{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T20:58:35Z","timestamp":1792011515687,"version":"4.4.0"},"reference-count":57,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2023,3,15]],"date-time":"2023-03-15T00:00:00Z","timestamp":1678838400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,3,15]],"date-time":"2023-03-15T00:00:00Z","timestamp":1678838400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"South African MRC","doi-asserted-by":"publisher","award":["R01 HD083040-02S1"],"award-info":[{"award-number":["R01 HD083040-02S1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"South African MRC","doi-asserted-by":"publisher","award":["R01 AI094586"],"award-info":[{"award-number":["R01 AI094586"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001713","name":"European Union","doi-asserted-by":"publisher","award":["TMA2020CDF-3192-VaViBa"],"award-info":[{"award-number":["TMA2020CDF-3192-VaViBa"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation Calestous Juma Scientific Leadership Fellowship","doi-asserted-by":"publisher","award":["INV-037612"],"award-info":[{"award-number":["INV-037612"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation","doi-asserted-by":"publisher","award":["17\/43"],"award-info":[{"award-number":["17\/43"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u201319 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\u2019s health.<\/jats:p>","DOI":"10.3390\/v15030758","type":"journal-article","created":{"date-parts":[[2023,3,16]],"date-time":"2023-03-16T03:50:45Z","timestamp":1678938645000},"page":"758","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Cervicovaginal Human Papillomavirus Genomes, Microbiota Composition and Cytokine Concentrations in South African Adolescents"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3658-8638","authenticated-orcid":false,"given":"Anna-Ursula","family":"Happel","sequence":"first","affiliation":[{"name":"Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3439-3992","authenticated-orcid":false,"given":"Christina","family":"Balle","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6185-8607","authenticated-orcid":false,"given":"Enock","family":"Havyarimana","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4476-6150","authenticated-orcid":false,"given":"Bryan","family":"Brown","sequence":"additional","affiliation":[{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3174-9036","authenticated-orcid":false,"given":"Brandon","family":"Maust","sequence":"additional","affiliation":[{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin","family":"Feng","sequence":"additional","affiliation":[{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byung","family":"Yi","sequence":"additional","affiliation":[{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Gill","sequence":"additional","affiliation":[{"name":"Desmond Tutu Health Foundation, 3 Woodlands Road, Woodstock, Cape Town 7915, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda-Gail","family":"Bekker","sequence":"additional","affiliation":[{"name":"Desmond Tutu Health Foundation, 3 Woodlands Road, Woodstock, Cape Town 7915, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo-Ann","family":"Passmore","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"},{"name":"National Health Laboratory Service, Observatory, Cape Town 7925, South Africa"},{"name":"NRF-DST Center of Excellence in HIV Prevention, Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Congella, Durban 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Jaspan","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa"},{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA"},{"name":"Department of Global Health, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4111-2415","authenticated-orcid":false,"given":"Arvind","family":"Varsani","sequence":"additional","affiliation":[{"name":"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"},{"name":"Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Wylie, K.M., Mihindukulasuriya, K.A., Zhou, Y., Sodergren, E., Storch, G.A., and Weinstock, G.M. 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