Characterization of the Virome in HIV-Positive Individuals with Opportunistic Coinfections in Tertiary Hospitals Across Southern Nigeria: Metagenomic and Epidemiological Perspectives

The human virome, comprising all viral communities inhabiting the human body, is profoundly altered by HIV-mediated immunosuppression and opportunistic coinfections, yet comprehensive virome characterization in Nigerian HIV-positive patient populations using modern metagenomics remains unpublished. This study characterized the virome in HIV-positive individuals with diverse opportunistic coinfections across tertiary hospitals in the South South (Rivers State), South East (Anambra State), and South West (Lagos State) geopolitical zones using viral metagenomics combined with classical epidemiological investigation. Blood, oral, and stool samples from 120 HIV-positive patients stratified by CD4 count (below 100, 100 to 350, and above 350 cells/mm³) and 40 HIV-negative controls were subjected to viral particle enrichment by ultracentrifugation, nuclease treatment, and total nucleic acid extraction. Viral metagenomics was performed using Illumina NovaSeq, with taxonomic classification by Diamond-MEGAN and VIPR databases. Virome diversity indices and correlations with CD4 count, opportunistic coinfection status, and ART exposure were analyzed. Results revealed a dramatically expanded and diversified virome in severely immunosuppressed patients (CD4 below 100), including novel anellovirus strains, human herpesvirus 8, and multiple enteric picornaviruses not previously reported in Nigerian patients. Beta-diversity analysis demonstrated distinct virome community structure separating severe immunosuppression from moderate and controlled disease groups. A novel divergent anellovirus clade was detected in 24 percent of patients and correlated inversely with CD4 count. These findings constitute an original virological and epidemiological contribution to understanding the consequences of HIV-related immunosuppression on the human virome in southern Nigeria. Keywords: virome, HIV, viral metagenomics, opportunistic infections, immunosuppression.