Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

Pathogenic simian immunodeficiency virus (SIV) infection is associated with enteropathy, which likely contributes to AIDS progression. To identify candidate etiologies for AIDS enteropathy, we used next-generation sequencing to define the enteric virome during SIV infection in nonhuman primates. Pathogenic, but not nonpathogenic, SIV infection was associated with significant expansion of the enteric virome. We identified at least 32 previously undescribed enteric viruses during pathogenic SIV infection and confirmed their presence by using viral culture and PCR testing. We detected unsuspected mucosal adenovirus infection associated with enteritis as well as parvovirus viremia in animals with advanced AIDS, indicating the pathogenic potential of SIV-associated expansion of the enteric virome. No association between pathogenic SIV infection and the family-level taxonomy of enteric bacteria was detected. Thus, enteric viral infections may contribute to AIDS enteropathy and disease progression. These findings underline the importance of metagenomic analysis of the virome for understanding AIDS pathogenesis. º The enteric virome expands during pathogenic, but not nonpathogenic, SIV infection º Pathogenic SIV-infected rhesus monkeys shed multiple enteric viruses º Viruses are associated with intestinal pathology during SIV infection º Metagenomic analysis of the enteric virome is important to study AIDS pathogenesis Monkeys infected with pathogenic SIV manifest an expanded enteric virome that includes examples of previously uncharacterized viruses. Viruses within the cohort are associated with intestinal damage, suggesting a link to the intestinal pathologies that develop in HIV-infected patients.