Search

Background: Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. Methods: We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. Results: We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value <30 (vs >35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged <5 (aOR 6.7, 95%CI1.4-31.2) and 5-12 years (aOR 6.6 95%CI2.6-16.7)(vs 19-39) and Ct value <30 (aOR 4.5, 95%CI 1.3-15.5) and 30-35 (aOR 6.0, 95%CI 2.3-15.7)(vs >35). Conclusions: Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness. [ABSTRACT FROM AUTHOR]

In 2012 the World Health Organization (WHO) aimed to eliminate measles in five regions by 2020. This retrospective descriptive study reviewed measles surveillance data in South Africa for the period 2015-2020 to document the epidemiology of measles and the progress made towards meeting the 2020 measles elimination goal.A total of 22,578 specimens were tested over the period 2015-2020 yielding 401 (1.8%) confirmed measles cases, 321 (1.4%) compatible and 21,856 (96.8%) discarded cases. The most affected age group was 0-4 year olds. At the provincial level, South Africa achieved adequate surveillance, defined as more than two cases of febrile rash notified annually per 100 000 popoulation, except for KwaZulu-Natal and Limpopo in 2020, probably due to COVID-19 lockdown restrictions. Of confirmed cases, only 26% were vaccinated, 3% were too young to receive vaccines, 5% were not vaccinated, and 65% had unknown vaccination status. Measles vaccine effectiveness amongst 1-4 year olds was 80%. Using the standard case definition, South Africa achieved the measles elimination target of less than one case per one million nationally in years 2015, 2016 and 2020. The years 2017 to 2019 had incidence rates exceeding one per million nationally. Using a narrow case definition, that excluded positive rubella cases, improved the indicators with only the year 2017 having an incidence rate of more than one per million.South Africa displays intermittent measles outbreaks approximately six-yearly interspersed by inter-epidemic periods in which the country meets measles elimination targets. Intense effort is needed to increase the vaccine coverage to avoid periodic outbreaks. Enhanced molecular testing of each case will be required as measles incidence declines regionally. [ABSTRACT FROM AUTHOR]

Background: Epidemics of infectious disease occur frequently in low-income and humanitarian settings and pose a serious threat to populations. However, relatively little is known about responses to these epidemics. Robust evaluations can generate evidence on response efforts and inform future improvements. This systematic review aimed to (i) identify epidemics reported in low-income and crisis settings, (ii) determine the frequency with which evaluations of responses to these epidemics were conducted, (iii) describe the main typologies of evaluations undertaken and (iv) identify key gaps and strengths of recent evaluation practice.Methods: Reported epidemics were extracted from the following sources: World Health Organization Disease Outbreak News (WHO DON), UNICEF Cholera platform, Reliefweb, PROMED and Global Incidence Map. A systematic review for evaluation reports was conducted using the MEDLINE, EMBASE, Global Health, Web of Science, WPRIM, Reliefweb, PDQ Evidence and CINAHL Plus databases, complemented by grey literature searches using Google and Google Scholar. Evaluation records were quality-scored and linked to epidemics based on time and place. The time period for the review was 2010-2019.Results: A total of 429 epidemics were identified, primarily in sub-Saharan Africa, the Middle East and Central Asia. A total of 15,424 potential evaluations records were screened, 699 assessed for eligibility and 132 included for narrative synthesis. Only one tenth of epidemics had a corresponding response evaluation. Overall, there was wide variability in the quality, content as well as in the disease coverage of evaluation reports.Conclusion: The current state of evaluations of responses to these epidemics reveals large gaps in coverage and quality and bears important implications for health equity and accountability to affected populations. The limited availability of epidemic response evaluations prevents improvements to future public health response. The diversity of emphasis and methods of available evaluations limits comparison across responses and time. In order to improve future response and save lives, there is a pressing need to develop a standardized and practical approach as well as governance arrangements to ensure the systematic conduct of epidemic response evaluations in low-income and crisis settings. [ABSTRACT FROM AUTHOR]

Background: The peritonitis rate among children treated with peritoneal dialysis (PD) has not been widely reported in Saudi Arabia. The study aim was to estimate the peritonitis rate per patient-year and investigate the factors associated with higher peritonitis rates in a sample of PD children at King Abdullah Specialist Children's Hospital-Riyadh (KASCH-R), Saudi Arabia.Methods: This retrospective cohort study included 27 PD children treated between September 2007 and December 2017 at KASCH-R. We recorded the children's demographic and clinical data, and the frequency of peritonitis.Results: The 27 PD children reviewed (63% girls; mean age = 7.32 years old; range, 1-14 years), resulted in 86 peritonitis diagnoses in which the overall recurrence rate (in at least one episode) was 58/86 (67.4%) with a 95% confidence interval (CI), 56.5 to 77.2%. The rate of peritonitis episodes per patient-year was 0.76 (1 episode per 1.31 patient-year). The generalized Poisson model identified older children (age >  10 years) (adjusted rate ratios [aRR] = 7.273, 95% CI: 1.562-33.860), congenital nephrosis (aRR = 4.677, 95% CI: 1.443-15.155), height below 3rd percentile (aRR = 4.689, 95% CI: 1.874-11.735), weight below 3rd percentile (aRR = 5.388, 95% CI: 1.678-17.302), low albumin level (aRR = 4.041, 95% CI: 2.053-7.956), two-week duration of antibiotic therapy (aRR = 2.947, 95% CI: 1.163-7.468), which were independently associated with a high peritonitis rate.Conclusions: This study showed a high peritonitis rate in our center. Older children, congenital nephrosis, height and weight below the 3rd percentile, low albumin level, and long duration of antibiotic therapy were associated with a higher rate of peritonitis. An optimal peritonitis prevention strategy or best-practice guideline is needed to reduce and prevent peritonitis occurrence in our center. [ABSTRACT FROM AUTHOR]

Background: Measles is a highly contagious viral infection causing large outbreaks all over the world. Despite the availability of safe and cost effective vaccine, measles remained endemic with persistent periodic outbreaks in the Horn of Africa. The aim of this study is to characterize laboratory confirmed measles cases in Amhara Regional State, which was one of the highly affected regions in Ethiopia.Method: A suspected measles case was defined as any person presenting with fever, maculopapular rash and one or more of the three symptoms cough, coryza or conjunctivitis or a patient in whom a clinician suspects measles. A blood sample was collected for any measles suspected patient with a case based investigation form and specimen transported to the National Measles Laboratory in good condition where it was to be tested for Measles IgM antibody by ELISA technique. Data was entered and analyzed using Epi-Info 3.5.4 software.Result: A total of 6579 samples were tested for measles IgM among 7296 samples collected in Amhara Regional State over 11 years (2004-2014). Of the tested samples, 2412 (36.7%) were found positive, while 3965 and 202 samples were found to be negative and equivocal (compatible) respectively. Patients with age ≥ 10 years were the most affected. The highest number of laboratory confirmed measles cases were detected in 2014 and cases were occurred in all of the 11 zones of the state. A seasonal peak was noted in the hot-dry season of the year.Conclusion: Measles remains to be a public health problem in Amhara Regional State of Ethiopia, mostly affecting people ≥ 10 years of age. Measles virus was detected in all zones of the state, reaching its peak in the hot-dry season. To reduce the incidence of measles, it is highly recommended to improve routine immunization, and conduct a wide age group campaign. Additional research to evaluate the knowledge, attitudes and practices of the general population and health care professionals about measles infection and vaccination is important. Genotyping of circulating measles virus strain is recommended. [ABSTRACT FROM AUTHOR]

Background: Anthropogenic habitat change often results in altered landscapes that can provide new environments where hosts, parasites and pathogens can interact. The latter can have implications for human and animal health when in close proximity to developed areas. We recorded the helminth species richness and level of infestation in the peri-domestic rodent, Rhabdomys pumilio, in three different human linked landscapes. The aim was, to investigate the potential of R. pumilio to act as a reservoir host for zoonotic helminths and to compare the effect of anthropogenic habitat change on its parasite infestation patterns. Methods: Rodents (n = 518) were trapped in natural areas (nature reserves) and in three human linked landscapes (crop, livestock and urban fragments). Gastrointestinal parasite burdens were recovered and helminths identified from each animal. Generalized linear models were applied to investigate the effect of different landscape types on helminth infestation. Results: Rhabdomys pumilio was the most abundant rodent species within each landscape type. Eight helminths species were recovered and overall helminth prevalence was 86.68%. Mean helminth species richness, prevalence and abundance were significantly higher in crop fragments compared to natural landscapes and overall lower for nematodes in livestock and urban areas. Cestode prevalence showed a tendency to be elevated at anthropogenic linked landscape types. Conclusions: Host parameters and parasite infestations were strongly influenced by landscape characteristics. Resource-rich landscapes (crop fragments) provide favorable conditions for helminth infestations, while landscapes that are more closely associated with humans (livestock and urban landscapes) pose a larger risk by zoonotic species. [ABSTRACT FROM AUTHOR]

Background African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and "unbiased" deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses. Results We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals coinfected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more. Conclusions Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of "unbiased" deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses. [ABSTRACT FROM AUTHOR]

Background: Due to the difficult geographic terrain with lack of roads and transport, the Sikkim State in India finds difficulties in contending the respiratory diseases especially during the rainy seasons. Findings: A case-control study was conducted for two months at the Central Referral Hospital of East Sikkim involving 110 individuals in the age group of 10 years and above. Due to feasibility constraints, 55 cases and 55 controls were selected by applying the non-probability sampling method with age and sex matching. The collected data were tabulated and analyzed by using the SPSS (Statistical Package for Social Sciences) version 10.0 for windows. Findings were expressed in terms of proportion, Chi Square Test and Multiple Logistic Regression Analysis. Here, p-value <0.05 was considered as statistically significant. This study revealed that the presence of overcrowding, chronic exposure to allergens, smoking habits, chronic respiratory illnesses within last 5 years, family history of chronic respiratory illnesses and mental illnesses were independently associated with respiratory diseases. Conclusion: This study should be replicated in other parts of Sikkim to obtain more confirmatory evidence on determinants of respiratory diseases. [ABSTRACT FROM AUTHOR]

Background: M.tuberculosis (M.tb) is associated with enhanced T helper cell type 1 (Th1) immune responses while helminth infection is associated with T helper cell type 2 (Th2) immune responses. Our aim was to investigate whether helminth infection could influence the ability to generate an appropriate Th1 immune response that is characterized by a positive tuberculin skin test (TST), in M.tb exposed children.Methods: We completed a community-based, cross sectional household contact tracing study, using matched enrolment of HIV negative children with and without documented household M.tb exposure. We documenteddemographics, clinical characteristics, HIV status, M.tb exposure (using a standard contact score) and M.tb infection status (TST > = 10 mm). Ascaris lumbricoides-specific IgE was used as proxy for Ascaris infection/exposure.Results: Of 271 children (median age 4 years (range: 4 months to 15 years)) enrolled, 65 participants (24%) were serum positive for Ascaris IgE. There were 168 (62%) children with a documented household tuberculosis contact and 107 (40%) were (TST) positive overall.A positive TST was associated with increasing age (Odds Ratio (OR) =1.17, p < 0.001), increasing M.tb contact score(OR = 1.17, p < 0.001), previous tuberculosis treatment (OR = 4.8, p = 0.06) and previous isoniazid preventive treatment (OR = 3.16, p = 0.01). A visible bacillus Calmette-Guérin (BCG) scar was associated with reduced odds of being TST positive (OR = 0.42, p = 0.01).Ascaris IgE was not associated with TST status in univariate analysis (OR = 0.9, p = 0.6), but multivariable logistic regression analysis suggested an inverse association between Ascaris IgE status and a positive TST (OR = 0.6,p = 0.08), when adjusted for age, and M.tb contact score. The addition of an age interaction term to the model suggested that the age effect was stronger among Ascaris IgE positive children; the effect of being Ascaris IgE positive significantly reduced the odds of being TST positive amongst younger children while this effect weakened with increasing age.Conclusions: Our preliminary findings highlight a high prevalence of both Ascaris exposure/infection and M.tb infection in children in an urban setting. Helminth exposure/infection may reduce the immune response following M.tb exposure when controlling for epidemiological and clinical covariates. These findings might be relevant to the interpretation of immunological tests of M.tb infection in children. [ABSTRACT FROM AUTHOR]

Background: Ascariasis and HIV/AIDS are often co-endemic under conditions of poverty in South Africa; and discordant immune responses to the respective infections could theoretically be affecting the epidemic of HIV/AIDS in various ways. It is well-known that sensitisation to helminthic antigens can aggravate or ameliorate several non-helminthic diseases and impair immunisation against cholera, tetanus and tuberculosis. The human genotype can influence immune responses to Ascaris strongly. With these factors in mind, we have started to document the extent of long-term exposure to Ascaris and other helminths in a community where HIV/AIDS is highly prevalent. In more advanced studies, objectives are to analyse relevant immunological variables (e.g. cytokine activity and immunoglobulin levels). We postulate that when Ascaris is hyperendemic, analysis of possible consequences of co-infection by HIV cannot be based primarily on excretion vs nonexcretion of eggs. Methods: Recall of worms seen in faeces was documented in relation to the age of adult volunteers who were either seropositive (n = 170) or seronegative (n = 65) for HIV. Reasons for HIV testing, deworming treatments used or not used, date and place of birth, and duration of residence in Cape Town, were recorded. Confidence intervals were calculated both for group percentages and the inter-group differences, and were used to make statistical comparisons. Results: In both groups, more than 70% of participants were aware of having passed worms, often both when a child and as an adult. Most of the descriptions fitted Ascaris. Evidence for significantly prolonged exposure to helminthic infection in HIV-positives was supported by more recall of deworming treatment in this group (p < 0.05). Over 90% of the participants had moved to the city from rural areas. [ABSTRACT FROM AUTHOR]

Background: Low- and middle-income countries often lack the fiscal, infrastructural and human resources to conduct evidence-based research; similar constraints may also hinder the application of good clinical practice guidelines based on research findings from high-income countries. While the context of health organizations is increasingly recognized as an important consideration when such guidelines are implemented, there is a paucity of studies that have considered local contexts of resource-scarcity against recommended clinical guidelines.Methods: This paper sets out to explore the implementation of the NICE Guideline 11 on family interventions when working with persons with intellectual disability and challenging behavior by a group of psychologists employed in a government health facility in Cape Town, South Africa.Results: In the absence of evidence-based South African research, we argue that aspects of the guidelines, in particular those that informed our ethos and conceptual thinking, could be applied by clinical psychologists in a meaningful manner notwithstanding the relative scarcity of resources.Conclusion: We have argued that where guidelines such as the NICE Guidelines do not apply contextually throughout, it remains important to retain the principles behind these guidelines in local contexts. Limitations of this study exist in that the data were drawn only from the clinical experience of authors. Some of the implications for future research in resource-constrained contexts such as ours are discussed. Smaller descriptive, qualitative studies are necessary to explore the contextual limitations and resource strengths that exist in low- and middle-income settings, and these studies should be more systematic than drawing only on the clinical experience of authors, as has been done in this study. [ABSTRACT FROM AUTHOR]

Background: Frailty is a key predictor of death and dependency, yet little is known about frailty in sub-Saharan Africa despite rapid population ageing. We describe the prevalence and correlates of phenotypic frailty using data from the Health and Aging in Africa: Longitudinal Studies of an INDEPTH Community cohort., Methods: We analysed data from rural South Africans aged 40 and over. We used low grip strength, slow gait speed, low body mass index, and combinations of self-reported exhaustion, decline in health, low physical activity and high self-reported sedentariness to derive nine variants of a phenotypic frailty score. Each frailty category was compared with self-reported health, subjective wellbeing, impairment in activities of daily living and the presence of multimorbidity. Cox regression analyses were used to compare subsequent all-cause mortality for non-frail (score 0), pre-frail (score 1-2) and frail participants (score 3+)., Results: Five thousand fifty nine individuals (mean age 61.7 years, 2714 female) were included in the analyses. The nine frailty score variants yielded a range of frailty prevalences (5.4% to 13.2%). For all variants, rates were higher in women than in men, and rose steeply with age. Frailty was associated with worse subjective wellbeing, and worse self-reported health. Both prefrailty and frailty were associated with a higher risk of death during a mean 17 month follow up for all score variants (hazard ratios 1.29 to 2.41 for pre-frail vs non-frail; hazard ratios 2.65 to 8.91 for frail vs non-frail)., Conclusions: Phenotypic frailty could be measured in this older South African population, and was associated with worse health, wellbeing and earlier death.

Background: Tuberculosis (TB) continues to be a major global health problem. While progress has been made to improve TB cure rates, South Africa's 76 % smear-positive pulmonary TB (PTB) case cure rate remains below the WHO target of 85 %. We report on the trends of TB smear non-conversion and their predictors at the end of an intensive phase of treatment, and how this impacted on treatment outcomes of smear-positive PTB cases in Eden District, Western Cape Province, South Africa., Methods: Routinely collected, retrospective data of smear-positive PTB cases from the electronic TB register in Eden District between 2007 and 2013 was extracted. Non-conversion was defined as persistent sputum smear-positive PTB cases at the end of the two or three month intensive phase of treatment. Chi-square test for linear trend and simple linear regression analysis were used to analyse the change in percentages and slope of TB smear non-conversion rates over time. Risk factors for TB non-conversion, and their impact on treatment outcomes, were evaluated using logistic regression models., Results: Of 12,742 total smear-positive PTB cases included in our study, 12.8 % (n = 1627) did not sputum smear convert; 13.3 % (1411 of 10,574) of new cases and 9.9 % (216 of 2168) of re-treatment cases. Although not statistically significant in either new or re-treatment cases, between 2007 and 2013, smear non-conversion decreased from 16.4 to 12.7 % (slope = -0.60; 95 % CI: -1.49 to 0.29; p = 0.142) in new cases, and from 11.3 to 10.8 % in re-treatment cases (slope = -0.29; 95 % CI: -1.06 to 0.48; p = 0.376). Male gender, HIV co-infection and a >2+ acid fast bacilli (AFB) smear grading at the start of TB treatment were independent risk factors for non-conversion (p < 0.001). Age was a risk factor for non-conversion in new cases, but not for re-treatment cases. Non-conversion was also associated with unsuccessful treatment outcomes (p < 0.01), including treatment default and treatment failure., Conclusions: Smear-positive PTB cases, especially men and those with identified risk factors for non-conversion, should be closely monitored throughout their treatment period. The South African TB control program should invest in patient adherence counselling and education to mitigate TB non-conversion risk factors, and to improve conversion and TB cure rates.

Background: Epilepsy is a common neurological disorder, with over 80 % of cases found in low- and middle-income countries (LMICs). Studies from high-income countries find a significant economic burden associated with epilepsy, yet few studies from LMICs, where out-of-pocket costs for general healthcare can be substantial, have assessed out-of-pocket costs and health care utilization for outpatient epilepsy care., Methods: Within an established health and socio-demographic surveillance system in rural South Africa, a questionnaire to assess self-reported health care utilization and time spent traveling to and waiting to be seen at health facilities was administered to 250 individuals, previously diagnosed with active convulsive epilepsy. Epilepsy patients' out-of-pocket, medical and non-medical costs and frequency of outpatient care visits during the previous 12-months were determined., Results: Within the last year, 132 (53 %) individuals reported consulting at a clinic, 162 (65 %) at a hospital and 34 (14 %) with traditional healers for epilepsy care. Sixty-seven percent of individuals reported previously consulting with both biomedical caregivers and traditional healers. Direct outpatient, median costs per visit varied significantly (p < 0.001) between hospital (2010 International dollar ($) 9.08; IQR: $6.41-$12.83) and clinic consultations ($1.74; IQR: $0-$5.58). Traditional healer fees per visit were found to cost $52.36 (IQR: $34.90-$87.26) per visit. Average annual outpatient, clinic and hospital out-of-pocket costs totaled $58.41. Traveling to and from and waiting to be seen by the caregiver at the hospital took significantly longer than at the clinic., Conclusions: Rural South Africans with epilepsy consult with both biomedical caregivers and traditional healers for both epilepsy and non-epilepsy care. Traditional healers were the most expensive mode of care, though utilized less often. While higher out-of-pocket costs were incurred at hospital visits, more people with ACE visited hospitals than clinics for epilepsy care. Promoting increased use and effective care at clinics and reducing travel and waiting times could substantially reduce the out-of-pocket costs of outpatient epilepsy care.