Characterization of cervicovaginal HPV virome and bacteriome in HIV -i infected women in Northern South Africa

Abstract

BACKGROUND: The presence of a highly diverse bacterial species in the cervicovaginal niche is linked to a higher risk of contracting human immunodeficiency virus (HIV), persistent infection with human papillomavirus (HPV) and consequently cervical cancer. It is unknown how cervicovaginal bacterial species associate and interact with other viruses. This study hypothesized that HIV/HPV co-infected women have an increased diversity of cervicovaginal virome and bacteriome. OBJECTIVES: The study’s primary objective was to characterize cervicovaginal HPV virome and bacteriome in HIV-infected women from selected health care facilities in Northern South Africa. Specific objectives were to determine the presence of HPV virome in HIV-infected women and HIV-noninfected women, to determine the presence of bacteriome in HIV-infected women and HIV-noninfected women, and to determine the relational occurrence of virome and bacteriome according to HIV status. METHODOLOGY: Cervical swabs from 50 HIV/HPV co-infected women; 50 HIV-infected, HPV-noninfected women; and from 50 HPV-infected, HIV-noninfected women were used to extract total deoxyribonucleic acid (DNA). To determine HPV virome, total DNA was enriched by rolling circle amplification (RCA) using an illustra TempliPhi amplification kit. To determine bacteriome, a two-round polymerase chain reaction (PCR) was employed targeting a bacterial 16S rRNA gene. Amplification products obtained from RCA and PCR were purified and sequenced by Next Generation Sequencing (NGS) using a MiniSeq platform (Illumina). The quality of the sequences was validated using the FastQC program. Sequences of good quality were assigned to viral family and genera using the Dragen metagenomics online tool with BaseSpace Sequence Hub. Bacterial sequences were assigned and categorised into vaginal community state types (CSTs) using the Dragen metagenomics online tool with BaseSpace Sequence Hub. The relational occurrence of virome and bacteriome according to HIV status was assessed through Chi-square statistical analysis available in GraphPad Prism version 9.3.1. Differences in occurrence were expressed as probability (P)-values. RESULTS: A diverse group of viral families was observed among HIV/HPV co-infected women. Papillomaviridae (14/34; 41%) was the most prevalent (P<0.0001), followed by Herpesviridae and Phycodnaviridae (12/34; 35%) each, Poxviridae (10/34; 29%), Mimiviridae (7/34; 20%), Maiseilleviridae (3/34; 9%) and Anelloviridae (2/34; 6%) in order of decreasing prevalence. A highly diverse group of bacteriophages was observed, with Myoviridae (31/34, 91%) being the most prevalent (P<0.0001). Among HPV-infected HIV-noninfected women, v Papillomaviridae (8/26; 31%) was the most prevalent (P<0.0001), followed by Anelloviridae (4/26; 15%), Phycodnaviridae (4/26; 15%), Poxviridae and Herpesviridae (2/26; 8%) each in order of decreasing prevalence. Myoviridae (6/26; 23%) was the most prevalent bacteriophage family detected (P=0.0005). Among HIV-infected HPV-noninfected women, a small group of viral families was observed, with Myoviridae (3/11,27%) and Siphoviridae (3/11, 27%) being the most prevalent viral families detected (P=0.0005 each). HPV 16 was the most common high risk (hr) HPV type in HIV-infected women and HIV-noninfected women of this study. This genotype co-existed with other hrHPV or probable hr types including HPV 54, HPV 53, and HPV 26. Overall, hrHPV types were more prevalent in HIV-infected women than in HIV-noninfected women, although this difference was not statistically significant (P=0.2832). When the occurrence of hrHPV types were considered individually, HPV 54 occurred more significantly in HIV-noninfected women than in HIV-infected women (P<0.0003). Bacteriome revealed the presence of community state types (CSTs) one, two, three, four and five among study participants. Among HIV/HPV co-infected women, CST one (L. crispatus), CST three (L. iners) and CST four (high bacterial diversity) were observed, with CST four being the most prevalent. Among HPV-infected, HIV-noninfected women, CST one, three, four and five (L. jensenni) were observed, with CST four, also being the most prevalent. Among HIV-infected, HPV noninfected women, CST three and four were observed. CST three and four were associated with viral infections. Gardnerella vaginalis (75%), Pretovella spp (54%), Atopobium spp (50%), Bifidobacterium spp (27%), Porphyromonas spp (53%), Pseudomonas spp (50%), Faecalibacterium prausnitzii (47%) and Bacteroides spp (35%) were the most prevalent anaerobic bacterial species detected in CST four. A diverse group of bacterial families occurred more significantly among HIV-infected women as compared to HIV-noninfected women for NGS data of RCA products (P<0.0001) and NGS data of 16S amplification products (P<0.0001). CONCLUSION: In conclusion, this study showed a higher diversity of cervicovaginal virome and bacteriome in women who were HIV/HPV co-infected than in those singly infected with HIV or HPV. The relationship between viral infections and a high diversity of bacterial species (CST four) observed herein may be a useful indicator of the individual’s disease state, indicating the likelihood of developing cervical lesions and cervical cancer. As a result, additional research is necessary to uncover the association between viral infections and CST four with disease state. Vaccine development and antiviral research should also target compounds that boost the cervicovaginal environment and maintain vaginal homeostasis.