Gut Virome Alterations in HIV-Infected Individuals on Long-Term Antiretroviral Therapy in Lagos State

The human gut virome, composed predominantly of bacteriophages and eukaryotic viruses, plays an important but poorly understood role in modulating gut immune homeostasis. In HIV-infected individuals on long-term antiretroviral therapy (ART), persistent gut immune activation despite viral suppression may be linked to gut virome dysbiosis. This study characterises gut virome alterations in HIV-infected adults on ART compared to HIV-uninfected controls at the Lagos University Teaching Hospital, Lagos State, South West Nigeria. A case-control design will recruit 60 HIV-positive adults on suppressive ART (minimum three years, undetectable viral load) and 60 HIV-uninfected controls matched for age, sex, and diet. Stool samples will be collected, viral nucleic acids extracted, and metagenomic next-generation sequencing performed using the Illumina NovaSeq platform. Bioinformatics analysis using VirSorter2 and vConTACT2 will characterise virome composition, alpha and beta diversity, and abundance of specific bacteriophage taxa. Gut microbiome (16S rRNA) data will be co-analysed to identify associations between virome and bacteriome disruption. This study addresses a virtually unexplored research frontier in West African HIV cohorts, where virome studies are absent despite well-described gut dysbiosis in HIV. Findings will contribute fundamental virome data from a Nigerian HIV cohort and identify virome signatures associated with immune activation, potentially informing future microbiome-targeted adjunctive therapies. Keywords: gut virome, HIV, antiretroviral therapy, metagenomics, Lagos State