Point-of-Care Tenofovir Urine Testing for the Prediction of Treatment Failure and Drug Resistance During Initial Treatment for Human Immunodeficiency Virus Type 1 (HIV-1) Infection.

BACKGROUND: Viral rebound during antiretroviral treatment (ART) is most often driven by suboptimal adherence in the absence of drug resistance. We assessed the diagnostic performance of point-of-care (POC) tenofovir (TFV) detection in urine for the prediction of viral rebound and drug resistance during ART. METHODS: We performed a nested case-control study within the ADVANCE randomized clinical trial (NCT03122262) in Johannesburg, South Africa. Adults with human immunodeficiency virus (HIV) and newly initiating ART were randomized to receive either dolutegravir or efavirenz, tenofovir disoproxil fumarate or alafenamide, and emtricitabine. All participants with rebound ≥200 copies/mL between 24 and 96 weeks of follow-up were selected as cases and matched to controls with virological suppression <50 copies/mL. Rapid POC urine-TFV detection was performed retrospectively. RESULTS: We included 281 samples from 198 participants. Urine-TFV was detectable in 30.7% (70/228) of cases and in 100% (53/53) of controls. Undetectable urine-TFV predicted rebound with a sensitivity of 69% [95% confidence interval {CI}: 63-75] and specificity of 100% [93-100]. In cases with virological failure and sequencing data (n = 42), NRTI drug resistance was detected in 50% (10/20) of cases with detectable urine-TFV versus in 8.3% (2/24) of cases with undetectable urine-TFV. Detectable urine-TFV predicted NRTI resistance (odds ratio [OR] 10.4 [1.8-114.4] P = .005) with a sensitivity of 83% [52-98] and specificity of 69% [50-84]. CONCLUSIONS: POC objective adherence testing using a urine-TFV test predicted viral rebound with high specificity. In participants with rebound, urine-TFV testing predicted the selection of drug resistance. Objective adherence testing may be used to rapidly provide insight into adherence, suppression, and drug resistance during ART.

Unmasking a silent killer: Prevalence of diagnosed and undiagnosed diabetes mellitus among people living with HIV in rural South Africa.

OBJECTIVES: To document the prevalence of impaired glucose tolerance (IGT) and undiagnosed diabetes mellitus (DM) and to identify factors associated with undiagnosed DM in people living with HIV (PLWH). METHODS: Cross-sectional study performed at Ndlovu Medical Center, Limpopo, South Africa including PLWH aged ≥18 years. Between August and November 2017, 356 HIV-positive participants were included. Information was collected on socio-demographics, DM symptoms and risk factors for DM. IGT and DM were diagnosed using random plasma glucose and/or HbA1c. Factors associated with undiagnosed DM were assessed by comparing participants with newly diagnosed DM to participants without DM. RESULTS: IGT was diagnosed in 172 (48.3%) participants. Twenty-nine (8.1%) participants met the definition of DM, of whom 17 (58.6%) were newly diagnosed. Compared to participants without DM, participants with DM were on average 5 years older, were more likely to have a positive family history for DM, were less physically active and had higher systolic blood pressure, body mass index and waist circumference. Factors associated with undiagnosed DM included age ≥45 years (odds ratio [OR] = 3.59) and physical inactivity (OR = 3.17). CONCLUSIONS: The prevalence of IGT and DM among PLWH is high and more than half of DM cases were undiagnosed. Regular screening for DM in PLWH is recommended, especially in an ageing population with additional cardiovascular disease risk factors.

Prevalence, incidence and recurrence of sexually transmitted infections in HIV-negative adult women in a rural South African setting.

OBJECTIVE: Sexually transmitted infections (STIs), including syphilis, chlamydia, gonorrhoea and trichomoniasis, are of global public health concern. While STI incidence rates in sub-Saharan Africa are high, longitudinal data on incidence and recurrence of STIs are scarce, particularly in rural areas. We determined the incidence rates of curable STIs in HIV-negative women during 96 weeks in a rural South African setting. METHODS: We prospectively followed participants enrolled in a randomised controlled trial to evaluate the safety and efficacy of a dapivirine-containing vaginal ring for HIV prevention in Limpopo province, South Africa. Participants were included if they were female, aged 18-45, sexually active, not pregnant and HIV-negative. Twelve-weekly laboratory STI testing was performed during 96 weeks of follow-up. Treatment was provided based on vaginal discharge by physical examination or after a laboratory-confirmed STI. RESULTS: A total of 119 women were included in the study. Prevalence of one or more STIs at baseline was 35.3%. Over 182 person-years at risk (PYAR), a total of 149 incident STIs were diagnosed in 75 (65.2%) women with incidence rates of 45.6 events/PYAR for chlamydia, 27.4 events/100 PYAR for gonorrhoea and 8.2 events/100 PYAR for trichomoniasis. Forty-four women developed ≥2 incident STIs. Risk factors for incident STI were in a relationship ≤3 years (adjusted hazard ratio [aHR]: 1.86; 95% confidece interval [CI]: 1.04-2.65) and having an STI at baseline (aHR: 1.66; 95% CI: 1.17-2.96). Sensitivity and specificity of vaginal discharge for laboratory-confirmed STI were 23.6% and 87.7%, respectively. CONCLUSION: This study demonstrates high STI incidence in HIV-negative women in rural South Africa. Sensitivity of vaginal discharge was poor and STI recurrence rates were high, highlighting the shortcomings of syndromic management in the face of asymptomatic STIs in this setting.

Predictors of Treatment Adherence and Virological Failure Among People Living with HIV Receiving Antiretroviral Therapy in a South African Rural Community: A Sub-study of the ITREMA Randomised Clinical Trial.

A large proportion of people living with HIV (PLHIV) in sub-Saharan Africa reside in rural areas. Knowledge of enablers and barriers of adherence to antiretroviral treatment (ART) in these populations is limited. We conducted a cohort study of 501 adult PLHIV on ART at a rural South African treatment facility as a sub-study of a clinical trial (ClinicalTrials.gov NCT03357588). Socio-economic, psychosocial and behavioral characteristics were assessed as covariates of self-reported adherence difficulties, suboptimal pill count adherence and virological failure during 96 weeks of follow-up. Male gender was an independent risk factor for all outcomes. Food insecurity was associated with virological failure in males. Depressive symptoms were independently associated with virological failure in both males and females. Household income and task-oriented coping score were protective against suboptimal pill-count adherence. These results underscore the impact of low household income, food insecurity and depression on outcomes of ART in rural settings and confirm other previously described risk factors. Recognition of these factors and targeted adherence support strategies may improve patient health and treatment outcomes.

2021 update to HIV-TRePS: a highly flexible and accurate system for the prediction of treatment response from incomplete baseline information in different healthcare settings.

OBJECTIVES: With the goal of facilitating the use of HIV-TRePS to optimize therapy in settings with limited healthcare resources, we aimed to develop computational models to predict treatment responses accurately in the absence of commonly used baseline data. METHODS: Twelve sets of random forest models were trained using very large, global datasets to predict either the probability of virological response (classifier models) or the absolute change in viral load in response to a new regimen (absolute models) following virological failure. Two 'standard' models were developed with all baseline variables present and 10 others developed without HIV genotype, time on therapy, CD4 count or any combination of the above. RESULTS: The standard classifier models achieved an AUC of 0.89 in cross-validation and independent testing. Models with missing variables achieved AUC values of 0.78-0.90. The standard absolute models made predictions that correlated significantly with observed changes in viral load with a mean absolute error of 0.65 log10 copies HIV RNA/mL in cross-validation and 0.69 log10 copies HIV RNA/mL in independent testing. Models with missing variables achieved values of 0.65-0.75 log10 copies HIV RNA/mL. All models identified alternative regimens that were predicted to be effective for the vast majority of cases where the new regimen prescribed in the clinic failed. All models were significantly better predictors of treatment response than genotyping with rules-based interpretation. CONCLUSIONS: These latest models that predict treatment responses accurately, even when a number of baseline variables are not available, are a major advance with greatly enhanced potential benefit, particularly in resource-limited settings. The only obstacle to realizing this potential is the willingness of healthcare professions to use the system.

Virological suppression and clinical management in response to viremia in South African HIV treatment program: A multicenter cohort study.

BACKGROUND: Uptake of antiretroviral treatment (ART) is expanding rapidly in low- and middle-income countries (LMIC). Monitoring of virological suppression is recommended at 6 months of treatment and annually thereafter. In case of confirmed virological failure, a switch to second-line ART is indicated. There is a paucity of data on virological suppression and clinical management of patients experiencing viremia in clinical practice in LMIC. We report a large-scale multicenter assessment of virological suppression over time and management of viremia under programmatic conditions. METHODS AND FINDINGS: Linked medical record and laboratory source data from adult patients on first-line ART at 52 South African centers between 1 January 2007 and 1 May 2018 were studied. Virological suppression, switch to second-line ART, death, and loss to follow-up were analyzed. Multistate models and Cox proportional hazard models were used to assess suppression over time and predictors of treatment outcomes. A total of 104,719 patients were included. Patients were predominantly female (67.6%). Median age was 35.7 years (interquartile range [IQR]: 29.9-43.0). In on-treatment analysis, suppression below 1,000 copies/mL was 89.0% at month 12 and 90.4% at month 72. Suppression below 50 copies/mL was 73.1% at month 12 and 77.5% at month 72. Intention-to-treat suppression was 75.0% and 64.3% below 1,000 and 50 copies/mL at month 72, respectively. Viremia occurred in 19.8% (20,766/104,719) of patients during a median follow-up of 152 (IQR: 61-265) weeks. Being male and below 35 years of age and having a CD4 count below 200 cells/µL prior to start of ART were risk factors for viremia. After detection of viremia, confirmatory testing took 29 weeks (IQR: 16-54). Viral resuppression to below 1,000 copies/mL without switch of ART occurred frequently (45.6%; 6,030/13,210) but was associated with renewed viral rebound and switch. Of patients with confirmed failure who remained in care, only 41.5% (1,872/4,510) were switched. The median time to switch was 68 weeks (IQR: 35-127), resulting in 12,325 person-years spent with a viral load above 1,000 copies/mL. Limitations of this study include potential missing data, which is in part addressed by the use of cross-matched laboratory source data, and the possibility of unmeasured confounding. CONCLUSIONS: In this study, 90% virological suppression below the threshold of 1,000 copies/mL was observed in on-treatment analysis. However, this target was not met at the 50-copies/mL threshold or in intention-to-treat analysis. Clinical management in response to viremia was profoundly delayed, prolonging the duration of viremia and potential for transmission. Diagnostic tools to establish the cause of viremia are urgently needed to accelerate clinical decision-making.

Safety and Efficacy of a Dapivirine Vaginal Ring for HIV Prevention in Women.

BACKGROUND: The incidence of human immunodeficiency virus (HIV) infection remains high among women in sub-Saharan Africa. We evaluated the safety and efficacy of extended use of a vaginal ring containing dapivirine for the prevention of HIV infection in 1959 healthy, sexually active women, 18 to 45 years of age, from seven communities in South Africa and Uganda. METHODS: In this randomized, double-blind, placebo-controlled, phase 3 trial, we randomly assigned participants in a 2:1 ratio to receive vaginal rings containing either 25 mg of dapivirine or placebo. Participants inserted the rings themselves every 4 weeks for up to 24 months. The primary efficacy end point was the rate of HIV type 1 (HIV-1) seroconversion. RESULTS: A total of 77 participants in the dapivirine group underwent HIV-1 seroconversion during 1888 person-years of follow-up (4.1 seroconversions per 100 person-years), as compared with 56 in the placebo group who underwent HIV-1 seroconversion during 917 person-years of follow-up (6.1 seroconversions per 100 person-years). The incidence of HIV-1 infection was 31% lower in the dapivirine group than in the placebo group (hazard ratio, 0.69; 95% confidence interval [CI], 0.49 to 0.99; P=0.04). There was no significant difference in efficacy of the dapivirine ring among women older than 21 years of age (hazard ratio for infection, 0.63; 95% CI, 0.41 to 0.97) and those 21 years of age or younger (hazard ratio, 0.85; 95% CI, 0.45 to 1.60; P=0.43 for treatment-by-age interaction). Among participants with HIV-1 infection, nonnucleoside reverse-transcriptase inhibitor resistance mutations were detected in 14 of 77 participants in the dapivirine group (18.2%) and in 9 of 56 (16.1%) in the placebo group. Serious adverse events occurred more often in the dapivirine group (in 38 participants [2.9%]) than in the placebo group (in 6 [0.9%]). However, no clear pattern was identified. CONCLUSIONS: Among women in sub-Saharan Africa, the dapivirine ring was not associated with any safety concerns and was associated with a rate of acquisition of HIV-1 infection that was lower than the rate with placebo. (Funded by the International Partnership for Microbicides; ClinicalTrials.gov number, NCT01539226 .).

Hypertension in a rural community in South Africa: what they know, what they think they know and what they recommend.

BACKGROUND: Hypertension is one of the most important risk factors for cardiovascular disease and has a high prevalence in South Africa and other low- and middle-income countries. However, awareness of hypertension has been reported to be low. Health programmes can increase awareness of hypertension and its causes, but hinge on the knowledge and perception of the targeted community. Therefore, this study investigated knowledge on and perceptions about hypertension of community members in a rural area in Limpopo, South Africa with the aim to increase awareness of hypertension and cardiovascular disease in the local population. METHODS: Using a mixed methods study approach, 451 participants of the Ndlovu Cohort Study, attending a follow-up visit between August 2017 and January 2018, completed a questionnaire on cardiovascular risk perception. A knowledge score was calculated for all participants. Sixty participants were invited to participate in six focus group discussions, of which 56 participated. Audio recordings were transcribed verbatim, transcripts coded, and thematic analysis of the data undertaken to obtain an understanding of knowledge and perception of hypertension in the community. RESULTS: Most members of the community seemed to have intermediate (74.3%) or good (14.0%) knowledge of hypertension based on the knowledge score, and only 11.8% of the population had poor knowledge. The risk factors of hypertension seemed to be well known in the community. Poverty was identified as a major vulnerability in this community limiting choices for healthy lifestyles such as nutritious foods, recreational physical activity and accessing health care timely. Participants proposed community-based activities as an effective way to reach out to community members for prevention and management of hypertension. CONCLUSION: This study highlights the need for improved health promotion efforts to increase knowledge of hypertension in rural communities, and to address poverty as a major obstacle to healthy life-style choices.

2018 update to the HIV-TRePS system: the development of new computational models to predict HIV treatment outcomes, with or without a genotype, with enhanced usability for low-income settings.

Objectives: Optimizing antiretroviral drug combination on an individual basis can be challenging, particularly in settings with limited access to drugs and genotypic resistance testing. Here we describe our latest computational models to predict treatment responses, with or without a genotype, and compare their predictive accuracy with that of genotyping. Methods: Random forest models were trained to predict the probability of virological response to a new therapy introduced following virological failure using up to 50 000 treatment change episodes (TCEs) without a genotype and 18 000 TCEs including genotypes. Independent data sets were used to evaluate the models. This study tested the effects on model accuracy of relaxing the baseline data timing windows, the use of a new filter to exclude probable non-adherent cases and the addition of maraviroc, tipranavir and elvitegravir to the system. Results: The no-genotype models achieved area under the receiver operator characteristic curve (AUC) values of 0.82 and 0.81 using the standard and relaxed baseline data windows, respectively. The genotype models achieved AUC values of 0.86 with the new non-adherence filter and 0.84 without. Both sets of models were significantly more accurate than genotyping with rules-based interpretation, which achieved AUC values of only 0.55-0.63, and were marginally more accurate than previous models. The models were able to identify alternative regimens that were predicted to be effective for the vast majority of cases in which the new regimen prescribed in the clinic failed. Conclusions: These latest global models predict treatment responses accurately even without a genotype and have the potential to help optimize therapy, particularly in resource-limited settings.

An update to the HIV-TRePS system: the development and evaluation of new global and local computational models to predict HIV treatment outcomes, with or without a genotype.

OBJECTIVES: Optimizing antiretroviral drug combination on an individual basis in resource-limited settings is challenging because of the limited availability of drugs and genotypic resistance testing. Here, we describe our latest computational models to predict treatment responses, with or without a genotype, and compare the potential utility of global and local models as a treatment tool for South Africa. METHODS: Global random forest models were trained to predict the probability of virological response to therapy following virological failure using 29 574 treatment change episodes (TCEs) without a genotype, 3179 of which were from South Africa and were used to develop local models. In addition, 15 130 TCEs including genotypes were used to develop another set of models. The 'no-genotype' models were tested with an independent global test set (n = 1700) plus a subset from South Africa (n = 222). The genotype models were tested with 750 independent cases. RESULTS: The global no-genotype models achieved area under the receiver-operating characteristic curve (AUC) values of 0.82 and 0.79 with the global and South African tests sets, respectively, and the South African models achieved AUCs of 0.70 and 0.79. The genotype models achieved an AUC of 0.84. The global no-genotype models identified more alternative, locally available regimens that were predicted to be effective for cases that failed their new regimen in the South African clinics than the local models. Both sets of models were significantly more accurate predictors of outcomes than genotyping with rules-based interpretation. CONCLUSIONS: These latest global models predict treatment responses accurately even without a genotype, out-performed the local South African models and have the potential to help optimize therapy, particularly in resource-limited settings.

Carotid Intima Media Thickness in Mainly Female HIV-Infected Subjects in Rural South Africa: Association With Cardiovascular but Not HIV-Related Factors.

BACKGROUND: In sub-Saharan Africa, the number of persons living with human immunodeficiency virus (HIV) has increased immensely. In parallel, rates of noncommunicable diseases, especially cardiovascular disease, are rising rapidly in resource-limited settings. This study aims to evaluate the relation between subclinical atherosclerosis and HIV-related and traditional cardiovascular risk factors in HIV-infected patients in rural South Africa. METHODS: A cross-sectional study was performed among HIV-infected patients visiting a health center in Limpopo, South Africa. Demographic and HIV-related information was collected, and cardiovascular risk was assessed. Carotid intima media thickness (CIMT) was measured and the prevalence of subclinical atherosclerosis (CIMT >0.78 mm) was calculated. The association between cardiovascular or HIV-related determinants with CIMT was analyzed using linear and logistic regression models adjusted for age and sex. RESULTS: The median CIMT in 866 subjects (median age [interquartile range], 41 [35-48] years; 69% female) was 0.589 mm (interquartile range, 0.524-0.678 mm), and values seemed higher than in healthy Western reference populations. In fact 12% of subjects (106 of 866) had subclinical atherosclerosis. Hypertension, high body mass index, previous cardiovascular event, diabetes mellitus, total and low-density lipoprotein cholesterol, estimated glomerular filtration rate, metabolic syndrome, and the Framingham Heart Risk score were independently associated with CIMT. No HIV-related determinants were associated with CIMT. CONCLUSIONS: In a predominantly female HIV-infected population in South Africa, CIMT values are considerably high and associated with cardiovascular risk factors, rather than HIV-related factors. This finding emphasizes the need to screen for cardiovascular disease among persons with HIV infection in resource-limited settings. Ideally, this screening would be integrated into care for chronic HIV infection, posing a major challenge for the future.

An update to the HIV-TRePS system: the development of new computational models that do not require a genotype to predict HIV treatment outcomes.

OBJECTIVES: The optimal individualized selection of antiretroviral drugs in resource-limited settings is challenging because of the limited availability of drugs and genotyping. Here we describe the development of the latest computational models to predict the response to combination antiretroviral therapy without a genotype, for potential use in such settings. METHODS: Random forest models were trained to predict the probability of a virological response to therapy (<50 copies HIV RNA/mL) following virological failure using the following data from 22,567 treatment-change episodes including 1090 from southern Africa: baseline viral load and CD4 cell count, treatment history, drugs in the new regimen, time to follow-up and follow-up viral load. The models were assessed during cross-validation and with an independent global test set of 1000 cases including 100 from southern Africa. The models' accuracy [area under the receiver-operating characteristic curve (AUC)] was evaluated and compared with genotyping using rules-based interpretation systems for those cases with genotypes available. RESULTS: The models achieved AUCs of 0.79-0.84 (mean 0.82) during cross-validation, 0.80 with the global test set and 0.78 with the southern African subset. The AUCs were significantly lower (0.56-0.57) for genotyping. CONCLUSIONS: The models predicted virological response to HIV therapy without a genotype as accurately as previous models that included a genotype. They were accurate for cases from southern Africa and significantly more accurate than genotyping. These models will be accessible via the online treatment support tool HIV-TRePS and have the potential to help optimize antiretroviral therapy in resource-limited settings where genotyping is not generally available.

Trends in body mass index in the pre-dolutegravir period in South Africa.

Background: Antiretroviral therapy (ART) is associated with weight gain, but this has been shown to be more marked with dolutegravir and other integrase strand transfer inhibitors. Objectives: We studied weight gain in people living with HIV (PLWH) on ART compared to the general population in the period before dolutegravir was introduced in a rural South African cohort. Method: Longitudinal analysis of the Ndlovu Cohort Study including 36-48 months' follow-up data. From 2014 to 2019, data were collected annually in Limpopo, rural South Africa. Linear mixed models using HIV status, demographics, ART use and cardiovascular risk factors were used to estimate trends in body mass index (BMI) over time. Results: In total, 1518 adult, non-pregnant participants were included, of whom 518 were PLWH on ART (79.8%), 135 PLWH not yet on ART (20.2%) and 865 HIV-negative. HIV-negative participants had significantly higher BMIs than PLWH on ART at all study visits. There was a significant increase in BMI in all subgroups after 36 months (PLWH on ART, BMI +1.2 kg/m2, P < 0.001; PLWH not on ART, BMI +1.8 kg/m2, P < 0.001 and HIV-negative, BMI +1.3 kg/m2, P < 0.001). Conclusion: The increase in BMI in PLWH and HIV-negative participants is a serious warning signal as obesity results in morbidity and mortality.

No Evidence for an Association of HIV and Antiviral Treatment With Changes in Framingham Cardiovascular Risk Score in the Ndlovu Cohort Study.

BACKGROUND: HIV and antiretroviral therapy (ART) have been associated with increased cardiovascular disease (CVD) risk in high-income countries. The authors studied the longitudinal association between HIV and ART and nonlaboratory Framingham Risk Score (FRS) in a middle-income country. METHODS AND RESULTS: This longitudinal analysis of the NCS (Ndlovu Cohort Study), South Africa used baseline to 36-month follow-up data. Demographics, HIV, ART status, and cardiometabolic measures were obtained. FRS was used as a CVD risk measure. Through linear mixed models, FRS trends over time and the association with HIV were studied. Analysis included 1136 participants, with 609 (54%) having HIV, and 495 (81%) taking ART. At baseline, 9.8% of participants had a high FRS. People living with HIV (PLHIV) had a 3.2% lower FRS than HIV-negative participants (P<0.001). FRS increased similarly for both groups over time. Other factors associated with FRS were secondary and higher education (ß value: -0.075, P<0.001; ß value: -0.084, P<0.001) and alcohol consumption (ß value: 0.011, P<0.001). CONCLUSIONS: CVD risk increased for all participants over 36 months, suggesting classic risk factors rather than HIV status or ART to be drivers of CVD risk. People living with HIV had a significantly lower FRS than their HIV-negative counterparts, possibly related to HIV itself or a more frequent interaction with healthcare services. No association of HIV and ART with changes in FRS over 36 months was observed, suggesting the need for research using clinical endpoints to elucidate the effects of HIV and ART on CVD risk. Population-based prevention of CVD risk factors in sub-Saharan Africa is warranted, regardless of HIV status.

Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings.

The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.

HIV-1 pretreatment drug resistance negatively impacts outcomes of first-line antiretroviral treatment.

INTRODUCTION: Pretreatment drug resistance (PDR) prevalence in sub-Saharan Africa is rising, but evidence of its impact on efavirenz (EFV)-based antiretroviral treatment (ART) is inconclusive. We determined the impact of PDR on outcomes of EFV-based ART in a subanalysis of a randomized clinical trial comparing different ART monitoring strategies implemented at a rural treatment facility in Limpopo, South Africa. METHODS: Participants initiating EFV-based first-line ART (2015-2017) were enrolled and received 96 weeks follow-up. Resistance to nucleos(t)ide reverse transcriptase inhibitors (NRTIs) and non-NRTI's (NNRTIs) was retrospectively assessed by population-based sequencing. Virological failure was defined as a viral load of at least 1000 copies/ml after at least 24 weeks of ART. RESULTS: A total of 207 participants were included, 60.4% (125/207) of whom were female. Median age was 38.8 (interquartile range: 31.4-46.7) years. Median CD4+ cell count was 191 (interquartile range: 70-355) cells/µl. PDR was detected in 12.9% (25/194) of participants with available sequencing results; 19 had NNRTI-resistance, and six had NRTI- and NNRTI-resistance. 26.0% of participants (40/154) with sequencing results and virological follow-up developed virological failure. PDR was independently associated with failure (adjusted hazard ratio: 3.7 [95% confidence interval: 1.68.5], P = 0.002). At failure, 87.5% (7/8) of participants with PDR harboured dual-class resistant virus, versus 16.7% (4/24) of participants without PDR (P = 0.0007). Virological resuppression after failure on first-line ART occurred in 57.7% (15/26) of participants without PDR versus 14.3% (1/7) of participants with PDR (P = 0.09). CONCLUSION: PDR was detected in 13% of study participants. PDR significantly increased the risk of virological failure of EFV-based ART. Accumulation of resistance at failure and inability to achieve virological resuppression illustrates the profound impact of PDR on treatment outcomes.

Comparative performance of cardiovascular risk prediction models in people living with HIV.

Background: Current cardiovascular risk assessment in people living with HIV is based on general risk assessment tools; however, whether these tools can be applied in sub-Saharan African populations has been questioned. Objectives: The study aimed to assess cardiovascular risk classification of common cardiovascular disease (CVD) risk prediction models compared to the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) 2010 and 2016 models in people living with HIV. Method: Cardiovascular disease risk was estimated by Framingham Cardiovascular and Heart Disease (FHS-CVD, FHS-CHD), Atherosclerotic Cardiovascular Disease (ASCVD) and D:A:D 2010 and 2016 risk prediction models for HIV-infected participants of the Ndlovu Cohort Study, Limpopo, rural South Africa. Participants were classified to be at low (< 10%), moderate (10% - 20%), or high-risk (> 20%) of CVD within 10 years for general CVD and five years for D:A:D models. Kappa statistics were used to determine agreement between CVD risk prediction models. Subgroup analysis was performed according to age. Results: The analysis comprised 735 HIV-infected individuals, predominantly women (56.7%), average age 43.9 (8.8) years. The median predicted CVD risk for D:A:D 2010 and FHS-CVD was 4% and for ASCVD and FHS-CHD models, 3%. For the D:A:D 2016 risk prediction model, the figure was 5%. High 10-year CVD risk was predicted for 2.9%, 0.5%, 0.7%, 3.1% and 6.6% of the study participants by FHS-CVD, FHS-CHD, ASCVD, and D:A:D 2010 and 2016. Kappa statistics ranged from 0.34 for ASCVD to 0.60 for FHS-CVD as compared to the D:A:D 2010 risk prediction model. Conclusion: Overall, predicted CVD risk is low in this population. Compared to D:A:D 2010, CVD risk estimated by the FHS-CVD model showed similar overall results for risk classification. With the exception of the D:A:D model, all other risk prediction models classified fewer people to be at high estimated CVD risk. Prospective studies are needed to develop and validate CVD risk algorithms in people living with HIV in sub-Saharan Africa.

A randomized study of intensified antiretroviral treatment monitoring versus standard-of-care for prevention of drug resistance and antiretroviral treatment switch.

INTRODUCTION: Standard-of-care antiretroviral treatment (ART) monitoring in low and middle-income countries consists of annual determination of HIV-RNA viral load with confirmatory viral load testing in case of viral rebound. We evaluated an intensified monitoring strategy of three-monthly viral load testing with additional drug exposure and drug resistance testing in case of viral rebound. METHODS: We performed an open-label randomized controlled trial (RCT) at a rural South African healthcare clinic, enrolling adults already receiving or newly initiating first-line ART. During 96 weeks follow-up, intervention participants received three-monthly viral load testing and sequential point-of-care drug exposure testing and DBS-based drug resistance testing in case of rebound above 1000 copies/ml. Control participants received standard-of-care monitoring according to the WHO guidelines. RESULTS: Five hundred one participants were included, of whom 416 (83.0%) were randomized at 24 weeks. Four hundred one participants were available for intention-to-treat analysis. Viral rebound occurred in 9.0% (18/199) of intervention participants and in 11.9% (24/202) of controls ( P  = 0.445). Time to detection of rebound was 375 days [interquartile range (IQR): 348-515] in intervention participants and 360 days [IQR: 338-464] in controls [hazard ratio: 0.88 (95% confidence interval (95% CI): 0.46-1.66]; P  = 0.683]. Duration of viral rebound was 87 days [IQR: 70-110] in intervention participants and 101 days [IQR: 78-213] in controls ( P  = 0.423). In the control arm, three patients with confirmed failure were switched to second-line ART. In the intervention arm, of three patients with confirmed failure, switch could initially be avoided in two cases. CONCLUSION: Three-monthly viral load testing did not significantly reduce the duration of viraemia when compared with standard-of-care annual viral load testing, providing randomized trial evidence in support of annual viral load monitoring.

Presence of occult HBV, but near absence of active HBV and HCV infections in people infected with HIV in rural South Africa.

Human immunodeficiency (HIV), hepatitis B (HBV), and hepatitis C (HCV) viruses are endemic in Sub-Saharan Africa, but data regarding the prevalence of hepatitis co-infections in HIV-positive individuals residing there are limited. The aim of the study was to determine the prevalence of HBV, HCV, and occult HBV (presence of HBV-DNA in the absence of HBsAg) in a rural, South African cohort. The results were compared to various ethnic groups in a Dutch cohort of people infected with HIV. Antiretroviral-naïve individuals with HIV from both a rural South African clinic (n = 258), and a Dutch University hospital (n = 782), were included. Both serological (HBV and HCV) and molecular (occult HBV) assays were performed. Logistic regression analysis was used to define independent predictors of a hepatitis co-infection. HBV and HCV prevalence rates in the South African cohort were exceptionally low (0.4%, 1/242 and 0.8%, 2/242, respectively), compared to those observed in Caucasians (HBV 4.4% and HCV 10.9%) and African immigrants (HBV 8.9% and HCV 4.8%). Conversely, occult HBV was observed in a considerable proportion (10%, 6/60) of South African patients who were anti-HBc-positive but HBsAg-negative. Occult infections were less frequent in Caucasians and Africans in the Dutch cohort (3.2% and 1.4%, respectively). Independent predictors for occult HBV were not identified, but a trend towards more occult HBV at lower CD4 counts was observed. Local HBV/HCV prevalence data are needed to optimize vaccination and antiretroviral treatment strategies. Occult HBV in patients with HIV may be missed regularly when molecular analyses are not available.

Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis.

OBJECTIVE: The objective was to examine the use of a tailor-made DNA microarray containing probes representing the vaginal microbiota to examine bacterial vaginosis. STUDY DESIGN: One hundred one women attending a health center for HIV testing in South Africa were enrolled. Stained, liquid-based cytology slides were scored for bacterial vaginosis. An inventory of organisms was obtained using microarray technology, probing genera associated with bacterial vaginosis in more detail, namely Gardnerella, Atopobium, Dialister, Leptotrichia, Megasphaera, Mobiluncus, Peptostreptococcus, Prevotella, and Sneathia. RESULTS: Of 101 women, 34 were diagnosed positive for bacterial vaginosis. This condition was associated with an increased microbial diversity. It is no longer useful to base the diagnosis of bacterial vaginosis on Gardnerella alone. Rather, its presence with Leptotrichia and Prevotella species, and especially Atopobium was more indicative of an aberrant state of the vaginal flora. CONCLUSION: To understand the vaginal microbiota in more detail, microarray-based identification can be used after microscopic scoring.