Large expansion of plasma commensal viruses is associated with SIV pathogenesis in <i>Macaca leonina</i>

Human immunodeficiency virus-1 (HIV-1) infection disrupts the homeostatic equilibrium between the host and commensal microbes. However, the dynamic changes of plasma commensal viruses and their role in HIV/simian immunodeficiency virus (SIV) pathogenesis are rarely reported. Here, we investigated the longitudinal changes of plasma virome, inflammation levels, and disease markers using an SIV-infected <i>Macaca leonina</i> model. Large expansions of plasma <i>Anelloviridae</i>, <i>Parvoviridae</i>, <i>Circoviridae</i> and other commensal viruses, and elevated levels of inflammation and D-dimer were observed since the chronic phase of SIV infection. <i>Anelloviridae</i> abundance appears to correlate positively with the CD4⁺ T cell count but negatively with SIV load especially at the acute phase, whereas other commensal viruses' abundances show opposite correlations with the two disease markers. Antiretroviral therapy slightly reduces but does not substantially reverse the expansion of commensal viruses. Furthermore, 1387 primate anellovirus open reading frame 1 sequences of more than 1500 nucleotides were annotated. The data reveal different roles of commensal viruses in SIV pathogenesis.