Assessment of haemoglobin, red cell distribution width and calculated Mentzer ratios suggested underlying iron deficiency in 14.2% of participants. Conclusion. Paediatric immunohaematological reference intervals observed in this study are similar to, and support continued use of, international paediatric reference intervals. Underlying iron and related nutritional deficiencies may be contributing to lower haemoglobin levels noted in local children. A larger nationwide study, including all ethnic groups, is recommended.
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    Systematic review of statistically-derived models of immunological response in HIV-infected adults on antiretroviral therapy in Sub-Saharan Africa
    (Public Library of Science, 2017-02-15) Sempa, Joseph B.; Ujeneza, Eva L.; Nieuwoudt, Martin
    Introduction: In Sub-Saharan African (SSA) resource limited settings, Cluster of Differentiation 4 (CD4) counts continue to be used for clinical decision making in antiretroviral therapy (ART). Here, HIV-infected people often remain with CD4 counts <350 cells/μL even after 5 years of viral load suppression. Ongoing immunological monitoring is necessary. Due to varying statistical modeling methods comparing immune response to ART across different cohorts is difficult. We systematically review such models and detail the similarities, differences and problems. Methods: ‘Preferred Reporting Items for Systematic Review and Meta-Analyses’ guidelines were used. Only studies of immune-response after ART initiation from SSA in adults were included. Data was extracted from each study and tabulated. Outcomes were categorized into 3 groups: ‘slope’, ‘survival’, and ‘asymptote’ models. Wordclouds were drawn wherein the frequency of variables occurring in the reviewed models is indicated by their size and color. Results: 69 covariates were identified in the final models of 35 studies. Effect sizes of covariates were not directly quantitatively comparable in view of the combination of differing variables and scale transformation methods across models. Wordclouds enabled the identification of qualitative and semi-quantitative covariate sets for each outcome category. Comparison across categories identified sex, baseline age, baseline log viral load, baseline CD4, ART initiation regimen and ART duration as a minimal consensus set. Conclusion: Most models were different with respect to covariates included, variable transformations and scales, model assumptions, modelling strategies and reporting methods, even for the same outcomes. To enable comparison across cohorts, statistical models would benefit from the application of more uniform modelling techniques. Historic efforts have produced results that are anecdotal to individual cohorts only. This study was able to define ‘prior’ knowledge in the Bayesian sense. Such information has value for prospective modelling efforts.