Advancing HIV Drug Resistance Technologies and Strategies: Insights from South Africa's Experience and Future Directions for Resource-Limited Settings.

Monitoring of HIV drug resistance (HIVDR) remains critical for ensuring countries attain and sustain the global goals for ending HIV as a public health threat by 2030. On an individual patient level, drug resistance results assist in ensuring unnecessary treatment switches are avoided and subsequent regimens are tailored on a case-by-case basis, should resistance be detected. Although there is a disparity in access to HIVDR testing in high-income countries compared to low- and middle-income countries (LMICS), more LMICs have now included HIVDR testing for individual patient management in some groups of patients. In this review, we describe different strategies for surveillance as well as where HIVDR testing can be implemented for individual patient management. In addition, we briefly review available technologies for HIVDR testing in LMICs, including Sanger sequencing, next-generation sequencing, and some point-of-care options. Finally, we describe how South Africa has implemented HIVDR testing in the public sector.

Level of viral suppression and the cascade of HIV care in a South African semi-urban setting in 2012.

OBJECTIVE: In 2012, 7 years after the introduction of antiretroviral treatment (ART) in the South African township of Orange Farm, we measured the proportion of HIV-positive people who were virally suppressed, especially among high-risk groups (women 18-29 years and men 25-34 years). DESIGN: A community-based cross-sectional representative survey was conducted among 3293 men and 3473 women. METHODS: Study procedures included a face-to-face interview and collection of blood samples that were tested for HIV, 11 antiretroviral drugs and HIV-viral load. RESULTS: HIV prevalence was 17.0% [95% confidence interval: 15.7-18.3%] among men and 30.1% [28.5-31.6%] among women. Overall, 59.1% [57.4-60.8%] of men and 79.5% [78.2-80.9%] of women had previously been tested for HIV. When controlling for age, circumcised men were more likely to have been tested compared with uncircumcised men (66.1 vs 53.6%; P < 0.001). Among HIV+, 21.0% [17.7-24.6%] of men and 30.5% [27.7-33.3%] of women tested positive for one or more antiretroviral drugs. Using basic calculations, we estimated that, between 2005 and 2012, ART programs prevented between 46 and 63% of AIDS-related deaths in the community. Among antiretroviral-positive, 91.9% [88.7-94.3%] had viral suppression (viral load <400 copies/ml). The proportion of viral suppression among HIV+ was 27.0% [24.3-29.9%] among women and 17.5% [14.4-20.9%] among men. These proportions were lower among the high-risk groups: 15.6% [12.1-19.7%] among women and 8.4% [5.0-13.1%] among men. CONCLUSION: In Orange Farm, between 2005 and 2012, ART programs were suboptimal and, among those living with HIV, the proportion with viral suppression was still low, especially among the young age groups. However, our study showed that, in reality, antiretroviral drugs are highly effective in viral suppression at an individual level.

Design and implementation of an external quality assessment program for HIV viral load measurements using dried blood spots.

An external quality assurance program was developed for HIV-1 RNA viral load measurements taken from dried blood spots using a reference panel and field-collected specimens. The program demonstrated that accurate and reproducible quantitation can be obtained from field-collected specimens. Residual proviral DNA may confound interpretation in virologically suppressed subjects.

Association of low-risk human papillomavirus infection with male circumcision in young men: results from a longitudinal study conducted in Orange Farm (South Africa).

BACKGROUND: Low-Risk Human Papillomavirus (LR-HPV) genotypes 6 and 11 cause genital warts. This study investigated the association of LR-HPV infection with male circumcision (MC). METHODS: We used data from the South African MC trial conducted among young men. Urethral swabs, collected among intervention (circumcised) and control (uncircumcised) groups, were analyzed using HPV linear array. Adjusted LR-HPV prevalence rate ratio (aPPR) and Poisson mean ratio (aPMR) of number of LR-HPV genotypes were estimated using log-Poisson regression, controlling for background characteristics, sexual behaviour, and HIV and HSV-2 statuses. RESULTS: Compared to controls, LR-HPV prevalence and mean number of genotypes were significantly lower among the intervention group ((8.5% versus 15.8%; aPRR: 0.54, P < .001) and (0.33 versus 0.18; aPMR: 0.54, P < .001), resp.). Mean number of LR-HPV genotypes increased with number of lifetime sexual partners and decreased with education level and consistent condom use. CONCLUSIONS: This study shows a reduction in LR-HPV infection among circumcised men.

Association of oncogenic and nononcogenic human papillomavirus with HIV incidence.

OBJECTIVE: Little is known about the interaction between human papillomavirus (HPV) and HIV. This study aimed to explore the association of oncogenic (high risk) and nononcogenic (low risk) HPV with HIV incidence. METHODS: We used 1683 urethral swabs collected at the last follow-up visit of a male circumcision trial conducted in Orange Farm (South Africa). Swabs analyses and HPV genotyping were performed by polymerase chain reaction. We estimated HIV adjusted incidence rate ratios (aIRRs) and 95% confidence intervals (CIs) using survival analysis. Background characteristics, male circumcision status, sexual behavior, HPV status, and other sexually transmitted infections were used as covariates. RESULTS: The prevalence of HR and LR HPV was 14.0% (95% CI: 12.4 to 15.7) and 17.3% (95% CI: 15.6 to 19.2), respectively. When controlling for HR-HPV status, LR-HPV status was not associated with HIV incidence (aIRR = 1.13, 95% CI: 0.40 to 3.16; P = 0.82). When controlling for all covariates, HIV incidence increased significantly with HR-HPV positivity (aIRR = 3.76, 95% CI: 1.83 to 7.73, P < 0.001) and with the number of HR-HPV genotypes (adjusted-P linear trend = 0.0074). CONCLUSIONS: Several explanations could account for our findings. One is that HR-HPV facilitates HIV acquisition. The association of HPV with HIV acquisition requires further investigations.

Comparison of lavage and swabs for the collection of genital ulcer specimens to measure HIV RNA shedding.

BACKGROUND: The optimum collection procedure for the evaluation of HIV-1 burden in ulcer secretions has not been well defined. OBJECTIVES: The objective of this study was to compare ulcer swabs and ulcer lavages for the detection and quantitation of HIV-1 RNA in genital ulcers. STUDY DESIGN: A convenience sample of the first 84 HIV-positive participants in a randomized double blind placebo controlled trial of acyclovir episodic treatment among men with genital ulcer disease were included in this evaluation. At baseline, participants were screened for HIV, syphilis and HSV-2 by serology and for ulcer etiology by PCR. Ulcer specimens were collected by using (1) a non-traumatic washing procedure with 10ml of PBS, and (2) sterile dry swabs. Ulcer samples were tested with HIV-1 Amplicor 1.5 Ultra Sensitive Assay with a lower threshold of 50 copies/ml. RESULTS: Of ulcer samples 35 (41.7%) had HIV detected by ulcer lavage and 32 (38.1%) by swabs (p=0.68). Overall, 45 (53.6%) were positive by one or both methods. The overall proportion of agreement was 73% (61/84). The chance-corrected proportion of agreement was 0.46 (95% CI: 0.26, 0.65) as estimated by the Kappa statistic. The log mean viral load from lavages (1.49log(10) copies/ml, 95% CI: 1.17-1.81) did not differ significantly from that of swabs (1.41log(10) copies/ml, 95% CI: 1.16-1.71) (p=0.29) with a mean difference of 0.08log copies/ml (SD 0.96). CONCLUSION: Ulcer lavage and ulcer swab performed in moderate agreement in the detection and quantitation of HIV RNA from ulcer specimens.

Effect of male circumcision on the prevalence of high-risk human papillomavirus in young men: results of a randomized controlled trial conducted in Orange Farm, South Africa.

BACKGROUND: A causal association links high-risk human papillomavirus (HR-HPV) and cervical cancer, which is a major public health problem. The objective of the present study was to investigate the association between male circumcision (MC) and the prevalence of HR-HPV among young men. METHODS: We used data from a MC trial conducted in Orange Farm, South Africa, among men aged 18-24 years. Urethral swab samples were collected during a period of 262 consecutive days from participants in the intervention (circumcised) and control (uncircumcised) groups who were reporting for a scheduled follow-up visit. Swab samples were analyzed using polymerase chain reaction. HR-HPV prevalence rate ratios (PRRs) were assessed using univariate and multivariate log Poisson regression. RESULTS: In an intention-to-treat analysis, the prevalences of HR-HPV among the intervention and control groups were 14.8% (94/637) and 22.3% (140/627), respectively, with a PRR of 0.66 (0.51-0.86) (P = .002). Controlling for propensity score and confounders (ethnic group, age, education, sexual behavior [including condom use], marital status, and human immunodeficiency virus status) had no effect on the results. CONCLUSIONS: This is the first randomized controlled trial to show a reduction in the prevalence of urethral HR-HPV infection after MC. This finding explains why women with circumcised partners are at a lower risk of cervical cancer than other women.