Oligonucleotide Ligation Assay (OLA)-Simple: Field Implementation, Usability, and Performance of a near Point-of-Care HIV Drug Resistance Assay in Kenya

Laboratories · 2026-02-04

A point-of-care (POC) HIV drug resistance (HIV-DR) test is needed for low- and middle-income countries (LMICs). Oligonucleotide Ligation Assay (OLA)-Simple, designed as a near-POC HIV-DR test, was assessed for its overall usability in Kenya by technicians with and without molecular laboratory PCR experience. Further, its diagnostic accuracy was evaluated by PCR-experienced technicians utilizing 147 plasma samples with known Sanger sequence genotypes-based on seven major HIV-DR mutations of nucleotide and non-nucleoside reverse transcriptase inhibitors. Thirteen laboratory technicians were recruited, including five with prior PCR experience. Twelve technicians completed the training and attained OLA-Simple testing competency, ten of whom were able to perform the OLA-Simple test within 6 h. Technicians' survey feedback indicated the user-friendliness of OLA-Simple, citing straightforward reagent reconstitution, concise instructions in prompts, and a shorter sample-to-result test time compared to standard genotyping assays. Of the 147 archived plasma samples tested, 132 (90%) yielded interpretable results. OLA-Simple assay demonstrated a sensitivity of 97.3% (95% CI 94.5, 98.9), a specificity of 97.2% (95% CI 95.5, 98.3), and a percent agreement of 97.1% (95% CI 95.9, 98.2) compared to Sanger sequencing. This evaluation found that OLA-Simple was user-friendly among intended end-users and performed well. LMIC HIV programs would benefit from strategizing on case-use scenarios for such near-POC HIV-DR assays to improve HIV outcomes.

Comparison of gut virome in Kenyan infants born to women with and without HIV

iScience · 2026-02-04

The gut virome develops in infancy, seeded from numerous sources including the maternal virome. Altered infant virome development from exposure to maternal HIV infection could contribute to the higher observed morbidity among children who are HIV-exposed, uninfected (CHEU) versus HIV-unexposed (CHUU). To assess whether infant HIV exposure affects gut virome development, we sequenced the DNA virome in stool samples collected between birth-2 years from 37 CHUU and 32 CHEU whose mothers received optimized antiretroviral therapy (ART). Richness and Shannon diversity increased with age and introduction of foods other than breastmilk, and Bray-Curtis distances varied by age. Virome richness was lower among CHEU than CHUU, but Shannon diversity and Bray-Curtis distances did not differ by HIV exposure. These findings suggest that HIV exposure is not a major determinant of the infant virome when mothers receive optimized ART.

HIV viral non-suppression and drug resistance among persons who inject drugs on dolutegravir antiretroviral therapy in Kenya

medRxiv · 2026-03-02

Background: )-based regimens. We evaluated PWID taking DTG to assess longitudinal rates of viral non-suppression and emergence of drug resistance mutations in Kenya. Methods: ) every 6 months for 2 years. We used univariable Cox proportional hazards to assess longitudinal risk for viremia (VL >200 copies/ml). Plasma specimens with viremia were genotyped for HIV drug resistance, including minority variants, using a lab-developed PacBio sequencing assay, and referenced by the Stanford HIVdb program. Results: Among 250 participants, 125 were receiving methadone, 199 (79.6) reported heroin use, 70% were male, and median age was 39 years. 194 (77.6%) participants completed all five study visits, 41 (16.4%) were lost to follow-up and 15 (6.0%) died. Across all study visits, 166 (66.0%) of the 250 participants were always suppressed, and 84 (33.6%) were viremic at least once during follow-up, including 8 (3.2%) who were always viremic and 76 (30.4%) who were intermittently suppressed. Living in an improvised shelter or outdoors was significantly associated with a higher risk of viremia (HR=4.35, 95% CI: 1.52-12.53). 93 specimens had drug resistance genotyping, 27 (29%) of which were from participants with incomplete follow-up. NNRTI resistance was frequent (37-41% across visits), whereas major resistance mutations were infrequent to tenofovir (4.3%), lamivudine (7.5%), and DTG (1%, minority variant S153F detected at 1% frequency). Accessory DTG mutations, which do not independently reduce susceptibility, were more common, observed in 41% (38/93) of genotyped specimens, most often T97A, E138K, and L74M. Conclusion: Among PWID living with HIV on TLD in Kenya, one-third had intermittent or sustained viral non-suppression across two years of follow-up. While NNRTI resistance was common, DTG resistance mutations were rare. Improving viral suppression among PWID living with HIV will reduce transmission risks and improve clinical outcomes.

Initiation of Oral Pre-exposure Prophylaxis Associated With Changes in Genital Tract T Cell Phenotypes in Women Exposed to HIV

The Journal of Infectious Diseases · 2026-04-03

Oral tenofovir-based HIV-pre-exposure prophylaxis (PrEP), approved for use in preventing human immunodeficiency virus (HIV) infection, has been implicated in altering the immune landscape. We leveraged longitudinal samples from heterosexual couples with the male partner living with HIV and the female partner without HIV initiating PrEP after enrollment. Applying high parameter flow cytometry to cells from ectocervical and vaginal biopsies and peripheral blood samples, we found a decrease in activated ectocervical CD8+ and CD4+ T cell subsets after oral PrEP exposure. Our data expand the understanding of the immunological impact of oral PrEP and potential protective mechanisms of PrEP usage.

Early Structural Cardiovascular Disease, HIV, and Tuberculosis in East Africa (ASANTE): Cross-sectional study protocol for a multimodal cardiac imaging study in Nairobi, Kenya

medRxiv · 2025-03-17 · 1 citations

Abstract Introduction Persons living with HIV (PLWH) have an augmented risk of cardiovascular disease, including atherosclerosis and myocardial dysfunction, despite effective viral suppression with antiretroviral therapy (ART). Despite the majority of PLWH residing in sub-Saharan Africa, there are limited reports from the region on structural cardiovascular changes due to this residual risk. Methods and analysis The Early Structural Cardiovascular Disease, HIV, and Tuberculosis (ASANTE) cross-sectional study will be conducted in a public hospital in Nairobi, Kenya. It will enroll 400 participants (50% female, 50% PLWH) to undergo comprehensive cardiovascular phenotyping using multimodal imaging (coronary CT angiography [CCTA], echocardiography) and banking of biological samples (whole blood, peripheral blood mononuclear cells, serum, and urine). We will define the prevalence of subclinical coronary atherosclerosis by coronary CT angiography (CCTA) and subclinical myocardial dysfunction by transthoracic echocardiography, and evaluate both traditional and non-traditional risk factors, including endemic infections such as latent tuberculosis. This study will contribute important data on phenotypes of and risk factors for HIV-associated cardiovascular disease in this under-studied region. Ethics and dissemination Ethical approval for the ASANTE study was granted by the University of Nairobi-Kenyatta National Hospital Ethical Review Committee, Nairobi, Kenya. Results will be submitted for publication in peer-reviewed journals. Key messages What is already known on this topic In studies from high-income countries, HIV infection is an independent risk factor for structural cardiovascular abnormalities (atherosclerosis, myocardial remodeling) and corresponding incident cardiovascular events. Emerging data from sub-Saharan Africa suggest there may be a unique epidemiological profile, in which HIV and traditional cardiometabolic risk factors (e.g., hypertension, diabetes, overweight/obesity, smoking) are not associated with coronary atherosclerosis. Unique endemic risk factors for cardiovascular disease in HIV have yet to be defined in sub-Saharan Africa. What this study adds We will define the prevalence of and risk factors for subclinical coronary atherosclerosis and myocardial disease in a cohort of Kenyan adults with and without HIV who have been enriched for cardiometabolic risk factors using multimodal imaging (coronary CT angiography, speckle tracking echocardiography). We will assess the contribution of latent tuberculosis infection as a potential endemic risk factor for subclinical cardiovascular abnormalities identified on multimodal imaging. How this study might affect research, practice, or policy Delineating the burden, phenotypes, and unique risk factors for early cardiovascular disease in this setting will facilitate tailored interventions for screening, monitoring, and management among persons with HIV. Developing multimodal cardiac imaging infrastructure in this resource-limited setting will expand tools for understanding the natural history of cardiovascular disease among persons with HIV in this unique setting. This study will yield a diverse collection of stored biological samples, including peripheral blood mononuclear cells, plasma, whole blood RNA, and urine. In combination with the cardiac imaging repository, this biobank will facilitate future collaborative efforts to identify mechanisms underlying phenotypes of cardiovascular disease in this population.

HIV Resistance to Dolutegravir Varies With Coadministered Agents

Clinical Infectious Diseases · 2025-08-30 · 2 citations

We hypothesized that HIV-dolutegravir resistance is more frequent when coadministered with nucleos(t)ides with shorter intracellular half-lives. Multivariable analysis of 183 viremic (≥200 c/mL) participants from 4 cohorts (N = 660 participants) found dolutegravir resistance in 21 (11.5%). Dolutegravir resistance was greater with dolutegravir + lamivudine + zidovudine/(1 on stavudine) (odds ratio [OR] = 19.4, 95% confidence interval [CI]: 5.1-74.3) or dolutegravir + lamivudine +abacavir (OR = 5.4, 95% CI: 1.1-25.8), compared with dolutegravir + lamivudine + tenofovir.

Genital herpes shedding episodes associate with altered spatial organization and activation of mucosal immune cells

JCI Insight · 2025-11-18

Herpes Simplex Virus 2 (HSV-2) infection results in variable rates of local viral shedding in anogenital skin. The effect of episodic viral exposures on immune cells in adjacent mucosal tissues, including the genital tract, is unknown. However, any immune responses at this site could affect protective mucosal immunity, tissue homeostasis, and adverse health outcomes. To investigate the effect of HSV-2 on cervicovaginal tract immunity, we applied flow cytometry, immunofluorescence imaging, analysis of soluble immune factors, and spatial transcriptomics to cervicovaginal tissue and blood samples provided by a total of 232 HSV-2-seropositive and seronegative participants, with genital HSV-2 shedding evaluated at the time of biopsy. This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics. HSV-2 seropositivity alone was associated with minimal differences in cervicovaginal and circulating T cell phenotypes. However, the vaginal mucosa during active HSV-2 shedding was associated with alterations in T cell, macrophage, and DC localization and gene expression, consistent with increased immune surveillance, with immune activating and suppressing signals potentially reinforcing mucosal tissue homeostasis.

Genital herpes shedding episodes associate with alterations in the spatial organization and activation of mucosal immune cells

bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-27

Abstract Herpes Simplex Virus 2 (HSV-2) infection results in variable rates of local viral shedding in anogenital skin. The impact of episodic viral exposures on immune cells in adjacent mucosal tissues, including the genital tract, is unknown. However, any immune responses at this site could impact protective mucosal immunity, tissue homeostasis, and adverse health outcomes. To investigate the impact of HSV-2 on cervicovaginal tract immunity, we applied flow cytometry, immunofluorescent imaging, analysis of soluble immune factors, and spatial transcriptomics to cervicovaginal tissue and blood samples provided by a total of 232 HSV-2 seropositive and seronegative participants, with genital HSV-2 shedding evaluated at the time of biopsy. This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics. HSV-2 seropositivity alone was associated with minimal differences in cervicovaginal and circulating T cell phenotypes. However, the vaginal mucosa during active HSV-2 shedding was associated with alterations in T cell, macrophage, and dendritic cell localization and gene expression consistent with increased immune surveillance, with immune activating and suppressing signals potentially reinforcing mucosal tissue homeostasis. Summary In context of episodic HSV-2 shedding, immune cells mobilize and co-localize in the vaginal epithelium, expressing cytotoxic and inflammatory genes and immunoregulatory genes that collectively may promote tissue homeostasis in settings of episodic viral shedding to limit damage.

Early structural cardiovascular disease, HIV, and tuberculosis in East Africa (ASANTE): cross-sectional study protocol for a multimodal cardiac imaging study in Nairobi, Kenya

BMJ Open · 2025-07-01

INTRODUCTION: Persons living with HIV (PLWH) have an augmented risk of cardiovascular disease, including atherosclerosis and myocardial dysfunction, despite effective viral suppression with antiretroviral therapy. Despite the majority of PLWH residing in sub-Saharan Africa, there are limited reports from the region on structural cardiovascular changes due to this residual risk. METHODS AND ANALYSIS: The Early Structural Cardiovascular Disease, HIV, and Tuberculosis in East Africa (ASANTE) cross-sectional study will be conducted in a public hospital in Nairobi, Kenya. It will enrol 400 participants (50% women, 50% PLWH) to undergo cardiovascular phenotyping using multimodal imaging (coronary CT angiography (CCTA) and echocardiography) and banking of biological samples (whole blood, peripheral blood mononuclear cells, plasma and urine). We will define the prevalence of subclinical coronary atherosclerosis by CCTA and subclinical myocardial dysfunction by transthoracic echocardiography and evaluate both traditional and non-traditional risk factors, including endemic infections such as latent tuberculosis. This study will contribute important data on phenotypes of and risk factors for HIV-associated cardiovascular disease in this understudied region. ETHICS AND DISSEMINATION: Ethical approval for the ASANTE study was granted by the University of Nairobi-Kenyatta National Hospital Ethical Review Committee, Nairobi, Kenya, and the University of Washington Institutional Review Board, USA. Results will be submitted for publication in peer-reviewed journals.

Clinical, Psychosocial, and Structural Factors Associated with the Detection of HIV Drug Resistance in Children Living with HIV in Kisumu, Kenya: Secondary Analysis of Data from the Opt4Kids Study

Viruses · 2025-09-16

BACKGROUND: HIV drug resistance (DR) mutations can compromise antiretroviral therapy (ART) success among children living with HIV (CLHIV). We conducted a secondary analysis using data from a randomized control trial for ART monitoring among CLHIV in Kisumu County, Kenya from 2019 to 2023, to assess clinical, psychosocial, and structural factors associated with HIV DR. METHODS: 704 CLHIV were followed for 12+ months, with characteristics captured at enrollment and follow-up visits in the "parent" randomized-controlled-trial (of point-of-care plasma viral load testing and for viremias ≥ 1000 copies/mL HIV genotyping for DR vs. standard-of-care) and an observational "extension" substudy (of participants on a dolutegravir-containing ART with genotyping performed on viremic specimens ≥ 200 copies/mL). A multivariate modified Poisson regression model was used to analyze factors associated with sequences yielding a Stanford HIVDR database DR penalty score (DR-PS) ≥ 30 to a nucleos(t)ides and/or non-nucleoside reverse transcriptase inhibitor, protease inhibitor (PI), and/or integrase inhibitor (INSTI). RESULTS: Among 113 (16.1%) participants who underwent genotyping, 93 (82.3%) had a DR-PS ≥ 30. DR-PS ≥ 30 were associated with age 1-5 years (adjusted risk ratio (ARR) = 1.84; 95% confidence interval (CI): 1.07, 3.14), history of viremia ≥ 1000 copies/mL (ARR = 4.18; 95% CI: 2.77, 6.31), prescription of a PI- (ARR = 6.05; 95% CI: 3.43, 10.68) or INSTI-containing regimen (ARR = 1.83; 95% CI: 1.08, 3.11), poor adherence to ART (ARR = 1.91; 95% CI: 1.32, 2.76), lack of caregiver confidence in ART administration (ARR = 1.89; 95% CI: 1.11, 3.22), and mid-sized clinic populations (ARR = 0.55; 95% CI: 0.33, 0.92). CONCLUSION: Addressing social factors associated with DR-PS ≥ 30 may improve ART success among CLHIV.