Doctoral Degrees (Medical Virology)
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Browsing Doctoral Degrees (Medical Virology) by browse.metadata.advisor "De Beer, Corena"
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- ItemInvestigating pathogens of the gastrointestinal tract in sudden and unexpected death in infancy cases at the Tygerberg medico-legal mortuary, compared to an age-matched healthy control group.(Stellenbosch : Stellenbosch University, 2023-07) Cupido, Danielle Tiffany; De Beer, Corena; Whitelaw, Andrew; Dempers, Johan; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology.ENGLISH ABSTRACT: Background: Sudden and unexpected deaths in infancy (SUDI) includes infants under the age of one year that die suddenly and without apparent cause. Childhood diarrhoea is one of the leading causes of death for children under five, with around 1.7 billion cases worldwide each year and is often reported prior to death in SUDI cases. Poor socioeconomic conditions and inadequate water supplies in developing countries contribute to diarrhoea, and diarrhoeagenic Escherichia coli (DEC) were detected in 30-40% of these cases, while acute viral gastroenteritis causes ± 70% of all episodes. The microbiome influences host immunity, infectious susceptibility, and health, disease, and death outcomes. Limited information is available on the gastrointestinal tract (GIT) pathology, as well as the GIT microbiome as contributory factors to SUDI in South Africa. This study aims to investigate the bacterial and viral pathogens and colonisation of the GIT in SUDI cases admitted to the Tygerberg Medico-Legal Mortuary in the Western Cape in the process of determining the cause of death. Finally, the SUDI microbiome was compared to age-matched, apparently healthy infants. Methods: Swabs of the GIT and stool samples were collected from SUDI cases at Tygerberg Medico-legal Mortuary between June 2017 and May 2018. To serve as controls, stool samples were collected from the nappies of 45 healthy and age-matched infants. In stool and swab samples positive for Escherichia coli, DEC were detected using the AllplexTM GI-Bacteria (II) Assay and gastrointestinal viruses were detected in stool samples using the Allplex™ GI-Viral Assay. Positive rotavirus samples were genotyped and the intestinal microbiome was characterised by full-length 16S rRNA sequencing, on the PacBio Sequel IIe System platform. Results: This study included 186 SUDI cases (107 males and 79 females) and 45 controls (24 males and 21 females). Several known demographic factors increase the risk for SUDI, including age between 2-4 months, male sex, cold season, bedsharing, prone and side sleeping positions, as well as informal housing. Enteroaggregative Escherichia coli (EAEC) ) were detected in 87.3% of cases and enteropathogenic Escherichia coli (EPEC) were detected in 78.2% of cases. Co-infections between DEC pathotypes were observed in 85.2% of cases. Rotavirus was detected in 38.6%, of cases followed by norovirus GI and GII (30.0%), whereas norovirus GII was more prevalent in the controls (36.7%). Forty-eight cases had enteric virus co-detections. The association between most viruses and seasons was highly significant. Among the rotavirus genotypes, combinations of the G type and the P type, G1P[8] had the highest prevalence (40%), followed by G2P[4] (30%), while G9P[8] (20%) and G8P[4] (10%) genotypes had the lowest prevalence. Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria were found to be the most common organisms in the GIT. Significant differences were observed in alpha diversity and beta diversity between cases and controls, as well as the different final diagnoses. Conclusion: This study demonstrated that autopsy sampling procedures should include other sampling sites, e.g., GIT, as these pathogens may contribute to death, particularly with virus and bacterium co-infections. Determining the cause of death based on GIT pathogens, may decrease the number of Sudden Infant Death Syndrome (SIDS) cases reported in the future.
- ItemA Longitudinal Perspective on the Impact of Immune Status on the HIV-1 Latent Reservoir and Neurocognitive Outcomes in Virologically Suppressed Children(Stellenbosch : Stellenbosch University, 2022-04) Naidoo, Shalena; Glashoff, Richard; De Beer, Corena; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology.ENGLISH SUMMARY: Background: Children remain the most vulnerable population affected by the Human Immunodeficiency Virus-1 (HIV-1) pandemic whose reliance on lifelong therapy is accompanied by several immune abnormalities. In the absence of an effective vaccine, there is currently a strong emphasis on HIV-1 “cure” and although cART leads to viral suppression the virus is still able to establish latent reservoirs within host cells and this is considered the major barrier to achieving cure. Immune factors are considered critically important for the establishment and maintenance of HIV-1 latent reservoirs, but these factors are not well characterised, particularly in children. Delineating and understanding the immunological mechanisms that drive HIV-1 persistence and other chronic diseases such as metabolic, cardiovascular and neurodegenerative diseases is important in children approaching adolescence. Longitudinal studies evaluating the relationship between immune status, the HIV-1 latent reservoir and neurocognitive outcomes are limited, and inadequately studied, specifically within the South African subtype C context. The aim of this study was to longitudinally investigate and characterise host immune status before and after early initiated, delayed and interrupted cART in relation to HIV-1 latent reservoir size and neurocognitive outcomes in perinatally HIV-1 infected children. Methods: Study participants originated from the well-characterised Children with HIV Early AntiRetroviral Therapy (CHER) randomised controlled trial. This was a descriptive study that employed both a longitudinal (birth to 8 years of age) and cross-sectional study design and analysed samples collected retrospectively and prospectively. For the extensive longitudinal evaluation of immunological biomarker (cytokine, chemokine and receptor antagonist) profiling, we utilised Luminex® Multiplex Assays as well as Enzyme Linked ImmunoSorbent Assays (ELISAs). Multiparameter flow cytometry was utilised for the analysis of monocyte subset distribution. The quantitative viral outgrowth assay (QVOA) was implemented on a subset of participants for measuring of the HIV-1 replication-competent viral reservoir in conjunction with a novel highly sensitive RT-qPCR single copy assay targeted at HIV-1 integrase (iSCA). In addition, HIV-1 cell-associated DNA, specific for integrase (iCAD), were measured longitudinally as a molecular biomarker of HIV-1 persistence and correlated to immune and neurocognitive parameters. Longitudinal neurocognitive assessments were completed independently and correlated to immune, virological and clinical parameters. Age and demographically matched HIV exposed uninfected (HEU) and HIV unexposed uninfected (HUU) were included at the last time point (8 years of age). Key Findings: HIV-1 infected (HIV+) children showed significantly higher levels of biomarkers associated with generalised chronic inflammation, particularly those associated with myeloid cell activation compared to HEU and HUU controls at 8 years of age. These included hsCRP (p=0.01), MIP-1β (p=0.03), IL-1α (p<0.001), INF-α (p<0.001), CD40L (p<0.001), sCD14, sCD163, IL-18, IL-17F (p<0.001) and PDGF-BB (p<0.00001). We also observed a significant elevation of soluble calcium binding alarmin protein involved in the regulation of the inflammatory process and immune response, s100A8/A9, in the HIV+ group compared to the two study control groups (p<0.001). Within the HIV+ group, significant elevation of biomarkers associated with gut epithelial damage was observed at 8 years of age. IL-18 was the only immune biomarker that significantly correlated with HIV-1 CAD at baseline (r = +0.35; p=0.04) and at the 8-year follow-up (r = +0.38; p=0.02) and associated to the innate IL-1 family of immune biomarkers including IL-1RA (r = +0.33; p<0.01), IL-1α (r = +0.22; p<0.01), IL-1β (r = +0.26; p<0.01), and IL-1RA (r = +0.32; p<0.01). IL-18 also significantly correlated with biomarkers of monocyte/macrophage activation and gut damage, including: sCD14 (r = +0.50; p<0.01), sCD163 (r = +0.40; p<0.01), LBP (r = +0.26; p<0.01) and MIP-1β (r = +0.19; p=0.02). IL-18 showed significant negative associations (p<0.01) with CD4 % at baseline, longitudinal CD4 count and CD4:CD8 ratio at 8 years (r = +0.35; p=0.04). For longitudinal cytokine analysis, principal component analysis indicated that about 36% of the soluble biomarkers measured including: IL-15, TNFβ, GCSF, IL-1RA, IL-5, IL-4, IL-8, IL-10 and RANTES contributed to the largest parameter change over time across all treatment groups. The key early clinical predictors of plasma biomarker expression over time include time to therapy initiation, time to viral suppression, longitudinal CD4% and absolute count and CD4 and CD8% and absolute counts at birth. Neurocognitive outcomes can be predicted by early immunological, virological and clinical parameters. Conclusion: By investigating and profiling participants from the CHER randomised control trial cohort, we were able to provide important insights into immunological mechanisms that contribute to driving HIV-1 persistence during long-term suppressive therapy. The findings reported in this thesis have highlighted some key features of immune abnormalities that persists after early initiated long-term ART in paediatric populations. The evaluation of the persistence of any of the key associations through and beyond adolescence will aid in building a lifelong profile of immune changes in the MTCT-infected children. This research also provides important knowledge to further exploring PHIV children as potential “cure” and remission candidates.