OpenUCT :: Browsing by Subject "Epidemiology "

Browsing by Subject "Epidemiology "

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Open Access
A centile chart for birth weight for an urban population of the Western Cape
(1995) Theron, G B; Thompson, M L
Evidence from large epidemiological studies has supported concern that being born light for gestational age (LiGA) may be detrimental. The incidence of LiGA babies is an important indicator of the health of women of reproductive age in deprived communities. In the assessment of LiGA in the Western Cape, centile charts constructed for populations in other parts of the world are generally used. These charts, however, may not be appropriate. Patients residing in the area served by the Tygerberg Hospital obstetric service, who booked early with singleton pregnancies, had their gestational age confirmed by early ultrasound and delivered between 1 March 1989 and 28 February 1990 were included in the study. The sample consisted of 3 643 patients. The mean birth weight was 2 995 g (SD 573 g) and the range 760 - 5 080 g. The distribution of birth weight at each week of gestation from 28 to 42 weeks was not normal. The 4-parameter Johnson family of densities was used to model the distribution of birth weight at each gestational age. A comparison of the distribution of birth weight in the study relative to the perinatal growth chart for international reference constructed by Dunn was also made. In addition to considering an overall chart, the sample was subdivided according to a number of characteristics (e.g. gender, firstborn and latter-born babies, smoking habit, hypertensive disorders and induction of labour) in order to explore their impact on the distribution of birth weight. Having explored the potential impact of all these factors, it was concluded that a single chart including all patients could be constructed.
Open Access
A longitudinal analysis of neonatal and infant diagnostic HIV-PCR uptake and associations during three sequential policy periods in Mitchell’s Plain, Cape Town
(2018) Kalk, Emma; Davies, Mary-Ann
Background: Despite technological and programmatic advances in the prevention of vertical transmission of HIV and early infant diagnosis (EID), paediatric HIV continues to have a significant impact on infant and child survival in low- and middle-income countries. Many EID programmes follow the WHO recommendation of initial infant HIV testing with a nucleic acid assay at 4-6 weeks old. In general this strategy has been poorly implemented with substantial attrition after birth such that, according to UNAIDS, only 51% of HIV-exposed infants received a virological test in the first two months of life in 2015. In addition, there is concern about the sensitivity of the nucleic acid assays at six weeks in the context of exposure to prolonged multidrug antiretroviral therapy as infant post-exposure prophylaxis, and in breast milk. HIV-PCR testing at birth has been promoted as a means of maximizing the number of infants who receive an HIV test as well as identifying in utero-infected infants in whom HIV infection may follow an aggressive course. Evidence from pilot studies and modelling data was sufficiently compelling for the WHO to include a conditional recommendation for the addition of a birth HIV-PCR (either routine or targeted at high risk groups) to its EID algorithms in 2015. The Western Cape introduced targeted birth HIV testing for high risk infants in August 2014 and expanded this in line with the South African National Prevention of Mother-to-Child Transmission Guidelines, to include all HIV-exposed infants in December 2015. Methods: Between 2013 and 2016 we conducted an implementation science project to iteratively assess the implementation and effectiveness of the vertical transmission prevention of HIV in a chain of referral facilities in Cape Town (i.e. from primary to tertiary care). The e-register provided a single longitudinal record for each woman (linked to her infant after birth) and enabled assessment of HIV testing and treatment from first antenatal visit through delivery to infant HIV testing. Using a cohort of HIV-exposed live infants from this database, a protocol was designed (Section A: Protocol) to assess the implementation and outcome of effectively three different EID policy periods in the facility chain. i.e. an initial period of birth HIV-PCR at the clinician’s discretion if evidence of HIV infection; a period of targeted birth testing of high risk infants and lastly, of routine birth HIV-PCR for all HIV-exposed infants. A critical review of the literature appraised published assessments of birth HIV testing programmes in low- and middle-income countries (Section B: Literature Review) with the aim of assessing in utero transmission rates, follow-up testing and transmission rates and the resources required for implementation. Studies that modelled the impact of birth HIV testing were specifically reviewed. The manuscript (Section C: Manuscript) presented an analysis of the HIV-infected/exposed mother/infant dyads from the e-register of the Closing the Gaps study. Using this database adherence to guidelines in each period was assessed as well as the outcome of HIV-PCR at four delivery sites and the impact of the policies on return for follow-up EID. Results: South Africa is the first country in sub-Saharan Africa to implement birth HIV testing and most of the studies in support of this strategy were generated here. There was limited literature which highlighted the need for further investigation into the implementation and effectiveness of such programmes. No prospective data addressed targeted birth testing and those reporting on more routine birth HIV-PCR demonstrated success in timeous diagnosis and treatment although significant additional project resources were required. The retrospective laboratory data indicated that receipt of a birth HIV-PCR reduced the likelihood for follow-up at later testing time-points. This is important as the modelling studies suggested that the clinical and financial benefits of adding birth testing to existing algorithms would be lost if follow-up was poor. In the cohort of 2012 HIV-exposed infants in the study presented in the manuscript, the proportion who received birth testing increased with the progression of the EID policies but guideline implementation was poor, especially in primary care, with only 60% of infants being tested as recommended. The proportion of infants with positive HIV-PCR decreased as the pool of HIV-exposed infants undergoing testing expanded, being highest during the periods of targeted birth testing. In concurrence with the South African literature, receipt of a birth HIV-PCR decreased the likelihood of follow-up testing at 6-10 weeks. Among infants tested at 6-10 weeks old, the proportion who were positive for the first time at this time- point increased with the introduction of routine birth testing for all HIV-exposed infants, emphasizing the importance of the follow-up EID time-points. Conclusion: Virological testing at birth effectively increased the number of HIV-exposed infants who received an HIV test and was effective in identifying in utero infection in high risk infants (who could start treatment early with the attendant benefits.) The Western Cape EID policies were incompletely implemented in the study facilities over this time with many infants not being tested as indicated. Birth HIV-PCR decreased follow-up testing, an unintended consequence of serious concern. Adherence to the provincial and national guidelines needs to be re-enforced at delivery sites and at the primary care facilities where follow-up EID occurs.
Open Access
A retrospective study of the prehospital burden of trauma managed by the Western Cape Government emergency medical service
(2019) Abdullah, Mohammed Naseef; Saunders, Colleen; McCaul, Michael; Nyasulu, Peter
Introduction: Trauma is one of the leading causes of premature death and disability in South Africa. There is a paucity of data describing the prehospital trauma burden in sub-Saharan Africa. The aim of this study was to describe the epidemiology and common trauma emergencies managed by the Western Cape Government emergency medical service (WCG EMS) in South Africa. Methods: The WCG EMS call centre registry was retrospectively analysed for all trauma patients managed between 01 July 2017 to 30 June 2018. A descriptive analysis of the data was performed using standard procedures for all variables. To date, this was the first analysis of this dataset or any prehospital trauma burden managed in the Western Cape of South Africa. Results: The WCG EMS managed 492 303 cases during the study period. Of these cases, 168 980 (34.3%) or 25.9 per 1000 population were trauma related. However, only 91 196 met the inclusion criteria for the study. The majority of patients (66.4%) were males and between the socio-economically active ages of 21-40 years old (54.0%). Assaults were the most common cause of trauma emergencies, accounting for 50.2% of the EMS case load managed. The patient acuity was categorised as being urgent for 47.5% of the cases, and 74.9% of the prehospital trauma burden was transported to a secondary level health care facility for definitive care. Conclusion: This is the first report of the prehospital trauma burden managed in the Western Cape of South Africa. The Western Cape suffers a unique trauma burden that differs from what is described by the WHO or any other LMIC. It also provides the foundation for further research towards understanding the emergency care needs in South Africa and to support Afrocentric health care solutions to decrease this public health crisis.
Open Access
A systematic review of the epidemiology of hepatitis A in Africa
(2019-07-22) Patterson, Jenna; Abdullahi, Leila; Hussey, Gregory D; Muloiwa, Rudzani; Kagina, Benjamin M
Abstract Background Hepatitis A, caused by the hepatitis A virus (HAV), is a vaccine preventable disease. In Low and Middle-Income Countries (LMICs), poor hygiene and sanitation conditions are the main risk factors contributing to HAV infection. There have been, however, notable improvements in hygiene and sanitation conditions in many LMICs. As a result, there are studies showing a possible transition of some LMICs from high to intermediate HAV endemicity. The World Health Organization (WHO) recommends that countries should routinely collect, analyse and review local factors (including disease burden) to guide the development of hepatitis A vaccination programs. Up-to-date information on hepatitis A burden is, therefore, critical in aiding the development of country-specific recommendations on hepatitis A vaccination. Methods We conducted a systematic review to present an up-to-date, comprehensive synthesis of hepatitis A epidemiological data in Africa. Results The main results of this review include: 1) the reported HAV seroprevalence data suggests that Africa, as a whole, should not be considered as a high HAV endemic region; 2) the IgM anti-HAV seroprevalence data showed similar risk of acute hepatitis A infection among all age-groups; 3) South Africa could be experiencing a possible transition from high to intermediate HAV endemicity. The results of this review should be interpreted with caution as the reported data represents research work with significant sociocultural, economic and environmental diversity from 13 out of 54 African countries. Conclusions Our findings show that priority should be given to collecting HAV seroprevalence data and re-assessing the current hepatitis A control strategies in Africa to prevent future disease outbreaks.
Open Access
AFROStrep (SA): a surveillance system for group A streptococcal infection in South Africa
(2018) Barth, Dylan Dominic; Engel, Mark E; Mayosi, Bongani M
BACKGROUND AND AIMS OF THE THESIS: Group A β-haemolytic Streptococcus (GAS) also known as Streptococcus pyogenes, is responsible for a wide range of invasive and non-invasive GAS diseases. Prevalence and incidence data on GAS from developing countries are largely lacking when compared with industrialised nations. This thesis sought to (1) establish the South African arm of the AFROStrep biorepository and clinical database for patients with invasive and non-invasive GAS infection, (2) identify and summarize all published studies of laboratory-confirmed GAS infection in Africa, (3) describe, from national laboratory data, the incidence of invasive and non-invasive GAS in South Africa and, (4) conduct a prospective, surveillance study in order to determine the molecular epidemiology of GAS in Cape Town, South Africa over a 12-month period. METHODS: A systematic review was conducted on population-based studies reporting on the prevalence of laboratory-confirmed GAS infection among patients living in Africa (Study 1). A retrospective study of the incidence of GAS infection was conducted on data obtained from the National Health Laboratory Service between 2003 – 2015 (Study 2). The AFROStrep registry and biorepository (based in Cape Town) was established and through passive surveillance, laboratory confirmed invasive and non-invasive GAS cases were collected over a 12-month period. The molecular analysis of invasive and non-invasive infection was determined using emm type sequencing to provide insight into vaccine development (Study 3). RESULTS AND DISCUSSION: The pooled prevalence of GAS pharyngitis in Africa was determined to be 21% (95% CI, 17% to 26%). The incidence rates of laboratory-confirmed non-invasive GAS infection in the South African public sector appears to have declined over the last 13 years. Given the possibility that the lower incidence of invasive and non-invasive GAS infection found in our study is due to infrequent submission of specimens for microbiological culture by health practitioners, our findings may be an underestimate of the true burden of disease in South Africa. In our prospective surveillance study, 46 different emm types were identified. The most prevalent emm types were M76 (16% of isolates), M81 (10%), M80 (6%), M43 (6%), and M183 (6%) and were almost evenly distributed between invasive and non-invasive GAS isolates. When compared against the putative 30-valent vaccine under development, four of our most prevalent emm types are not included; vaccine coverage (i.e. vaccine type and non-vaccine type-killing) for non-invasive and invasive GAS infection in our setting was 60% and 59% respectively, notably lower than coverage in developed countries. CONCLUSION: This work provides evidence for a significantly high prevalence of GAS pharyngitis in Africa. While GAS surveillance in South Africa indicates a declining incidence of GAS disease in parts of the country over the last thirteen years, the findings may be an underestimate of the true burden of disease, demonstrating the need for accurate and comprehensive surveillance of GAS in South Africa. Finally, this research showed a low potential vaccine coverage in our setting and thus, emphasises the need for a reworking of the potential vaccine formulation to improve coverage in areas where the burden of disease is high.
Open Access
Alcohol as a risk factor for train commuting fatalities
(2001) Matzopoulos, Richard; Peden, Margie; Bradshaw, Debbie
Railway fatalities are an important subset of transport-related fatalities, which account for about 60% of the fatal unintentional injuries occurring in Cape Town. The Medical Research Council reviewed three and a half years of rail injury data and found that alcohol was one of the main risk factors. Furthermore, 33% of South Africa’s national rail fatalities tested positive for alcohol in 1999. Despite the links between alcohol and all types of transport- related injury, prevention efforts have targeted motor vehicle (MV) drivers exclusively. This study aimed to clarify the relationship between alcohol and the risk of all types of transport-related injury (particularly rail injury). Post mortem reports for transport fatalities were collected retrospectively from the two cape Town mortuaries at Salt River and Tygerberg for the period 1 January 1994 to 31 December 1996. A case control study design was used with the cases comprising rail passenger and rail pedestrian fatalities, while motor vehicle drivers and passengers were the controls for the passenger group and motor vehicle pedestrians were the controls for rail pedestrians. Blood alcohol concentration was the dependent variable, the independent variables were age, sex, race, date of death, day of week, time of injury and mechanism of death and the odds ratio was used as the measure of relative risk The study showed that alcohol consumption is an important risk-factor for rail fatalities. The odds ratios imply that rail passengers are 5.23 or 2.3 times as likely to be intoxicated than motor vehicle passengers or motor vehicle drivers respectively, while rail pedestrians are 1.44 times more likely to be intoxicated than motor vehicle pedestrian fatalities. Alcohol plays as important a role, if not more so, for drunken rail passengers and pedestrians as it does for drunken drivers and road pedestrians. The role of alcohol in rail pedestrian fatalities is significant when compared to motor-vehicle pedestrians as a control group. The study has also demonstrated that data provided by the National injury Mortality Surveillance System can form the basis for analytic studies on the risk-factors of injury. The results complement a growing body of research that documents the adverse health effects of excessive alcohol consumption and provide more evidence for public health campaigners to tackle endemic alcohol abuse in South Africa.
Open Access
An apparent reduction in the incidence and severity of spinal cord injuries in schoolboy rugby players in the Western Cape since 1990
(1999) Noakes, Timothy; Jakoet, I; Baalbergen, E
OBJECTIVE: To determine the impact of the 1990 rugby law changes in South African schoolboy rugby on the number of schoolboys suffering paralysing spinal cord injuries in the subsequent eight rugby seasons (1990-1997) in the former Cape Province (now the Western Cape, but including Port Elizabeth and East London). METHODS: The study was a retrospective analysis of all patients with rugby-related spinal cord injuries admitted to the Conradie and Libertas Spinal Units, Cape Town, between 1990 and 1997. Data were initially collected annually from patient files. From 1993 patients were interviewed in hospital and a standardised questionnaire was completed. Data were collated and analysed. RESULTS: There were 67 spinal cord injuries in adult and schoolboy rugby players in the eight seasons studied. Fifty-four (80%) injuries were in adults and 13 (20%) in schoolboys, representing a 23% increase and a 46% reduction in the number of injured adults and schoolboys, respectively. Fifty-two per cent of those injuries for which the mechanism was recorded occurred in the tackle phase of the game; of these approximately equal numbers were due to vertex impact of the tackler's head with another object, or to illegal (high) tackles. Twenty-five per cent of injuries occurred in the ruck and maul and the remainder (23%) in the collapsed scrum. The only striking difference in the proportion of injuries occurring in the different phases of play was the absence of high-tackle injuries among schoolboys. The majority of injuries occurred at vertebral levels C4/5 (32%) and C5/6 (42%). Five players (8%) died, tetraplegia occurred in 48% and 35% recovered either fully or with minor residual disability. Playing position was recorded for half the injured players. Front-row forwards (props 33%, hookers 9%), locks (12%) wings and centres (21%) and loose forwards (15%), accounted for 90% of all injuries. CONCLUSIONS: Introduction of rugby law changes in South African schoolboy rugby in 1990 may have led to a 46% reduction in the number of spinal cord injuries in this group. In contrast, the number of these injuries in adult rugby players increased during the same time period due either to an increase in the number of adult players or to a real increase in the incidence of these injuries. More injured schoolboy than adult rugby players made total or near-complete recoveries from initially paralysing injuries (61% v. 28%). The reduced number of schoolboy injuries could not have resulted directly from the specific law changes introduced in 1990, which targeted scrum laws. Rather, the absence of illegal (high) tackle injuries among schoolboys appears to be the principal factor explaining fewer injuries in schoolboys, who suffered a higher proportion of injuries in the ruck and maul than did adult players. Accordingly we conclude that a further reduction in spinal cord injuries in adult and schoolboy rugby players in the Western Cape requires: (i) the elimination of injuries occurring in the ruck and maul, and to the tackler; (ii) the strict application of the high-tackle rule in adult rugby; and (iii) a continuing, high level of vigilance. Concern must be expressed about the continuing number of paralysing spinal cord injuries in adult rugby players.
Open Access
Anthropometric measurements, sexual development and serum reproductive hormonal levels among boys in the rural Western Cape
(2016) Mao, Jun; Dalvie, Mohamed Aqiel
Background: Our previous epidemiological study have investigated the effect of pesticides on growth of boys in the Western Cape rural area, in this cross-sectional study, we extend those initial observation into a more detailed exploration of t he growth pattern in anthropometric variables and hormonal indicators, and its relation to pubertal stage. Reference data in relation to pubertal stage are presented, and compared with other international findings. Objective: To investigate the anthrop ometric growth and reproductive hormones alternation of Western Cape Rural boys who are potentially exposed to agricultural pesticides. Methods: A cross-sectional study of 269 boys was conducted in the rural Western Cape in South Africa. Tests included serum gonadotrophin releasing hormone (GnRH), lutenizing hormone (LH), follicle stimulating hormone (FSH), testosterone, sex hormone binding globulin (SHBG) and estradiol (E2); a physical examination of height, weight and BMI measurements; sexual matura tional assessment and a questionnaire (demographics and general medical history). Median of anthropometric variables and hormone levels by pubertal stage were compared with international references. Results: Median age of pubertal onset is 11.6 years old, later than African American boys and Urban South African boys. Western Cape rural boys were apparently shorter and lighter compared with the CDC and the WHO growth standards in the prepubertal and early pubertal stage, and then catch-up evidently in the mid and late puberty. Compared with previous pubertal hormonal studies, our boys were low in serum levels of testosterone were low and high in oestradiol levels throughout entire pubertal stages and the classic endocrine Negative Feedback Loops in hy pothalamic pituitary gonadal axis were established earlier. Conclusion: The results provide further evidence for the effects potentially from agricultural pesticides exposure in the pattern of growth in height and weight, and hormonal fluctuations dur ing the development of puberty.
Open Access
Antiretroviral therapy use during pregnancy and adverse birth outcomes in South African women
(2017) Malaba, Thokozile Rosemary; Myer, Landon
Background Studies suggest antiretroviral therapy (ART) use during pregnancy may be associated with adverse pregnancy outcomes. Given the large numbers of pregnancies exposed to ART, better understandings of potential associations with commonly used ART regimens and adverse pregnancy outcomes is critical. With the number of women on ART initiated before conception rapidly increasing, understanding how current recommended regimens and timing of ART initiation may influence pregnancy outcomes is critically important. Methods This mini-dissertation presents a research protocol (Section A), literature view (Section B) and journalformatted manuscript (Section C) for a study of ART use and birth outcomes among HIV-infected women and a comparator cohort of HIV-uninfected women. Pregnant women seeking care at the Gugulethu MOU, a primary-level antenatal care facility in Cape Town, South Africa were enrolled between March 2013 and August 2015. Pregnancy dating was based on research ultrasound, or last menstrual period/clinical exam where ultrasound was unavailable. Women were followed from their 1st antenatal visit through delivery. Analyses compared birth outcomes (preterm (PTD), low birthweight (LBW) and small for gestational age (SGA) deliveries) between HIV-infected and uninfected women; and between women on ART initiated before conception versus those initiating ART during pregnancy. Results In 1554 women with live singleton births (mean birthweight, 3079g; 21% preterm; 13% LBW; 12% SGA), a higher prevalence of PTD (22% vs 13%, p=0.001) and LBW (14% vs 9%, p=0.030) were observed in the HIV-infected compared to HIV-uninfected women. Adverse birth outcomes (PTD, LBW and SGA) did not vary systematically among the HIV-infected women regardless of ART initiation timing (initiated ART before conception or initiated ART to during pregnancy). The absence of associations between the adverse birth outcomes and timing of ART initiation persisted after adjusting for maternal age, parity, height, CD4 cell count and viral load at 1st visit. Conclusions Levels of adverse birth outcomes, in particular PTD, remain high among HIV-infected women, however our findings from a routine care cohort demonstrate that the timing of initiation of widely used regimens before conception or during pregnancy do not appear to be associated with an increased risk in adverse pregnancy outcomes.
Open Access
Association between depression and perceived parental traits : results from a nationally representative South African survey
(2011) Srubisky, Catherine Filippa; Myer, Landon
With a growing burden of disease and disability stemming from mental disorders in South Africa, additional research into this area may be justified, with specific reference to depression. The effects of parental influences have been explored in the literature as a relevant and valid risk factor in the development and presence of depression. The literature has suggested two main underlying themes of parental styles that included parental overprotection and care. The concept of overprotection has been associated with depression. This thesis explored these constructs in their association with depression whilst highlighting the influence of control. Furthermore the influences of parental depression were also included.
Open Access
Baseline prevalence and incidence and risk factors for new-onset drug induced hearing loss in adults receiving drug-resistant tuberculosis (DR-TB) treatment in Khayelitsha, South Africa
(2013) Njuguna, Christine Wanjiku; Cox, Helen; Boulle, Andrew
Treatment for drug-resistant tuberculosis (DR-TB) is longer and associated with more significant side-effects than drug susceptible TB. Second line injectable therapy using kanamycin, amikacin or capreomycin is associated with irreversible hearing loss. There is a scarcity of literature regarding the frequency of hearing loss as well as associated risk factors, particularly with long term use. This study aimed to determine the incidence and risk factors for hearing loss among patients receiving second line injectable drugs.
Open Access
Characteristics of perinatal depression in rural central, India: a cross-sectional study
(BioMed Central, 2018-11-12) Rathod, Sujit D; Honikman, Simone; Hanlon, Charlotte; Shidhaye, Rahul
Background Perinatal depression is associated with negative effects on child behavioural, cognitive and emotional development, birth outcomes, and physical growth. In India, increased priority accorded to mental health programs mean it is now possible to reduce the population-level burden of perinatal depression. In this secondary analysis of two studies, we aimed to describe the epidemiological features of depression among community- and facility-based samples of perinatal women from rural central India, and to describe the help-seeking behaviours from those women who screened positive for depression. Methods The Community Study was a multi-round population-based cross-sectional survey (n = 6087). The Facility Study was a multi-round facility-based cross-sectional survey (n = 1577). Both studies were conducted in Sehore District, Madhya Pradesh between 2013 and 2017. Field workers conducted structured interviews with perinatal women. The questionnaire had sections relating to sociodemographic characteristics, depression screening using the Patient’s Health Questionnaire (PHQ9), treatment seeking for depression-related symptoms, and disability. Using data pooled from both studies, we tested each characteristic for association with the total screening score and with screening positive for depression. Results We identified 224 perinatal women from the Community Study and 130 perinatal women from the Facility Study, of whom 8.8% and 18.5% screened positive for depression, respectively. For the continuous PHQ9 score, there was evidence of a “U” shaped association with age, and positive associations with pregnancy, disability score, suicidality and being a health facility attendee. For the binary PHQ9 score, there was evidence of positive associations with pregnancy, disability score, suicidality and being a health facility attendee. Conclusions This study highlights where the largest population-level variations in perinatal depression symptoms are present in this Indian sample, for which mental health service provision should be made a priority. Epidemiological evidence generated by this study, as well as new evidence on peer-delivered interventions for perinatal depression, must be utilized by policy-makers to prioritize mental health services for mothers along with maternal and child health services.
Open Access
The clinical features and estimated incidence of MIS-C in Cape Town, South Africa
(2022-05-02) Butters, Claire; Abraham, Deepthi R; Stander, Raphaella; Facey-Thomas, Heidi; Abrahams, Debbie; Faleye, Ayodele; Allie, Nazneen; Soni, Khushbu; Rabie, Helena; Scott, Christiaan; Zühlke, Liesl; Webb, Kate
Background Multisystem inflammatory syndrome is a severe manifestation of SARS-CoV-2 in children. The incidence of MIS-C after infection is poorly understood. There are very few cohorts describing MIS-C in Africa despite MIS-C being more common in Black children worldwide. Methods A cohort of children with MIS-C and healthy children was recruited from May 2020 until May 2021 from the two main paediatric hospitals in Cape Town, South Africa. Clinical and demographic data were collected, and serum was tested for SARS-CoV-2 antibodies. The incidence of MIS-C was calculated using an estimation of population exposure from seroprevalence in the healthy group. Summary data, non-parametric comparisons and logistic regression analyses were performed. Results Sixty eight children with MIS-C were recruited with a median age of 7 years (3.6, 9.9). Ninety seven healthy children were recruited with a 30% seroprevalence. The estimated incidence of MIS-C was 22/100 000 exposures in the city in this time. Black children were over-represented in the MIS-C group (62% vs 37%, p = 0.002). The most common clinical features in MIS-C were fever (100%), tachycardia (98.5%), rash (85.3%), conjunctivitis (77.9%), abdominal pain (60.3%) and hypotension (60.3%). The median haemoglobin, sodium, neutrophil count, white cell count, CRP, ferritin, cardiac (pro-BNP, trop-T) and coagulation markers (D-dimer and fibrinogen) were markedly deranged in MIS-C. Cardiac, pulmonary, central nervous and renal organ systems were involved in 71%, 29.4%, 27.9% and 27.9% respectively. Ninety four percent received intravenous immune globulin, 64.7% received methylprednisolone and 61.7% received both. Forty percent required ICU admission, 38.2% required inotropic support, 38.2% required oxygen therapy, 11.8% required invasive ventilation and 6% required peritoneal dialysis. Older age was an independent predictor for the requirement for ionotropic support (OR = 1.523, CI 1.074, 2.16, p = 0.018). The median hospital stay duration was 7 days with no deaths. Conclusion The lack of reports from Southern Africa does not reflect a lack of cases of MIS-C. MIS-C poses a significant burden to children in the region as long as the pandemic continues. MIS-C disproportionately affects black children. The clinical manifestations and outcomes of MIS-C in this region highlight the need for improved surveillance, reporting and data to inform diagnosis and treatment.
Open Access
Clustering of longitudinal viral loads in the Western Cape
(2020) Arua, Eke Nnanna; Lesosky, Maia Rose; Myer, Landon
Introduction: Routine viral load (VL) monitoring is important for assessing the effectiveness of ART in South Africa. There is little information however, on how the longitudinal VL patterns change for subgroups of persons living with HIV (PLHIV) who have experienced at least one elevated VL. We investigated the possible longitudinal VL patterns that may exist among this unique population. Methods: This mini-dissertation offers three components; a research protocol (Section A), a literature review (Section B) and a journal ready manuscript (Section C). We examined HIV VL data for the Western Cape from 2008 to 2018, taken from the National Health Laboratory Services (NHLS). Using< 1000 copies/mL as a threshold for viral suppression, we identified 109092 individuals who had at least one instance of an elevated VL. A nonparametric (KML-Shape) and a model-based (LCMM) clustering technique were used to identify latent subgroups of longitudinal VL trajectories among these individuals. Results: Both the KML-Shape and LCMM clustering techniques identified five latent viral load trajectory subgroups. KML-Shape found majority of individuals' trajectories belonged to clusters that had a decreasing longitudinal VL trend (76.6% of individuals), while LCMM found a smaller proportion of individuals' trajectories belonged to clusters that had a decreasing longitudinal trend (52.5% of individuals). Most of the trajectory subgroups identified had long periods of low-level viremia. Conclusion: Although majority of individuals belonged to clusters that had downward trends, further research is needed to better understand factors contributing to membership of clusters that did not have a downward longitudinal trend. Understanding these factors may help in the development of targeted HIV prevention programs for these individuals.
Open Access
Completion of isoniazid preventive therapy and factors associated with non-completion in an antiretroviral therapy-naive HIV-infected cohort in Cape Town by Tolu Oni.
(2012) Oni, Tolu; Coetzee, David
TB incidence in South Africa remains high, despite high rates of successful treatment suggesting ongoing transmission and a large reservoir of latently infected persons. Isoniazid preventive therapy (IPT) is recommended as preventive therapy in HIV-infected persons. However, implementation has been slow, impeded by barriers and challenges including the fear of non-adherence. A protocol was therefore written to conduct a study to measure IPT completion rates and evaluate predictors of non-completion of a six-month IPT course in Khayelitsha, an informal township in Cape Town. Prior to data analysis, a structured literature review was conducted to assess available evidence particularly from high-burden settings on IPT completion rates and factors associated with loss to follow up.
Open Access
The concurrence of typhoid and malaria as compared to typhoid and other diagnoses in adult patients admitted in the medical wards at Iringa Regional Hospital, Tanzania
(2005) Kangolle, Alfred C T; Young, Taryn
Malaria and typhoid are two diseases caused by different infectious organisms. Both have symptoms and signs that are very similar, making it possible to diagnose one instead of the other. In some parts of the world these two diseases are very common and may coexist in one patient, hence making it difficult for health personnel once they have confirmed one disease, to always be aware of the possible presence of another. The patients' blood can be tested in the laboratory to confirm the presence or absence of these diseases.
Open Access
A description of HIV-exposed uninfected infants in the IeDEA Southern Africa Cohort and an examination of growth outcomes
(2014) Morden, Erna; Davies, Mary-Ann
Since the successful use of antiretroviral therapy for the prevention of mother-to-child transmission of human immunodeficiency virus (HIV), there has been a steady increase in the number of infants born to HIV-infected mothers who remain uninfected. The characteristics of these HIV-exposed uninfected infants are not well known, including growth and other health outcomes. The International Epidemiologic Databases to Evaluate AIDS Southern Africa (IeDEA-SA) research strategy 2011-2016 includes specific studies in pregnant women, infants, children and adolescents. This study addresses one of the IeDEA-SA objectives, namely to establish and describe a sub-cohort of HIV-infected pregnant women and their exposed infants. Part A, the protocol, includes background information on sites contributing to this cohort of HIV-exposed uninfected (HEU) infants. It also details the aims, objectives and methodology of this study. Part B, the literature review, discusses what is known about HIV-exposed uninfected infants to date. It includes maternal disease factors, the use of antiretroviral therapy and the association between feeding modality and growth, focussing on studies conducted on the African continent. Part C, the manuscript, details the methodology, results and their interpretation of longitudinal analysis of growth among HEU infants in the IeDEA-SA collaboration. This cohort of HEU infants included 2621 infants from two South African sites. The median birth WAZ was -0.65 (IQR -1.46; 0.0), 51% were male and there was a median of 2 visits per infant. The feeding modalities practised were as follows: 0.5% exclusive breastfeeding, 7.9% unknown breastfeeding exclusivity, 78.6% mixed breastfeeding and 10.6% formula feeding. Mothers with a CD4 <200 cells/μl delivered infants with a lower birth WAZ (adjusted ß -0.253 [95% CI -0.043; -0.072], p = 0.006) compared to mothers with a CD4 ≥500 cells/≧l. Similarly, iv mothers who did not receive antiretroviral (ARVs) drugs delivered infants with a lower birth WAZ (adjusted ß -0.49 [95% CI -0.78; -0.20], p = 0.001) compared to mothers who received antenatal ARVs. Antenatal maternal ARVs and CD4 cell count did not have an effect on postnatal growth. Mixed effects models using maximum likelihood estimation for the longitudinal analysis of growth showed that exposure to breast milk positively influenced growth, albeit the effect was small. Infants with a birth weight <2 500g (ß 0.069 [95% CI 0.061; 0.078], p <0.0001) experienced faster growth within the first 28 weeks of life compared to infants with a birth weight ≥2 500g. In this cohort of South African HEU infants, less severe maternal disease and the use of ARVs positively impacted birth weight. Mixed feeding was common, and any breastfeeding may have a positive effect on longitudinal growth.
Open Access
Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar
(2016) De Bruyn, Alexandre; Harimalala, Mireille; Zinga, Innocent; Mabvakure, Batsirai M; Hoareau, Murielle; Ravigné, Virginie; Walters, Matthew; Reynaud, Bernard; Varsani, Arvind; Harkins, Gordon W; Martin, Darren P; Lett, Jean-Michel; Lefeuvre, Pierre
Abstract Background Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. Results The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.
Open Access
Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study
(2021-10-07) Riou, Julien; Dupont, Carole; Bertagnolio, Silvia; Gupta, Ravindra K.; Kouyos, Roger D.; Egger, Matthias; L. Althaus, Christian
Introduction The rise of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI) threatens antiretroviral therapy's long-term success (ART). NNRTIs will remain an essential drug for the management of HIV-1 due to safety concerns associated with integrase inhibitors. We fitted a dynamic transmission model to historical data from 2000 to 2018 in nine countries of southern Africa to understand the mechanisms that have shaped the HIV-1 epidemic and the rise of pretreatment NNRTI resistance. Methods We included data on HIV-1 prevalence, ART coverage, HIV-related mortality, and survey data on pretreatment NNRTI resistance from nine southern Africa countries from a systematic review, UNAIDS and World Bank. Using a Bayesian hierarchical framework, we developed a dynamic transmission model linking data on the HIV-1 epidemic to survey data on NNRTI drug resistance in each country. We estimated the proportion of resistance attributable to unregulated, off-programme use of ART. We examined each national ART programme's vulnerability to NNRTI resistance by defining a fragility index: the ratio of the rate of NNRTI resistance emergence during first-line ART over the rate of switching to second-line ART. We explored associations between fragility and characteristics of the health system of each country. Results The model reliably described the dynamics of the HIV-1 epidemic and NNRTI resistance in each country. Predicted levels of resistance in 2018 ranged between 3.3% (95% credible interval 1.9–7.1) in Mozambique and 25.3% (17.9–33.8) in Eswatini. The proportion of pretreatment NNRTI resistance attributable to unregulated antiretroviral use ranged from 6% (2–14) in Eswatini to 64% (26–85) in Mozambique. The fragility index was low in Botswana (0.01; 0.0–0.11) but high in Namibia (0.48; 0.16–10.17), Eswatini (0.64; 0.23–11.8) and South Africa (1.21; 0.83–9.84). The combination of high fragility of ART programmes and high ART coverage levels was associated with a sharp increase in pretreatment NNRTI resistance. Conclusions This comparison of nine countries shows that pretreatment NNRTI resistance can be controlled despite high ART coverage levels. This was the case in Botswana, Mozambique, and Zambia, most likely because of better HIV care delivery, including rapid switching to second-line ART of patients failing first-line ART.
Open Access
Drug-drug interactions between antiretrovirals and bedaquiline
(2017) Pandie, Mishal; Coetzee, David
Tuberculosis (TB) is a leading cause of morbidity and mortality worldwide. People living with HIV are particularly susceptible to TB infection, and treatment of HIV-TB co-infection is challenging for multiple reasons, including potential drug-interactions. Drug-resistant TB is difficult to treat and is associated with high treatment failure rates, mainly because the antimycobacterial drugs currently available are ineffective against drug-resistant TB. Bedaquiline is a new antimycobacterial drug which has shown great promise through its excellent efficacy for treating drug-resistant TB. Being a new drug, however, potential drug interactions with antiretrovirals are a major concern. Bedaquiline is metabolized in the liver by an enzyme called cytochrome P450 3A (CYP3A). The antiretrovirals nevirapine, efavirenz, and lopinavir/ritonavir (LPV/r) can affect the activity of this enzyme, and consequently affect the concentration of bedaquiline in the patient's blood. Nevirapine and efavirenz increase the activity of CYP3A, which may result in increased metabolism of bedaquiline, thus decreasing the concentration of bedaquiline, with consequent risk of treatment failure or the further development of drug-resistance. LPV/r inhibits the CYP3A enzyme, which may result in decreased bedaquiline metabolism, thus causing high concentration of bedaquiline in the blood, with consequent risk of toxicity. We conducted a pharmacokinetic study in 43 adult patients with drug-resistant TB to evaluate the drug-interactions between bedaquiline and the antiretrovirals nevirapine and LPV/r. We did serial measurements of the bedaquiline concentration in their plasma over 48 hours, and compared these concentrations in patients who were on antiretroviral and those who were not on antiretrovirals. Our results showed that nevirapine had no significant effect on bedaquiline concentrations, while patients on LPV/r had bedaquiline concentrations 2 fold higher than patients not on antiretrovirals. We could not determine the clinical significance of this, but recommend that patients receiving LPV/r and bedaquiline in combination must be closely monitored for side-effects.