Presence, persistence and effects of pre-treatment HIV-1 drug resistance variants detected using next generation sequencing: A Retrospective longitudinal study from rural coastal Kenya.

BACKGROUND: The epidemiology of HIV-1 drug resistance (HIVDR) determined by Sanger capillary sequencing, has been widely studied. However, much less is known about HIVDR detected using next generation sequencing (NGS) methods. We aimed to determine the presence, persistence and effect of pre-treatment HIVDR variants detected using NGS in HIV-1 infected antiretroviral treatment (ART) naïve participants from rural Coastal Kenya. METHODS: In a retrospective longitudinal study, samples from HIV-1 infected participants collected prior [n = 2 time-points] and after [n = 1 time-point] ART initiation were considered. An ultra-deep amplicon-based NGS assay, calling for nucleotide variants at >2.0% frequency of viral population, was used. Suspected virologic failure (sVF) was defined as a one-off HIV-1 viral load of >1000 copies/ml whilst on ART. RESULTS: Of the 50 eligible participants, 12 (24.0% [95% CI: 13.1-38.2]) had at least one detectable pre-treatment HIVDR variant against Protease Inhibitors (PIs, n = 6 [12%]), Nucleoside Reverse Transcriptase Inhibitors (NRTIs, n = 4 [8.0%]) and Non-NRTIs (n = 3 [6.0%]). Overall, 15 pre-treatment resistance variants were detected (frequency, range: 2.3-92.0%). A positive correlation was observed between mutation frequency and absolute load for NRTI and/or NNRTI variants (r = 0.761 [p = 0.028]), but not for PI variants (r = -0.117 [p = 0.803]). Participants with pre-treatment NRTI and/or NNRTI resistance had increased odds of sVF (OR = 6.0; 95% CI = 1.0-36.9; p = 0.054). CONCLUSIONS: Using NGS, pre-treatment resistance variants were common, though observed PI variants were unlikely transmitted, but rather probably generated de novo. Even when detected from a low frequency, pre-treatment NRTI and/or NNRTI resistance variants may adversely affect treatment outcomes.

Prevalence and correlates of home delivery amongst HIV-infected women attending care at a rural public health facility in Coastal Kenya.

BACKGROUND: Home delivery, referring to pregnant women giving birth in the absence of a skilled birth attendant, is a significant contributor to maternal mortality, and is encouragingly reported to be on a decline in the general population in resource limited settings. However, much less is known about home delivery amongst HIV-infected women in sub-Saharan Africa (sSA). We described the prevalence and correlates of home delivery among HIV-infected women attending care at a rural public health facility in Kilifi, Coastal Kenya. METHODS: A cross-sectional design using mixed methods was used. Quantitative data were collected using interviewer-administered questionnaires from HIV-infected women with a recent pregnancy (within 5 years, n = 425), whilst qualitative data were collected using focused group discussions (FGD, n = 5). Data were analysed using logistic regression and a thematic framework approach respectively. RESULTS: Overall, 108 (25.4%, [95% CI: 21.3-29.8]) participants delivered at home. Correlates of home delivery included lack of formal education (aOR 12.4 [95% CI: 3.4-46.0], p<0.001), history of a previous home delivery (2.7 [95% CI:1.2-6.0], p = 0.019) and being on highly active antiretroviral therapy (HAART, 0.4 [95% CI:0.2-0.8], p = 0.006).Despite a strong endorsement against home delivery, major thematic challenges included consumer-associated barriers, health care provider associated barriers and structural barriers. CONCLUSION: A quarter of HIV-infected women delivered at home, which is comparable to estimates reported from the general population in this rural setting, and much lower than estimates from other sSA settings. A tailored package of care targeting women with no formal education and with a history of a previous home delivery, coupled with interventions towards scaling up HAART and improving the quality of maternal care in HIV-infected women may positively contribute to a decline in home delivery and subsequent maternal mortality in this setting.

Incidence and predictors of attrition from antiretroviral care among adults in a rural HIV clinic in Coastal Kenya: a retrospective cohort study.

BACKGROUND: Scale up of antiretroviral therapy (ART) has led to substantial declines in HIV related morbidity and mortality. However, attrition from ART care remains a major public health concern and has been identified as one of the key reportable indicators in assessing the success of ART programs. This study describes the incidence and predictors of attrition among adults initiating ART in a rural HIV clinic in Coastal Kenya. METHODS: A retrospective cohort study design was used. Adults (≥ 15 years) initiated ART between January 2008 and December 2010 were followed up for two years. Attrition was defined as individuals who were either reported dead or lost to follow up (LFU, ≥ 180 days late since the last clinic visit). Kaplan Meier survival probabilities and Weibull baseline hazard regression analyses were used to model the incidence and predictors of time to attrition. RESULTS: Of the 928 eligible participants, 308 (33.2% [95% CI, 30.2 - 36.3]) underwent attrition at an incident rate of 23.1 (95% CI, 20.6 - 25.8)/100 pyo. Attrition at 6 and 12 months was 18.4% (95% CI, 16.0 - 21.1) and 23.2% (95% CI, 19.9 - 25.3) respectively. Gender (male vs. female, adjusted hazard ratio [95% CI], p-value: 1.5 [1.1 - 2.0], p = 0.014), age (15 - 24 vs. ≥ 45 years, 2.2 [1.3 - 3.7], p = 0.034) and baseline CD4 T-cell count (100 - 350 cells/uL vs. < 100 cells/uL, 0.5 [0.3 - 0.7], p = 0.002) were independent predictors of time to attrition. CONCLUSIONS: A third of individuals initiating ART were either reported dead or LFU during two years of care, with more than a half of these occurring within six months of treatment initiation. Practical and sustainable biomedical interventions and psychosocial support systems are warranted to improve ART retention in this setting.