Infections In South Africa Research Articles

The prevalence of hepatitis B virus, human T-lymphotropic virus and human immunodeficiency virus in patients receiving blood transfusions in South Africa.

South Africa has a high prevalence of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) and to a lesser extent human T-lymphotropic virus (HTLV). Each of these agents is transfusion-transmissible (TT)but deciding whether to implement preventive screening depends upon knowledge of background prevalence in transfused patients. We determined the prevalence of HIV, HBV and HTLV I/II among blood transfusion recipients in South African hospitals. We obtained identity-unlinked samples used for blood cross-matching at 634 South African hospitals served by the South African National Blood Service (SANBS). The ABBOTT Alinity S® Immunochemiluminescent system measured HIV, HBV and HTLV I/II antibodies. Repeatedly reactive samples were confirmed using the Roche Cobas® 8000. Logistic regression was performed to investigate the determinants of associations for HIV, HBV and HTLV infections. The overall prevalences of HIV, HBV and HTLV were 37.8%, 7.4% and 0.6%, respectively. The HIV prevalence in blood recipients was twice as high as general population estimates. Public hospital patients had a significantly higher prevalence compared with private hospital patients for HIV and HBV. HIV prevalence was significantly higher in females, and HBV prevalence was significantly higher in males, excluding the unknown gender results. Patients receiving blood transfusions in South Africa have high rates of HIV and HBV infection that should be taken into consideration when determining donor screening strategies for other viral infections. Measurable prevalence of HTLV indicates endemicity of this infection in South Africa.

Longitudinal controlled attenuation parameter and liver stiffness in children with and without perinatal HIV infection in South Africa.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is an emerging cause of liver disease in HIV. Transient elastography (TE) with controlled attenuation parameter (CAP) measures liver stiffness as a marker of liver fibrosis and CAP as a measure of hepatic steatosis. Our aim was to evaluate longitudinal CAP and liver stiffness in children with perinatally acquired HIV (PHIV) on antiretroviral therapy (ART) from early life compared to children without HIV (HU). Prospective cohort study. PHIV and HU were followed annually for two years. During the study, 60% of PHIV switched from older ART regimens to tenofovir disoproxil, lamivudine and dolutegravir (TLD). Longitudinal evolution of CAP and liver stiffness were investigated in two PHIV groups - on older ART and on TLD - compared to HU children using linear mixed effects models. 263 children and adolescents (112 PHIV, 151 HU) aged 7-20 years were followed. PHIV on older ART had CAP 8.61% (95% CI 4.42-12.97, P < 0.001) greater than HU and no significant difference in CAP between PHIV on TLD and HU. No significant difference in liver stiffness was found between PHIV on older ART regimens and PHIV on TLD compared to HU. PHIV on older ART had higher CAP than HU, whereas in PHIV switched to TLD there was no difference in CAP compared to HU. There was no difference in liver stiffness between either PHIV group and HU. This suggests starting ART early in life might protect PHIV from developing hepatic fibrosis.

Adolescents’ behavioral changes and preventive practices against COVID-19 in South Africa: The influence of household characteristics

The South African government instituted a countermeasure against COVID-19 in March 2020, which had a significant impact on many individuals, particularly the youth. However, there is a limited understanding of how household characteristics influenced adolescents&amp;rsquo; behavioral changes and their adoption of preventive measures during the pandemic. This study aimed to explore the relationship between the role of household characteristics and adolescents&amp;rsquo; behavioral responses to COVID-19 in South Africa. Using the latest data from the South African National Income Dynamics-Coronavirus Rapid Mobile Survey (Wave 5), which includes responses from 5581 (99.9%) youths aged 15 &amp;ndash; 24, we analyzed changes in their behaviors and the preventive measures they adopted. The study controlled for various household, demographic, and socioeconomic characteristics of the respondents. We utilized cross-tabulations and an ordinal logistics regression model to determine the relationship between the covariates and the outcome of behavioral changes and preventive measures adopted. Our findings revealed that none of the respondents adopted all recommended precautionary measures for COVID-19, while 55.7% exhibited low behavioral changes, and only 2.7% exhibited higher behavioral changes throughout the pandemic. The results indicate that, at both the individual and household levels, factors such as gender, educational attainment, source of household income, and access to electricity increase the odds of behavioral changes against COVID-19 in South Africa. In addition, among household-level factors, adolescents without access to water were more likely to adopt one to three preventive measures compared to those with access to water (52.2% vs. 47.9%, p &lt; 0.001). Therefore, to effectively prevent the spread of infection in South Africa, it is pertinent to address these household characteristics and encourage preventive measures tailored to these factors.

Seroprevalence and associated risk factors for Neospora caninum infection in dairy cattle in South Africa

Bovine neosporosis is a widespread parasitic disease associated with significant economic losses. Its effects on the reproductive performance of cows have resulted in losses that run into the hundreds of millions of US dollars in dairy industries in various countries (Reichel et al., Int J Parasitol 43:133–142, 2013). Due to outdated and scant information on the occurrence of Neospora caninum infection in South Africa, the study aimed to determine the seroprevalence and risk factors associated with infection in dairy cattle in South Africa. A total of 1401 blood samples were randomly collected from cattle on 48 dairy farms in seven of the nine provinces in South Africa. A close-ended questionnaire was used in a cross-sectional study to obtain farm-level and animal-level data. Serological testing was done using a commercial IDvet Screen® Neospora caninum Indirect ELISA. An overall seroprevalence, adjusted for test sensitivity and specificity, of 2.3% (95% CI, 1.3–4.1) was detected and 48% (23/48) of sampled farms had at least one animal testing positive. The highest seroprevalence of N. caninum was in the KwaZulu-Natal province with 7.5% (95% CI, 3.8–14.3), and the lowest in Western Cape with 0.1% (95% CI, 0–1.2). The highest within-farm seroprevalence of 25% was detected on a farm in the North West Province. In a multivariable logistic regression model, the odds of N. caninum seropositivity were higher in Holstein–Friesian cattle when compared to other breeds. Good hygiene was identified as a protective factor. Cattle left out on pasture had increased odds of testing positive for N. caninum compared to those that were penned. The odds of testing seropositive for N. caninum was higher on farms that practised segregation of cattle into different age groups. The purchase of replacement animals was a significant risk factor, as open herds had increased odds of N. caninum seropositivity. Cattle on farms that did not have a specific calving location were more likely to be seropositive. This is the first such study in South Africa and shows that N. caninum is widely distributed in the country at a low seroprevalence, but it may be a cause of concern on certain farms.

The role of new hepatitis B vaccines in South Africa.

Vaccination is key to eliminating hepatitis B virus infection in South Africa (SA). Despite introducing immunisation in 1995, as part of the expanded programme of immunisation (EPI), hepatitis B virus infection remains endemic, and EPI vaccine coverage is incomplete. In addition to infants, non-immune adults at risk of infection through their occupation or with behavioural risk factors should receive vaccination. SA has many individuals with diabetes mellitus (a prevalence of almost 13%), obesity, HIV (8.45 million) or older age (5 million >60 years old), associated with a poorer vaccine response. Recently two new hepatitis B vaccines have been licensed: HEPLISAV-B includes an adjuvant that improves immunogenicity and has shown improved vaccine response in individuals with HIV, old age or diabetes mellitus. PreHevbrio, which includes three hepatitis B surface protein domains, instead of one, may also be more immunogenic, although clinical study data are still limited. These two novel vaccines have not yet been investigated in children and licensed in SA. Should HEPLISAV-B become available in SA, it may be particularly valuable to target high-risk groups in the country, such as people living with HIV, who show a poor response to the currently licensed vaccine.

Assessing the impact of human behavior towards preventative measures on COVID-19 dynamics for Gauteng, South Africa: a simulation and forecasting approach

&lt;abstract&gt;&lt;p&gt;Globally, the COVID-19 pandemic has claimed millions of lives. In this study, we develop a mathematical model to investigate the impact of human behavior on the dynamics of COVID-19 infection in South Africa. Specifically, our model examined the effects of positive versus negative human behavior. We parameterize the model using data from the COVID-19 fifth wave of Gauteng province, South Africa, from May 01, 2022, to July 23, 2022. To forecast new cases of COVID-19 infections, we compared three forecasting methods: exponential smoothing (ETS), long short-term memory (LSTM), and gated recurrent units (GRUs), using the dataset. Results from the time series analysis showed that the LSTM model has better performance and is well-suited for predicting the dynamics of COVID-19 compared to the other models. Sensitivity analysis and numerical simulations were also performed, revealing that noncompliant infected individuals contribute more to new infections than those who comply. It is envisaged that the insights from this work can better inform public health policy and enable better projections of disease spread.&lt;/p&gt;&lt;/abstract&gt;

Modeling and analyzing COVID-19 infections in South Africa

In this paper, we present a mathematical model that incorporates seasonal variations in COVID-19 transmission within South Africa. By fitting the model to real-world data, we estimate its parameters and demonstrate its enhanced accuracy in describing the local infection dynamics. We analyze the basic reproduction number and establish threshold dynamics through theoretical analysis, alongside investigating its numerical relationship with specific parameters. Furthermore, we conduct an optimal control analysis to evaluate the impact of intervention strategies, including quarantine, vaccination and medical treatment, on COVID-19 spread. Our findings emphasize the effectiveness of combining all three interventions in reducing the number of exposed and infected individuals. We identify that implementing these interventions when the infected population is at its lowest yields optimal results.

The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review.

To determine the performance and reliability of diagnostic tests for the identification of SARS-CoV-2 infection in South Africa, we conducted a scoping review to identify published studies undertaken in the English language from March 2020 to August 2022 that evaluated the performance of antigen- and antibody-based diagnostic tests for SARS-CoV-2 in South Africa. We identified 17 relevant peer-reviewed articles; six reported on SARS-CoV-2 gene and/or antigen detection whilst 11 reported on antibody detection. Of the SARS-CoV-2 gene and/or antigen-based tests, sensitivity ranged from 40% to 100%, whilst for the antibody-based tests, sensitivity ranged from 13% to 100%. All tests evaluated were highly dependent on the stage of infection and the timing of sample collection. This scoping review demonstrated that no single SARS-CoV-2 gene and/or antigen- or antibody-based assay was sufficiently sensitive and specific simultaneously. The sensitivity of the tests was highly dependent on the timing of sample collection with respect to SARS-CoV-2 infection. In the case of SARS-CoV-2 gene and/or antigen detection, the earlier the collection of samples, the greater the sensitivity, while antibody detection tests showed better sensitivity using samples from later stages of infection.

Effect of implementation strategies on pre-exposure prophylaxis persistence among female sex workers in South Africa: an interrupted time series study

A disproportionate number of new HIV infections in South Africa are among female sex workers; pre-exposure prophylaxis (PrEP) for HIV prevention is freely available to female sex workers in the country, but unique barriers challenge PrEP persistence. TB HIV Care, a large South African non-profit organisation that provides daily oral PrEP (tenofovir disoproxil fumarate and emtricitabine), has implemented multiple strategies to improve PrEP persistence. We aimed to evaluate the effect of different implementation strategies on PrEP persistence in a large-scale real-world setting. In this interrupted time series study, we estimated level changes in 1-month oral PrEP persistence associated with roll-out of various implementation strategies among female sex workers across nine districts in South Africa. We used routinely collected data from TB HIV Care programme files from June 7, 2016, to April 30, 2021. Poisson regression of 1-month persistence was used to assess the effect of these strategies. In secondary analyses, we tested the association between each of the strategies and 4-month persistence. The median 1-month PrEP persistence for female sex workers was 33% (IQR 27-40). SMS support and refill reminders were associated with an 11% relative increase in 1-month persistence (risk ratio [RR] 1·11, 95% CI 1·02-1·26) and clinical mentoring for PrEP providers was associated with a 127% relative increase (RR 2·27, 95% CI 1·94-2·66) among female sex workers. The loyalty rewards programme was negatively associated with 1-month persistence (RR 0·71, 95% CI 0·67-0·83). Although clinical mentoring improved 4-month persistence, SMS support text messages had no significant effect. Identification and subsequent use of clinical mentoring for PrEP providers and SMS support and refill reminders might improve the usefulness of PrEP overall to prevent new HIV infections among female sex workers. PrEP persistence remains an important issue, and strategies to build on our findings are needed. National Institute of Mental Health and National Institute of Allergy and Infectious Diseases.

Transient increased risk of influenza infection following RSV infection in South Africa: findings from the PHIRST study, South Africa, 2016–2018

BackgroundLarge-scale prevention of respiratory syncytial virus (RSV) infection may have ecological consequences for co-circulating pathogens, including influenza. We assessed if and for how long RSV infection alters the risk for subsequent influenza infection.MethodsWe analysed a prospective longitudinal cohort study conducted in South Africa between 2016 and 2018. For participating households, nasopharyngeal samples were taken twice weekly, irrespective of symptoms, across three respiratory virus seasons, and real-time polymerase chain reaction (PCR) was used to identify infection with RSV and/or influenza. We fitted an individual-level hidden Markov transmission model in order to estimate RSV and influenza infection rates and their interdependence.ResultsOf a total of 122,113 samples collected, 1265 (1.0%) were positive for influenza and 1002 (0.8%) positive for RSV, with 15 (0.01%) samples from 12 individuals positive for both influenza and RSV. We observed a 2.25-fold higher incidence of co-infection than expected if assuming infections were unrelated. We estimated that infection with influenza is 2.13 (95% CI 0.97–4.69) times more likely when already infected with, and for a week following, RSV infection, adjusted for age. This equates to 1.4% of influenza infections that may be attributable to RSV in this population. Due to the local seasonality (RSV season precedes the influenza season), we were unable to estimate changes in RSV infection risk following influenza infection.ConclusionsWe find no evidence to suggest that RSV was associated with a subsequent reduced risk of influenza infection. Instead, we observed an increased risk for influenza infection for a short period after infection. However, the impact on population-level transmission dynamics of this individual-level synergistic effect was not measurable in this setting.

Fabaceae: South African Medicinal Plant Species Used in the Treatment and Management of Sexually Transmitted and Related Opportunistic Infections Associated with HIV-AIDS

The use of medicinal plants, particularly in the treatment of sexually transmitted and related infections, is ancient. These plants may well be used as alternative and complementary medicine to a variety of antibiotics that may possess limitations mainly due to an emerging enormous antimicrobial resistance. Several computerized database literature sources such as ScienceDirect, Scopus, Scielo, PubMed, and Google Scholar were used to retrieve information on Fabaceae species used in the treatment and management of sexually transmitted and related infections in South Africa. The other information was sourced from various academic dissertations, theses, and botanical books. A total of 42 medicinal plant species belonging to the Fabaceae family, used in the treatment of sexually transmitted and related opportunistic infections associated with HIV-AIDS, have been documented. Trees were the most reported life form, yielding 47.62%, while Senna and Vachellia were the frequently cited genera yielding six and three species, respectively. Peltophorum africanum Sond. was the most preferred medicinal plant, yielding a frequency of citation of 14, while Vachellia karoo (Hayne) Banfi and Glasso as well as Elephantorrhiza burkei Benth. yielded 12 citations each. The most frequently used plant parts were roots, yielding 57.14%, while most of the plant species were administered orally after boiling (51.16%) until the infection subsided. Amazingly, many of the medicinal plant species are recommended for use to treat impotence (29.87%), while most common STI infections such as chlamydia (7.79%), gonorrhea (6.49%), syphilis (5.19%), genital warts (2.60%), and many other unidentified STIs that may include “Makgoma” and “Divhu” were less cited. Although there are widespread data on the in vitro evidence of the use of the Fabaceae species in the treatment of sexually transmitted and related infections, there is a need to explore the in vivo studies to further ascertain the use of species as a possible complementary and alternative medicine to the currently used antibiotics in both developing and underdeveloped countries. Furthermore, the toxicological profiles of many of these studies need to be further explored. The safety and efficacy of over-the-counter pharmaceutical products developed using these species also need to be explored.

The Roles of Youth in Intimate Partner Relationships and the Perceived Risk of HIV Infection in South Africa

Background: Young people in South Africa face multiple developmental challenges, including violence and HIV infection. Objective: This study examines the various roles of youth in violent intimate relationships (IPV) and its association with the perceived risk of HIV infection. Results from this study could assist in youth development programmes to increase HIV testing, as well as inform modifications to the South African Domestic Violence Act (No. 116 of 1998), which addresses all forms of intimate partner violence in the country. Methods: The study uses data from the South African National HIV Prevalence, HIV Incidence, Behaviour and Communication Survey (SABSSM) 2017. The study population is youth (15-24 years old) who responded to a question on their perceived risk of being infected with HIV. A weighted sample (N) of 1,301,550 youth is included. The main independent variable is the 'role in IPV', and the study controls for the demographic, socioeconomic, and HIV knowledge and sexual behaviours of youth. Cross-tabulations and a multivariate binary logistic regression model are used to determine the relationship between controls and the outcome. Results: About 20% of youth perceive themselves at risk of being with HIV. Their reasons for believing this are because they are sexually active, do not use condoms consistently, and do not trust their partners. Only about 4% of IPV perpetrators, compared to 23.71% of victims and 23.16% of bidirectional youth, think it is likely they will get infected with HIV. The odds of perceiving themselves at risk are higher (with p-values&lt;0.05) for victims (OR=1.21), 20-24 years old (OR=1.35), female (OR=1.25), those who responded do not think condoms reduce the risk of HIV (OR=1.49) and those who do not use condoms (OR=1.44) among others. Conclusion: IPV behaviours are associated with perceived HIV risk among young people in South Africa. For perception to change and allow youth to adopt protective behaviours against HIV, there is a need for policy to target the different roles of youth.

Greener Neighbourhoods Show Resilience to the Spread but Not Severity of COVID-19 Infection in South Africa

The outbreak of COVID-19 quickly spread around the globe, with staggering infection and mortality rates. Given the reported benefits of greenness to human health, we hypothesized that greener neighbourhoods would suffer less from COVID-19 infection and severity than not. We modelled COVID-19 infection and severity in South Africa by fitting Generalized Linear Mixed Effects models to various socio-demographic and greenness data (EVI, i.e., Enhanced Vegetation Index, and tree and grass covers) collected from January 2020 to June 2022 at local municipalities, Wards, and districts scales. We found that income level showed a significant negative association with COVID-19 prevalence at the Ward level, suggesting that poorer neighbourhoods are more susceptible to COVID-19 infection. We also found that EVI and tree cover consistently showed a significant negative correlation with COVID-19 infection rate, irrespective of the scale of analysis, whereas grass cover showed a similar pattern but only at the Ward scale. Finally, we found that neither EVI, grass cover, nor tree cover showed a significant association with COVID-19 severity. Overall, greener neighbourhoods show greater resilience to the spread of COVID-19, suggesting that exposure to greenness may boost natural killer cells in the human body, thus reinvigorating our defence system against infections. Our results re-enforced the need to establish and preserve greens paces particularly in the developing world, given their ability to buffer the spread of COVID-19.

Prevalence and risk factors of M tuberculosis infection in young people across 14 communities in Zambia and South Africa.

From 2018-2021 the TB Reduction through Expanded Antiretroviral Treatment and TB Screening (TREATS) project took place in 21 Zambian and South African communities. The TREATS Incidence of TB Infection Cohort Study was conducted in adolescents and young people (AYP), aged 15-24 years in 14 communities. We describe the baseline prevalence and risk factors of Mycobacterium tuberculosis (M. tuberculosis) infection among this cohort and explore the quantitative QFT-Plus interferon gamma (IFN-γ) responses. A random sample of approximately 300 AYP per community were recruited and information on TB/HIV risk factors, TB symptoms and social mixing patterns collected. QuantiFERON TB Gold Plus assay (QFT-Plus) was used to detect M. tuberculosis infection, following manufacturer's instructions. Logistic regression was used to determine factors associated with infection. 5577 eligible AYP were invited to participate across both countries, with 4648 enrolled. QFT-Plus results were available for 4529: 2552(Zambia) and 1977(South Africa). Overall, 47.6% (2156/4529) AYP had positive QFT-Plus results, the prevalence of infection in South Africa being twice that in Zambia (64.7% (1280/1977) vs 34.3% (867/2552) p<0.001). Infection was associated with age, household contact with TB and alcohol in Zambia but showed no associations in South Africa. The antigen tube differential (TB2-TB1>0.6 IU/ml) of the assay at baseline showed no evidence of association with recent TB exposure. The high prevalence of infection in AYP warrants urgent action to address TB control, especially in South Africa. Further research is required to delineate antigen tube responses of the QFT-Plus assay more precisely to fully realise the benefit of the additional TB2 tube in high TB/HIV burden settings.

Doxycycline post-exposure prophylaxis for sexually transmitted infections in South Africa.

South Africa has a large burden of bacterial sexually transmitted infections (STIs) with high rates among men who have sex with men (MSM). Randomised controlled trials have recently demonstrated high effectiveness of doxycycline post-exposure prophylaxis (PEP) for prevention of bacterial STIs in MSM, with 70% - 85% reductions in Chlamydia trachomatis infection and syphilis, and approximately 50% reduction in Neisseria gonorrhoeae infection. Doxycycline PEP was not demonstrated to be effective in reducing C. trachomatis and N. gonorrhoeae infection among Kenyan cisgender women. Although no worrisome trends in antimicrobial resistance (AMR) were observed in the trials, important concerns remain about doxycycline PEP and AMR development in STIs, other pathogens, commensals, and the microbiome. Tetracycline resistance in N. gonorrhoeae is already widespread in South Africa, but emergence of AMR in other STIs would be concerning. Larger sample sizes of doxycycline PEP users with longer follow-up time are needed to understand the impact that doxycycline PEP may have on AMR at individual and population level. In this opinion article, we weigh the benefits of doxycycline PEP for prevention of bacterial STIs against the existing AMR concerns and data gaps in the South African context. Based on the current evidence, we conclude that it would be reasonable to offer doxycycline PEP to high-risk MSM on a case-by-case basis, provided that it is offered by experienced sexual health clinicians in settings that have access to diagnostic STI testing and ongoing AMR surveillance.

The molecular epidemiology and antimicrobial resistance of Staphylococcus pseudintermedius canine clinical isolates submitted to a veterinary diagnostic laboratory in South Africa.

Staphylococcus pseudintermedius is an important cause of clinical infections in small-animal-veterinary medicine. Evolutionary changes of strains using multilocus sequence typing (MLST) have been observed among S. pseudintermedius in European countries and the United States. However, there are limited or no studies on the detection of methicillin resistant Staphylococcus pseudintermedius (MRSP) and predominating MLST strains in South Africa. Therefore, this study aimed to determine the molecular epidemiology of S. pseudintermedius in South Africa. Twenty-six, non-duplicate, clinical isolates from dogs were obtained as convenience samples from four provinces in South Africa. The Kirby Bauer disk diffusion test was used to determine antimicrobial susceptibility. We used Resfinder and the Comprehensive Antibiotic Resistance Database (CARD) to detect antimicrobial resistance genes. Virulence genes were identified using the virulence factor database and Basic Local Alignment Search Tool (BLASTN) on Geneious prime. geoBURST analysis was used to study relationships between MLST. Finally, the maximum likelihood phylogeny was determined using Randomized Axelerated Maximum Likelihood (RAxML). Twenty-three isolates were confirmed as S. pseudintermedius of which 14 were MRSP. In addition to β-lactam antimicrobials, MRSP isolates were resistant to tetracycline (85.7%), doxycycline (92.8%), kanamycin (92.8%), and gentamicin (85.7%). The isolates harbored antimicrobial resistance genes (tetM, ermB, drfG, cat, aac(6')-Ie-aph(2")-Ia, ant(6)-Ia, and aph(3')-III) and virulence genes (AdsA, geh, icaA, and lip). MLST analysis showed that ST2228, ST2229, ST2230, ST2231, ST2232, ST2318, ST2326 and ST2327 are unique sequence types in South Africa. Whereas, previously reported major STs including ST45, ST71, ST181, ST551 and ST496 were also detected. The geoBURST and phylogenetic analysis suggests that the isolates in South Africa are likely genetically related to isolates identified in other countries. Highly resistant MRSP strains (ST496, ST71, and ST45) were reported that could present challenges in the treatment of canine infections in South Africa. Hence, we have gained a better understanding of the epidemiology of MRSP in the African continent, the genes involved in resistance and virulence factors associated with these organisms.

Tuberculosis risk factors in South Africa, 2008 to 2017: A Generalised Estimating Equations approach

&#x0D; Background: Although, death due to tuberculosis has been on the decline. In 2016, 124 000 people died of tuberculosis in South Africa and the disease was declared the leading cause of death by Statistics South Africa. Continued efforts to use research to create a nation free of tuberculosis are underway. &#x0D; Methods: A repeated measures investigation was performed with the aim of identifying the persistent predictors and the long-term patterns of tuberculosis infection in South Africa for the period 2008 to 2017. The most suitable Generalised Estimating Equations that describe the population average probability of infection over time were applied to a sample of respondents taken from the National Income Dynamics Survey data, wave 1 to wave 5. The response variable was binary with the outcome of interest being the respondents that self-reported to have been diagnosed with tuberculosis. To improve estimation efficiency, the best working correlation matrix for this data was selected. &#x0D; Results: We used a sample of 8510 individuals followed for five waves, of these, 3.7%, 2.54%, 4.15%, 5.72% and 5.99% for waves 1, 2, 3, 4 and 5 respectively, reported to have been diagnosed with tuberculosis. Findings revealed that the independent working correlation matrix with the model-based standard error estimates gave the most robust results for the repeated measures tuberculosis data in South Africa. Furthermore, over the years, the average probability of being diagnosed with tuberculosis was positively associated with being single, male, middle-aged (30- 59 years), black African, unemployed, smoking, lower education levels, lack of regular exercise, asthma, suffering from other diseases, lack of access to improved sanitation, lower household income and expenditure. &#x0D; Conclusion: The probabilities of tuberculosis infection are independent within individuals over time. The inequalities in socioeconomic status in South Africa caused the poor to be more at risk of tuberculosis over time from 2008 to 2017. &#x0D;

Performance of rapid antigen tests in identifying Omicron BA.4 and BA.5 infections in South Africa.

Concerns around accuracy and performance of rapid antigen tests continue to be raised with the emergence of new SARS-CoV-2 variants. To evaluate the performance of two widely used SARS-CoV-2 rapid antigen tests during BA.4/BA.5 SARS-CoV-2 wave in South Africa (May - June 2022). A prospective field evaluation compared the SARS-CoV-2 Antigen Rapid test from Hangzhou AllTest Biotech (nasal swab) and the Standard Q COVID-19 Rapid Antigen test from SD Biosensor (nasopharyngeal swab) to the Abbott RealTime SARS-CoV-2 assay (nasopharyngeal swab) on samples collected from 540 study participants. Overall 28.52% (154/540) were SARS-CoV-2 RT-PCR positive with median cycle number value of 12.30 (IQR 9.30-19.40). Out of the 99 successfully sequenced SARS-CoV-2 positive samples, 18 were classified as BA.4 and 56 were classified as BA.5. The overall sensitivities of the AllTest SARS-CoV-2 Ag test and Standard Q COVID-19 Ag test were 73.38% (95% CI 65.89-79.73) and 74.03% (95% CI 66.58-80.31) and their specificities were 97.41% (95% CI 95.30-98.59) and 99.22% (95% CI 97.74-99.74) respectively. Sensitivity was >90% when the cycle number value was <20. The sensitivity of both rapid tests was >90% in samples infected with Omicron sub-lineage BA.4 and BA.5. Accuracy of tested rapid antigen tests that target the nucleocapsid SARS-CoV-2 protein, were not adversely affected by BA.4 and BA.5 Omicron sub-variants.

Protective factors for adolescent sexual risk behaviours and experiences linked to HIV infection in South Africa: a three-wave longitudinal analysis of caregiving, education, food security, and social protection

BackgroundStructural interventions are endorsed to enhance biomedical and behavioural HIV prevention programmes for adolescents. Aiming to inform future interventions, we evaluated longitudinal associations between six protective factors that link closely to existing structural HIV prevention interventions, and five sexual risk behaviours for HIV transmission in a cohort of adolescents in South Africa.MethodsWe used three rounds of data between 2014–2018 on 1046 adolescents living with HIV and 473 age-matched community peers in South Africa’s Eastern Cape (Observations = 4402). We estimated sex-specific associations between six time-varying protective factors − number of social grants, education enrolment, days with enough food, caregiver supervision, positive caregiving, and adolescent-caregiver communication; and five HIV risk behaviours − multiple sexual partners, transactional sex, age-disparate sex, condomless sex, and sex on substances. HIV risk behaviours were analysed separately in multivariable random effects within-between logistic regression models that accounted for correlation of repeated observations on the same individual. We calculated prevalence ratios (PR), contrasting adjusted probabilities of HIV risk behaviours at ‘No’ and ‘Yes’ for education enrolment, and average and maximum values for the other five protective factors.ResultsThe sample mean age was 15.29 (SD: 3.23) years and 58% were girls. Among girls, within-individuals, increases from mean to maximum scores in positive caregiving were associated with lower probability of transactional sex (PR = 0.79; 95%CI = 0.67–0.91); in caregiver supervision were associated with lower probability of transactional sex (PR = 0.75; 95%CI = 0.66–0.84), and age-disparate sex (PR = 0.84; 95%CI = 0.73–0.95); in adolescent-caregiver communication were associated with higher probability of transactional sex (PR = 1.70; 95%CI = 1.08–2.32); and in days with enough food at home were associated with lower probability of multiple sexual partners (PR = 0.89; 95%CI = 0.81–0.97), and transactional sex (PR = 0.82; 95%CI = 0.72–0.92). Change from non-enrolment in education to enrolment was associated with lower probability of age-disparate sex (PR = 0.49; 95%CI = 0.26–0.73). Between-individuals, relative to mean caregiver supervision scores, maximum scores were associated with lower probability of multiple sexual partners (PR = 0.59; 95%CI = 0.46–0.72), condomless sex (PR = 0.80; 95%CI = 0.69–0.91), and sex on substances (PR = 0.42; 95%CI = 0.26–0.59); and relative to non-enrolment, education enrolment was associated with lower probability of condomless sex (PR = 0.59; 95%CI = 0.39–0.78). Among boys, within-individuals, increases from mean to maximum scores in positive caregiving were associated with lower probability of transactional sex (PR = 0.77; 95%CI = 0.59–0.96), and higher probability of condomless sex (PR = 1.26; 95%CI = 1.08–1.43); in caregiver supervision were associated with lower probability of multiple sexual partners (PR = 0.73; 95%CI = 0.64–0.82), transactional sex (PR = 0.63; 95%CI = 0.50–0.76), age-disparate sex (PR = 0.67; 95%CI = 0.49–0.85), and sex on substances (PR = 0.61; 95%CI = 0.45–0.78), and in days with enough food at home were associated with lower probability of transactional sex (PR = 0.91; 95%CI = 0.84–0.98).ConclusionEffective structural interventions to improve food security and education enrolment among adolescent girls, and positive and supervisory caregiving among adolescent girls and boys are likely to translate into crucial reductions in sexual risk behaviours linked to HIV transmission in this population.

The Importance of the Individual in PrEP Uptake: Multilevel Correlates of PrEP Uptake Among Adolescent Girls and Young Women in Tshwane, South Africa.

Adolescent girls and young women (AGYW) account for 25% of new HIV infections in South Africa. Pre-exposure prophylaxis (PrEP) is approved by the South African Government, but the factors that promote PrEP uptake among AGYW are not well understood. This study examines multilevel factors associated with PrEP uptake among AGYW in six clinic catchment areas in Tshwane (Pretoria), South Africa. After consent/assent, PrEP-eligible AGYW (n = 448) completed a questionnaire assessing factors at the individual, network/interpersonal, and community levels and were prescribed PrEP in study clinics, if interested. A multivariable model, adjusting for clustering, assessed factors associated with PrEP uptake over a 9-month period. At the individual level, multiple partners in the past 3 months (OR = 0.47), perceived risk of HIV (OR = 0.71), and PrEP-related shame (OR = 0.63) were correlated with lower odds of PrEP uptake (ps ≤ 0.05). The findings highlight modifiable factors that should be addressed to support PrEP uptake efforts.