Cervicovaginal Human Papillomavirus Genomes, Microbiota Composition and Cytokine Concentrations in South African Adolescents
Anna-Ursula Happel,
Christina Balle,
Enock Havyarimana,
Bryan Brown,
Brandon S. Maust,
Colin Feng,
Byung H. Yi,
Katherine Gill,
Linda-Gail Bekker,
Jo-Ann S. Passmore,
Heather B. Jaspan,
Arvind Varsani
Affiliations
Anna-Ursula Happel
Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
Christina Balle
Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
Enock Havyarimana
Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
Bryan Brown
Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
Brandon S. Maust
Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
Colin Feng
Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
Byung H. Yi
Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA
Katherine Gill
Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town 7915, South Africa
Linda-Gail Bekker
Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town 7915, South Africa
Jo-Ann S. Passmore
Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
Heather B. Jaspan
Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
Arvind Varsani
The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
The interaction between cervicovaginal virome, bacteriome and genital inflammation has not been extensively investigated. We assessed the vaginal DNA virome from 33 South African adolescents (15–19 years old) using shotgun DNA sequencing of purified virions. We present analyses of eukaryote-infecting DNA viruses, with a focus on human papillomavirus (HPV) genomes and relate these to the vaginal bacterial microbiota (assessed by 16S rRNA gene sequencing) and cytokines (assessed by Luminex). The DNA virome included single-stranded (Anelloviridae, Genomoviridae) and double-stranded DNA viruses (Adenoviridae, Alloherpesviridae, Herpesviridae, Marseilleviridae, Mimiviridae, Polyomaviridae, Poxviridae). We identified 110 unique, complete HPV genomes within two genera (Alphapapillomavirus and Gammapapillomavirus) representing 40 HPV types and 12 species. Of the 40 HPV types identified, 35 showed positive co-infection patterns with at least one other type, mainly HPV-16. HPV-35, a high-risk genotype currently not targeted by available vaccines, was the most prevalent HPV type identified in this cohort. Bacterial taxa commonly associated with bacterial vaginosis also correlated with the presence of HPV. Bacterial vaginosis, rather than HPV, was associated with increased genital inflammation. This study lays the foundation for future work characterizing the vaginal virome and its role in women’s health.
