Long-Term Outcome of an HIV-Treatment Programme in Rural Africa: Viral Suppression despite Early Mortality

Objective. To define the long-term (2–4 years) clinical and virological outcome of an antiretroviral treatment (ART) programme in rural South Africa. Methods. We performed a retrospective observational cohort study, including 735 patients who initiated ART. Biannual monitoring, including HIV-RNA testing, was performed. Primary endpoint was patient retention; virological suppression (HIV-RNA < 50 copies/mL) and failure (HIV-RNA > 1000 copies/mL) were secondary endpoints. Moreover, possible predictors of treatment failure were analyzed. Results. 63% of patients (466/735) have a fully suppressed HIV-RNA, a median of three years after treatment initiation. Early mortality was high: 14% died within 3 months after treatment start. 16% of patients experienced virological failure, but only 4% was switched to second-line ART. Male gender and a low performance score were associated with treatment failure; immunological failure was a poor predictor of virological failure. Conclusions. An “all or nothing” phenomenon was observed in this rural South African ART programme: high early attrition, but good virological control in those remaining in care. Continued efforts are needed to enrol patients earlier. Furthermore, the observed viro-immunological dissociation emphasises the need to make HIV-RNA testing more widely available

Diagnosing pregnancy status using infrared spectra and milk composition in dairy cows

Data on Holstein (16,890), Brown Swiss (31,441), Simmental (25,845), and Alpine Grey (12,535) cows reared in northeastern Italy were used to assess the ability of milk components (fat, protein, casein, and lactose) and Fourier transform infrared (FTIR) spectral data to diagnose pregnancy. Pregnancy status was defined as whether a pregnancy was confirmed by a subsequent calving and no other subsequent inseminations within 90 d of the breeding of specific interest. Milk samples were analyzed for components and FTIR full-spectrum data using a MilkoScan FT+ 6000 (Foss Electric, Hiller\uf8d, Denmark). The spectrum covered 1,060 wavenumbers (wn) from 5,010 to 925 cm 121. Pregnancy status was predicted using generalized linear models with fat, protein, lactose, casein, and individual FTIR spectral bands or wavelengths as predictors. We also fitted a generalized linear model as a simultaneous function of all wavelengths (1,060 wn) with a Bayesian variable selection model using the BGLR R-package (https://r-forge.r-project.org/projects/bglr/). Prediction accuracy was determined using the area under a receiver operating characteristic curve based on a 10-fold cross-validation (CV-AUC) assessment based on sensitivities and specificities of phenotypic predictions. Overall, the best prediction accuracies were obtained for the model that included the complete FTIR spectral data. We observed similar patterns across breeds with small differences in prediction accuracy. The highest CV-AUC value was obtained for Alpine Grey cows (CV-AUC = 0.645), whereas Brown Swiss and Simmental cows had similar performance (CV-AUC = 0.630 and 0.628, respectively), followed by Holsteins (CV-AUC = 0.607). For single-wavelength analyses, important peaks were detected at wn 2,973 to 2,872 cm 121 where Fat-B (C-H stretch) is usually filtered, wn 1,773 cm 121 where Fat-A (C=O stretch) is filtered, wn 1,546 cm 121 where protein is filtered, wn 1,468 cm 121 associated with urea and fat, wn 1,399 and 1,245 cm 121 associated with acetone, and wn 1,025 to 1,013 cm 121 where lactose is filtered. In conclusion, this research provides new insight into alternative strategies for pregnancy screening of dairy cows

Changes in milk characteristics and fatty acid profile during the estrous cycle in dairy cows

The relationship of the estrous cycle to milk composition and milk physical properties was assessed on Holstein (n = 10,696), Brown Swiss (n = 20,501), Simmental (n = 17,837), and Alpine Grey (n = 8,595) cows reared in northeastern Italy. The first insemination after calving for each cow was chosen to be the day of estrus and insemination. Test days surrounding the insemination date (from 10 d before to 10 d after the day of the estrus) were selected and categorized in phases relative to estrus as diestrus high-progesterone, proestrus, estrus, metestrus, and diestrus increasing-progesterone phases. Milk components and physical properties were predicted on the basis of Fourier-transform infrared spectra of milk samples and were analyzed using a linear mixed model, which included the random effects of herd, the fixed classification effects of year-month, parity number, breed, estrous cycle phase, day nested within the estrous cycle phase, conception, partial regressions on linear and quadratic effects of days in milk nested within parity number, as well as the interactions between conception outcome with estrous cycle phase and breed with estrous cycle phase. Milk composition, particularly fat, protein, and lactose, showed clear differences among the estrous cycle phases. Fat increased by 0.14% from diestrus high-progesterone to estrous phase, whereas protein concomitantly decreased by 0.03%. Lactose appeared to remain relatively constant over diestrus high-progesterone, rising 1 d before the day of estrus followed by a gradual reduction over the subsequent phases. Specific fatty acids were also affected across the estrous cycle phases: C14:0 and C16:0 decreased ( 120.34 and 120.48%) from proestrus to estrus with a concomitant increase in C18:0 and C18:1 cis-9 (0.40 and 0.73%). More general categories of fatty acids showed a similar behavior; that is, unsaturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, trans fatty acids, and long-chain fatty acids increased, whereas the saturated fatty acids, mediumchain fatty acids, and short-chain fatty acids decreased during the estrous phase. Finally, urea, somatic cell score, freezing point, pH, and homogenization index were also affected indicating variation associated with the hormonal and behavioral changes of cows in standing estrus. Hence, the variation in milk profiles of cows showing estrus should potentially be taken into account for precision dairy farming management

Теоретичні та практичні аспекти приватизації в Україні

Цели статьи заключаются в изучении спроса покупателей на объекты приватизации и анализе финансового состояния предприятий к принятию решения об их приватизации (на основе данных за I квартал 2006 года), раскрытии основных критериев целесообразности принятия решения о приватизации объектов ведения хозяйства.Цілі статті полягають у вивченні попиту покупців на об'єкти приватизації та аналізі фінансового стану підприємств до прийняття рішення про їх приватизацію (на основі даних за I квартал 2006 року), розкритті основних критеріїв доцільності прийняття рішення про приватизацію об'єктів господарювання

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’ followup 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

Computational models as predictors of HIV treatment outcomes for the Phidisa cohort in South Africa

Background: Selecting the optimal combination of HIV drugs for an individual in resourcelimited settings is challenging because of the limited availability of drugs and genotyping.Objective: The evaluation as a potential treatment support tool of computational models that predict response to therapy without a genotype, using cases from the Phidisa cohort in South Africa.Methods: Cases from Phidisa of treatment change following failure were identified that had the following data available: baseline CD4 count and viral load, details of failing and previous antiretroviral drugs, drugs in new regimen and time to follow-up. The HIV Resistance Response Database Initiative’s (RDI’s) models used these data to predict the probability of a viral load &lt; 50 copies/mL at follow-up. The models were also used to identify effective alternative combinations of three locally available drugs.Results: The models achieved accuracy (area under the receiver–operator  characteristic curve) of 0.72 when predicting response to therapy, which is less accurate than for an independent global test set (0.80) but at least comparable to that of genotyping with rules-based interpretation. The models were able to identify alternative locally available three-drug regimens that were predicted to be effective in 69% of all cases and 62% of those whose new treatment failed in the clinic.Conclusion: The predictive accuracy of the models for these South African patients together with the results of previous studies suggest that the RDI’s models have the potential to optimise treatment selection and reduce virological failure in different patient populations, without the use of a genotype

AIDS awareness and VCT behaviour: An application of the integrated model of behaviour prediction

In order to limit the expansion of the HIV and AIDS epidemic in South Africa, it is important to develop targeted prevention strategies. The voluntary HIV counselling and testing (VCT) programme appears to be effective for preventing the spread of the HI virus. This study adapted guidelines of the integrated model of behaviour prediction (IMBP) into a questionnaire and examined the extent to which it predicts behaviour. A sample of 92 sports team members from Limpopo ranging from 14 to 30 years of age completed the questionnaire. Results suggested that beliefs about the outcomes of behaviour and beliefs about the expectations of others had a direct influence on the intention to undergo HIV counselling and testing. Efficacy beliefs, namely beliefs that there are factors that can facilitate behaviour, can lead to actual testing behaviour if accompanied by self-efficacy. Knowledge, intention and stigma are not related to VCT behaviour. Findings show that some constructs influence intention and test behaviour, but in ways not predicted by the model. Thus, the adequacy of the IMBP to determine HIV and AIDS-preventative behavioural intentions is questioned

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 SARSCoV-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

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

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