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Virome remodeling rewires epigenetic and metabolic pathways linked to infection-associated colorectal cancer risk
Damane, Botle Precious; Featherston, Jonathan; Kader, Shakeel; Alaouna, Mohammed; Naidoo, Pragalathan; Dlamini, Zodwa; Mkhize-Kwitshana, Zilungile Lynette (Elsevier, 2026-06)
BACKGROUND : Colorectal cancer (CRC) incidence is rising in sub-Saharan Africa, coinciding with the high prevalence of immune-modulating infections such as HIV and helminths. The gut virome, a critical yet understudied component of the microbiome, may influence oncogenic processes through epigenetic and metabolic alterations. However, the interplay between gut viral communities, HIV-helminth co-infection, and CRC risk remains poorly characterized in African populations. This study aimed to investigate gut virome-associated epigenetic and metabolic signatures linked to CRC susceptibility among South African adults, with a focus on HIV and helminth co-infection dynamics. METHODS : Untargeted shotgun metagenomic sequencing was performed on stool DNA samples from 62 adults stratified into five groups: uninfected controls (n = 10), HIV-only (n = 14), helminth-only (n = 15), HIV-helminth co-infected (n = 13), and CRC-confirmed patients (n = 10). Bioinformatic analyses were used to identify differentially abundant viral genes and to functionally annotate epigenetic and metabolic pathways associated with infection status and CRC occurrence. RESULTS AND DISCUSSION : Adenine-specific DNA methylase (COG2189) emerged as one of the most significantly enriched epigenetic markers across all infected and CRC groups, CRC (7.0 ± 1.26, q = 2.98e-06), helminth-only (7.1 ± 1.16, q = 1.30e-07), HIV-only (6.2 ± 1.21, q = 1.28e-05), and co-infected 6.5 ± 1.21, q = 6.11e-06), suggesting a shared viral epigenomic mechanism potentially contributing to tumorigenesis. Additionally, diverse metabolism-related genes were differentially abundant, particularly those linked to butyrate metabolism, oxidative stress response, and polyamine biosynthesis, metabolic pathways known to influence tumor initiation, immune evasion, and disease progression. These findings indicate that the gut virome may play an intermediary role in modulating host epigenetic and metabolic landscapes in infection-driven CRC risk. CONCLUSION : This study identifies novel gut virome-associated epigenetic and metabolic functional signatures that may serve as early, non-invasive biomarkers of CRC susceptibility in HIV- and helminth-endemic populations. Integrating such molecular indicators into cancer surveillance and prevention frameworks could enhance early detection strategies and precision cancer care in underrepresented, high-infection burden African regions. HIGHLIGHTS • To our knowledge, this is the first metagenomic profiling of the gut virome in HIV-helminth co-infected African adults. • Differential viral gene expression, including adenine-specific DNA methylase enrichment, suggests shared epigenomic mechanisms with CRC. • Distinct metabolic signatures associated with CRC risk, including butyrate and polyamine pathways, were identified. • Virome-associated epigenetic and metabolic markers show promise for early CRC risk detection in high-burden settings.
Virological failure and risk factors among people living with HIV taking second-line ART in Addis Ababa, Ethiopia
Feyissa, Bekelech Bayou; Sisay, Abay; Davids, Eugene Lee; Yalew, Anteneh; Setswe, Geoffrey (Public Library of Science, 2026-02)
BACKGROUND : Virological failure (VF) presents significant challenges in the emergence of drug resistance, and elevated risk of transmission, higher mortality rates, and a diminished quality of life. Various factors contribute to VF, but documented information on this issue is lacking in Ethiopia. Therefore, this study aimed to assess the prevalence of VF and identify the risk factors among people living with HIV who are on second-line antiretroviral treatment (ART). METHODS : A concurrent mixed-method study using quantitative and qualitative data was conducted at selected hospitals in Addis Ababa, Ethiopia. The analysis was conducted using SPSS version 28, Stata version 18.5, and R for quantitative data and thematic analysis with Atlas.ti version 24 software was used for qualitative data. RESULT : Among 369 adults living with HIV taking second-line ART enrolled in the study, 191 (52%) were male with a median age of 44 years. The prevalence of VF was 55 (14.9%, 95% CI: 11, 19), with an incidence density of 27.2 per 10,000 person months (95% CI 21.1, 35.5). Lost to follow-up significantly increased VF risk [AHR: 2.52 (95% CI: 1.35, 4.69, p-value: 0.004)]. Patients transferred from other health facilities were two times at higher risk of VF compared to those receiving ART at the same facility [AHR: 1.97 (95% CI: 1.07, 3-64, p-value: 0.029)]. Likewise, clients with a history of regimen change were at a higher risk of VF [AHR = 2.05, (95% CI: 1.08, 3.88, p-value = 0.027)]. The qualitative data also supported these findings. CONCLUSION : This study underscores the need for improved ART adherence and consistent care to reduce virological failure in PLHIV to improve the quality of life.
Validation of the primerdesign quantitative allele specific amplification kit for the detection of JAK2V617F mutation
Vaz, Deborah; Netshidzivhani, Tshiphiri; Potgieter, Johan (Wiley, 2026-03)
INTRODUCTION : Janus Kinase 2 (JAK2) is a tyrosine kinase involved in cellular signalling. A point mutation in codon 617 of JAK2 (JAK2V617F) causes a gain-of-function effect that stimulates proliferation of myeloid cells. The aim of this study was to evaluate the Primerdesign quantitative allele-specific amplification (Quasa) kit for the detection of JAK2V617F. METHODS : Specimens previously evaluated using real-time PCR with melting curve analysis were analysed using the Quasa kit on the Bio-Rad CFX 96 platform. Results of the two PCR tests were compared to evaluate the accuracy of the kit. For intra-assay precision, samples were analysed in duplicate on the same run, and for inter-assay variation, the same known samples were tested on three non-consecutive days. The analytical sensitivity and quantitative analysis of the assay were determined using the World Health Organization (WHO) 1st International Reference Panel for Genomic JAK2V617F (United Kingdom Official Medicines Control Laboratory) and the United Kingdom National External Quality Assessment Service (UK NEQAS) results of their JAK2 p.val617phe (V617F) Mutation Status Programme. RESULTS : Concordance of the qualitative test results between the test methods was 100%. Precision experiments confirmed repeatability and reproducibility. Analytical sensitivity was confirmed at 0.1%. CONCLUSION : The PrimerDesign Quasa kit for the detection of JAK2V617F is a sensitive and reliable assay that yields reproducible qualitative results. The kit is commercially available and has, in addition, the potential for quantitative analysis when samples are analysed in duplicate. This kit assay validation may be valuable to laboratories offering or interested in offering JAK2V617F mutational testing.
Utilizing nominal group technique to achieve consensus on a clinical decision-making tool for vocational rehabilitation at a grassroots level in South Africa
Harmse, Suzanne; Casteleijn, Daleen; Jacobs, Karen (Sage, 2026-03)
BACKGROUND : Barriers to the delivery of vocational rehabilitation have been reported as a lack of knowledge, skills and confidence in occupational therapists who deliver these services. A program aimed at overcoming these barriers was developed to provide training in the delivery of vocational rehabilitation services. The program includes three decision-making tools to facilitate not only knowledge translation but also practice changes. The tools are (1) Return-to-Work Decision Tree, (2) Performance-based Assessment Tool, (3) Job Match Tool. OBJECTIVE : The objective of the research was to obtain consensus on the acceptability and utility of the developed tools to facilitate clinical reasoning in the delivery of vocational rehabilitation services. METHODS : A nominal group technique was used to obtain consensus on the developed tools. During a second phase, participants were sent revised versions of the tools and asked to comment on the tools’ clinical utility using a four-point Likert scale. RESULTS : The Return-to-Work Decision Tree and the Performance-based Assessment Tool received a 100% agreement in terms of clinical utility with the Job Match Tool receiving a 90% agreement for clinical utility. Participants made valuable recommendations such as adding a user manual and a training workshop to facilitate implementation of the tools. CONCLUSION : The three tools developed to support clinical reasoning and decision making during the vocational rehabilitation process were reported to be acceptable by the expert participants. Further development of the Job Match Tool is recommended.
Using vignettes to understand teacher well-being, anxiety and the long-term effects of the COVID-19 pandemic
Otto, Leanda; Eloff, Irma F. (Routledge, 2026)
This study utilised vignettes to investigate the diverse experiences of anxiety among teachers during the COVID-19 pandemic in independent primary schools in Gauteng, South Africa. The study adopted a retrospective vignette research design, a phenomenological paradigm, and a broad qualitative research approach. Participants (n = 18) took part in focus groups and concurrent creative expressive art therapeutic (CEAT) processes. Data collection involved asking focus group participants to create artefacts based on their experiences of COVID-19-related anxiety in the classroom. Raw vignettes were developed into final vignettes from observation data through a series of vignette and resonance readings. Findings indicate the long-lasting challenges faced by teachers due to pandemic-induced anxiety. It also highlights increased collegiality and heightened mental health awareness among teachers. Their commitment to quality education, adaptability, and persistence was evident. The study aims to inform interventions for the long-term effects of COVID-19 on teachers, specifically regarding their experiences of COVID-19-related anxiety