Prevalence and factors associated with HIV-1 drug resistance mutations in treatment-experienced patients in Nairobi, Kenya: A cross-sectional study

Trends and factors associated with HIV viral load non-suppression among treatment-experienced female sex workers in Kenya

BACKGROUND

Transactional sexual relations in the absence of condom use is a well established behaviour that strongly contributes to HIV transmission if the infected person is not virally suppressed. In this study, we determined the trends and factors associated with viral load non-suppression (VLNS) among treatment-experienced FSWs in Kenya.

METHODS

This retrospective cohort study used data collected from seven sex workers' outreach clinics between 2015 and 2022. VLNS trends were determined using the Modified Mann-Kendall test, and the effects of covariates on VLNS odds were examined using generalized estimating equations (GEE) with a logit link.

RESULTS

Twelve thousand one hundred and seventeen viral load tests were performed on samples collected from 1947 FSWs. The prevalence of VLNS decreased from 25.5% [95% confidence interval (CI) 17.6-34.6] in 2016 to 4.3% (95% CI 2.5-6.7) in 2021. The odds of VLNS decreased by 9% per year during the study period in the multivariable GEE analysis adjusted for covariates [regimen, age, and sex worker outreach program (SWOP) clinic], [odds ratio (OR) 0.91, 95% CI 0.84-0.98; P  = 0.005]. Age was a significant factor associated with VLNS, with younger women (18-24 years) having 2.2 times higher odds of VLNS (OR 2.15 95% CI 1.10-4.20; P  = 0.025) than those aged over 55 years (reference). Participants on dolutegravir (DTG)-based cART regimen had 64% lower odds of VLNS (OR 0.36, 95% CI 0.25-0.52; P  < 0.001) compared to those on protease inhibitor-based regimen.

CONCLUSION

There is strong evidence of decreasing population-level viraemia among FSWs during the study period. To maintain the trend, it is necessary to continue supporting SWOP clinics in order to provide HIV treatment services to this key population.

Preclinical Profile of the HIV-1 Maturation Inhibitor VH3739937

The HIV-1 maturation inhibitor (MI) VH3739937 (VH-937) inhibits cleavage between capsid and spacer peptide 1 and exhibits an oral half-life in humans compatible with once-weekly dosing. Here, the antiviral properties of VH-937 are described. VH-937 exhibited potent antiviral activity against all HIV-1 laboratory strains, clinical isolates, and recombinant viruses examined, with half-maximal effective concentration (EC50) values ≤ 5.0 nM. In multiple-cycle assays, viruses less susceptible to other MIs, including A364V, were inhibited at EC50 values ≤ 8.0 nM and maximal percent inhibition (MPI) values ≥ 92%. However, VH-937 was less potent against A364V in single-cycle assays (EC50, 32.0 nM; MPI, 57%) and A364V emerged in one of four resistance selection cultures. Other substitutions were selected by VH-937, although re-engineered viruses with these sequences were non-functional in multiple-cycle assays. Measured dissociation rates from wild-type and A364V-containing VLPs help explain resistance to the A364V mutation. Overall, the in vitro antiviral activity of VH-937 supports its continued development as a treatment for HIV-1.

Virologic Nonsuppression and HIV Drug Resistance Among People Who Inject Drugs and Their Sexual and Injecting Partners in Kenya

We evaluated the prevalence and correlates of HIV viral nonsuppression and HIV drug resistance (HIV-DR) in a cohort of people who inject drugs living with HIV (PWID-LH) and their sexual and injecting partners living with HIV in Kenya. HIV-DR testing was performed on participants with viral nonsuppression. Of 859 PWID-LH and their partners, 623 (72.5%) were on antiretroviral therapy (ART) ≥4 months and 148/623 (23.8%) were not virally suppressed. Viral nonsuppression was more common among younger participants and those on ART for a shorter duration. Among 122/148 (82.4%) successfully sequenced samples, 55 (45.1%) had detectable major HIV-DR mutations, mainly to non-nucleoside and nucleotide reverse transcriptase inhibitors (NNRTI and NRTI). High levels of HIV-DR among those with viral nonsuppression suggests need for viral load monitoring, adherence counseling, and timely switching to alternate ART regimens in this key population.

Factors associated with viral load non-suppression among treatment-experienced pre-teenage children living with HIV in Kenya: a nationwide population-based cohort study, 2015-2021

Background

Viral load non-suppression (VLNS) in children is a major public health concern because of attendant HIV disease progression and risk of morbidity and mortality. Based on a nationally representative database we present estimates of the prevalence, trends and factors associated with VLNS in Kenyan pre-teenage children between 2015 and 2021.

Methods

Kenya National AIDS & STI Control Program's (NASCOP) maintains an early infant diagnosis and viral load (EID/VL) database for all persons living with HIV who are enrolled in the country's primary care clinics for purposes of monitoring progress towards achievement of the 95% viral suppression goals. Participants were eligible if they were children living with HIV (CLHIV), on combination ART (cART) treatment, and ≤12 years old. The modified Mann-Kendall trend test for serially correlated data was used to identify VLNS trends. Generalized estimating equations (GEE) with a logit link was used to assess the effects of covariates on the odds of VLNS (VL ≥1,000 copies/mL) over repeated points in time, allowing for the correlation among the repeated measures.

Findings

Between January 2015 and December 2021, 508,743 viral load tests were performed on samples collected from 109,682 pre-teenage children. The prevalence of VLNS decreased from 22.9% (95% CI 22.4-23.3) to 12.5% (95% CI 12.1-12.9), p < 0.0001, and mean age increased from 3.1 (4.2) to 8.0 (3.2) years in 2015 and 2021 respectively. A modified Mann-Kendall trend test for serially correlated data denotes a statistically significant decreasing trend (τ = -0.300, p < 0.0001) over the study period. In the multivariable GEE analysis adjusted for covariates, the odds of VLNS decreased by 11% per year during the study period, (GEE-aOR 0.89, 95% CI 0.88-0.90; p < 0.0001). Factors positively associated with VLNS were EFV/NVP-based first-line cART regimen (GEE-aOR 1.74, 95% CI 1.65-1.84, p < 0.0001), PI-based cART regimen (GEE-aOR 1.82, 95% CI 1.72-1.92, p < 0.0001), and children aged 1-3 years (toddlers) (GEE-aOR: 1.84, 95% CI 1.79-1.90, p < 0.0001). On the contrary, DTG-based cART regimen, were negatively associated with VLNS (GEE-aOR 0.70, 95% CI 0.65-0.75, p < 0.0001).

Interpretation

There is a strong evidence of decreasing viremia between 2015 and 2021. To sustain the decreasing trend, accelerating the switch from the suboptimal EVP/NVP first-line regimen to optimised DTG regimen is warranted.

Funding

U.S. President's Emergency Plan for AIDS Relief (PEPFAR) and Clinton Health Access Initiative (CHAI).

A Machine Learning Approach to Predict HIV Viral Load Hotspots in Kenya Using Real-World Data

Background

Machine learning models are not in routine use for predicting HIV status. Our objective is to describe the development of a machine learning model to predict HIV viral load (VL) hotspots as an early warning system in Kenya, based on routinely collected data by affiliate entities of the Ministry of Health. Based on World Health Organization's recommendations, hotspots are health facilities with ≥20% people living with HIV whose VL is not suppressed. Prediction of VL hotspots provides an early warning system to health administrators to optimize treatment and resources distribution.

Methods

A random forest model was built to predict the hotspot status of a health facility in the upcoming month, starting from 2016. Prior to model building, the datasets were cleaned and checked for outliers and multicollinearity at the patient level. The patient-level data were aggregated up to the facility level before model building. We analyzed data from 4 million tests and 4,265 facilities. The dataset at the health facility level was divided into train (75%) and test (25%) datasets.

Results

The model discriminates hotspots from non-hotspots with an accuracy of 78%. The F1 score of the model is 69% and the Brier score is 0.139. In December 2019, our model correctly predicted 434 VL hotspots in addition to the observed 446 VL hotspots.

Conclusion

The hotspot mapping model can be essential to antiretroviral therapy programs. This model can provide support to decision-makers to identify VL hotspots ahead in time using cost-efficient routinely collected data.

Second-Line Switch to Dolutegravir for Treatment of HIV Infection

BACKGROUND

Data to inform the switch from a ritonavir-boosted protease inhibitor (PI) to dolutegravir in patients living with human immunodeficiency virus (HIV) infection who do not have genotype information and who have viral suppression with second-line therapy containing a ritonavir-boosted PI have been limited.

METHODS

In a prospective, multicenter, open-label trial conducted at four sites in Kenya, we randomly assigned, in a 1:1 ratio, previously treated patients without genotype information who had viral suppression while receiving treatment containing a ritonavir-boosted PI to either switch to dolutegravir or continue the current regimen. The primary end point was a plasma HIV type 1 RNA level of at least 50 copies per milliliter at week 48, assessed on the basis of the Food and Drug Administration snapshot algorithm. The noninferiority margin for the between-group difference in the percentage of participants who met the primary end point was 4 percentage points. Safety up to week 48 was assessed.

RESULTS

A total of 795 participants were enrolled, with 398 assigned to switch to dolutegravir and 397 assigned to continue taking their ritonavir-boosted PI; 791 participants (397 in the dolutegravir group and 394 in the ritonavir-boosted PI group) were included in the intention-to-treat exposed population. At week 48, a total of 20 participants (5.0%) in the dolutegravir group and 20 (5.1%) in the ritonavir-boosted PI group met the primary end point (difference, -0.04 percentage points; 95% confidence interval, -3.1 to 3.0), a result that met the criterion for noninferiority. No mutations conferring resistance to dolutegravir or the ritonavir-boosted PI were detected at the time of treatment failure. The incidence of treatment-related grade 3 or 4 adverse events was similar in the dolutegravir group and the ritonavir-boosted PI group (5.7% and 6.9%, respectively).

CONCLUSIONS

In previously treated patients with viral suppression for whom there were no data regarding the presence of drug-resistance mutations, dolutegravir treatment was noninferior to a regimen containing a ritonavir-boosted PI when the patients were switched from a ritonavir-boosted PI-based regimen. (Funded by ViiV Healthcare; 2SD ClinicalTrials.gov number, NCT04229290.).

Age and CD4+ T cell counts are inversely associated with HIV drug resistance mutations in treatment naive female sex workers

The increasing prevalence of human immunodeficiency virus (HIV) drug resistance mutations (HIVDRM) in untreated seropositive persons has consequences for future treatment options. This is extremely important in key populations such as female sex workers (FSWs), where the prevalence of pretreatment drug resistance (PDR) and associated risk factors are unknown. In this study, we analyzed PDR and associated risk factors in recently diagnosed and treatment-naive FSWs in Nairobi, Kenya. In this cross-sectional study, we used 64 HIV-seropositive plasma samples collected from FSWs between November 2020 and April 2021. To identify HIVDRM, the pol gene was amplified and genotyped using sanger sequencing. The effects of age, tropism, CD4+ T cell count, subtype, and location on HIVDRM counts were examined using Poisson regression. Overall, the prevalence of PDR was 35.9% (95% CI: 24.3-48.9), which was strongly influenced by K103N and M184V mutations, which confer resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTI), respectively. Subtype A1 was predominant followed by subtype D with a notable increase in inter-subtype recombinants. We found statistically significant evidence that age was inversely related to HIVDRM. A FSW who is 1 year older had 12% less HIVDRM (incidence rate ratios [IRR]: 0.88; 95% CI: 0.82-0.95; P < .001), after adjusting for CD4+ T cell count, subtype, location, and tropism. Similarly, an increase in CD4+ T cell count by 1 unit, was associated with 0.4% fewer HIVDRM (IRR: 0.996; 95% CI: 0.994-0.998; P = .001), while controlling for the other variables. HIV-1 tropism was not associated with HIVDRM counts. In conclusion, our findings show a high prevalence of NNRTIs. Lower CD4+ T cell counts and younger age were significant risk factors that influenced HIVDRM loads. This finding underscores the relevance of targeted interventions and the importance of continuing to focus on FSWs as a way of addressing the HIV epidemic.

Net charge and position 22 of the V3 loop are associated with HIV-1 tropism in recently infected female sex workers in Nairobi, Kenya

Human immunodeficiency virus (HIV) infection affects around 37 million people worldwide, and in Kenya, key populations especially female sex workers (FSW), are thought to play a substantial role in the wider, mostly heterosexual HIV-1 transmission structure. Notably, HIV tropism has been found to correlate with HIV-1 transmission and disease progression in HIV-infected patients. In this study, recently infected FSWs from Nairobi, Kenya, were assessed for HIV tropism and the factors related to it. We used a cross-sectional study design to analyze 76 HIV-1 positive plasma samples obtained from FSWs enrolled in sex worker outreach program clinics in Nairobi between November 2020 and April 2021. The effects of clinical, demographic, and viral genetic characteristics were determined using multivariable logistic regression. HIV-1 subtype A1 accounted for 89.5% of all cases, with a prevalence of CXCR4-tropic viruses of 26.3%. WebPSSMR5X4 and Geno2Pheno [G2P:10-15% false positive rate] showed high concordance of 88%. Subjects infected with CXCR4-tropic viruses had statistically significant lower baseline CD4+T-cell counts than those infected with CCR5-tropic viruses (P = .044). Using multivariable logistic regression and adjusting for potential confounders, we found that net charge, the amino acid at position 22 of the V3 loop, and the geographic location of the subject were associated with tropism. A unit increase in V3 loop's net-charge increased the odds of a virus being CXCR4-tropic by 2.4 times (OR = 2.40, 95%CI = 1.35-5.00, P = .007). Second, amino acid threonine at position 22 of V3 loop increased the odds of a strain being X4 by 55.7 times compared to the alanine which occurred in CCR5-tropic strains (OR = 55.7, 95%CI = 4.04-84.1, P < .003). The Kawangware sex worker outreach program clinic was associated with CXCR4-tropic strains (P = .034), but there was there was no evidence of a distinct CXCR4-tropic transmission cluster. In conclusion, this study revealed a high concordance of WebPSSMR5X4 and Geno2Pheno in predicting HIV tropism. The most striking finding was that amino acid position 22 of the V3 loop is linked to tropism in HIV-1 subtype A1. Additional studies with a large dataset are warranted to confirm our findings.