Dissecting the Functional Virome of the Human Gut in HIV-Positive Nigerians on Long-Term Antiretroviral Therapy Using Viral Metagenomics

The human gut virome, comprising bacteriophages, eukaryotic viruses, and endogenous retroviruses, plays emerging roles in modulating immune homeostasis, bacterial microbiome composition, and systemic inflammation. In HIV-positive individuals on antiretroviral therapy (ART), persistent immune dysregulation may be influenced by virome alterations, yet gut virome characterization in Nigerian HIV cohorts is entirely unexplored. This study dissects the functional virome of the human gut in HIV-positive individuals on long-term ART compared with HIV-negative controls from Benue and Kogi States, North Central Nigeria. Stool samples were collected from 40 HIV-positive patients on ART for more than five years and 40 HIV-negative controls matched by age, sex, and geographic location. Viral-like particle (VLP) enrichment was performed by ultracentrifugation, followed by nuclease treatment and total nucleic acid extraction. Sequencing was performed on the Illumina NovaSeq platform. Bioinformatic pipeline employed VirSorter2 and VIBRANT for viral contig identification, followed by vConTACT2 for viral protein cluster taxonomy. Functional annotation used DRAM-v against VOG and PFAM databases. HIV-positive individuals demonstrated significant depletion of Caudoviricetes bacteriophages (p less than 0.001) and enrichment of Anelloviridae (p=0.003) compared to controls. Bacteriophage functional gene analysis revealed reduced CRISPR-mediated host defense gene content in HIV-positive virome assemblies. Novel virome-microbiome interaction networks were reconstructed using co-occurrence analysis, identifying phage-bacteria pairs significantly altered in HIV-ART subjects. These findings make an original contribution to the characterization of gut virome-immune axis dysregulation in long-term HIV-treated Nigerian populations. Keywords: gut virome, viral metagenomics, HIV, antiretroviral therapy, North Central Nigeria.