Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency

• Main Authors: Juliana D. Siqueira, Gislaine Curty, Deng Xutao, Cristina B. Hofer, Elizabeth S. Machado, Héctor N. Seuánez, Marcelo A. Soares, Eric Delwart, Esmeralda A. Soares
• Format: Article
• Language: English
• Published: MDPI AG 2019-05-01
• Series: Viruses
• Subjects: virome; microbiome; HPV; HIV; immunodeficiency
• Online Access: https://www.mdpi.com/1999-4915/11/5/422

The human cervical microbiome is complex, and its role in health and disease has just begun to be elucidated. In this study, 57 cervical swab samples from 19 HIV/HPV co-infected women were analyzed for both virome and bacteriome composition. Virome analysis focused on circular DNA viruses through rolling circle amplification followed by next-generation sequencing (NGS). Data were assigned to virus families and genera, and HPV types were identified. NGS data of bacterial 16S from a subset of 24 samples were assigned to operational taxonomic units and classified according to vaginal microbiome community state types (CSTs). Four viral families were found: <i>Papillomaviridae</i>, <i>Anelloviridae</i>, <i>Genomoviridae</i>, and <i>Herpesviridae</i>. Papillomavirus reads were more abundant in women with premalignant cervical lesions, which were also strongly associated with multiple (≥3) high-risk HPV infection. Anellovirus read abundance was negatively correlated with host CD4+ T-cell counts. The bacteriome revealed the presence of CST III and CST IV, and women with ≥1% frequency of genomovirus or herpesvirus reads displayed an increased risk of carrying CST IV. By characterizing the composition of the cervical circular DNA viruses and the bacteriome of HIV/HPV co-infected women, we identified putative interactions between these two microorganism communities and their associations with patients’ clinical characteristics, notably immunodeficiency status.