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Deep sequencing extends the diversity of human papillomaviruses in human skin

Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequenci...

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Published in:	Scientific reports 2014-07, Vol.4 (1), p.5807-5807, Article 5807
Main Authors:	Bzhalava, Davit, Mühr, Laila Sara Arroyo, Lagheden, Camilla, Ekström, Johanna, Forslund, Ola, Dillner, Joakim, Hultin, Emilie
Format:	Article
Language:	English
Subjects:	49/23 631/326/596/2560 692/308/2778 Alphapapillomavirus - genetics Annan klinisk medicin Basic Medicine Bayes Theorem Carcinoma, Squamous Cell - virology Clinical Medicine DNA, Viral - genetics Genetic Variation Genomes High-Throughput Nucleotide Sequencing Human papillomavirus Humanities and Social Sciences Humans Keratoacanthoma - virology Keratosis, Actinic - virology Klinisk medicin Lesions Medical and Health Sciences Medicin och hälsovetenskap Medicinska och farmaceutiska grundvetenskaper Metagenome Microbiology in the medical area Mikrobiologi inom det medicinska området multidisciplinary Other Clinical Medicine Papillomaviridae Phylogeny Polymerase chain reaction Science Sequence Analysis, DNA Skin - virology Skin diseases Skin Neoplasms - virology Vaccines
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description	Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.
doi_str_mv	10.1038/srep05807
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Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.</description><subject>49/23</subject><subject>631/326/596/2560</subject><subject>692/308/2778</subject><subject>Alphapapillomavirus - genetics</subject><subject>Annan klinisk medicin</subject><subject>Basic Medicine</subject><subject>Bayes Theorem</subject><subject>Carcinoma, Squamous Cell - virology</subject><subject>Clinical Medicine</subject><subject>DNA, Viral - genetics</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Human papillomavirus</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Keratoacanthoma - virology</subject><subject>Keratosis, Actinic - virology</subject><subject>Klinisk medicin</subject><subject>Lesions</subject><subject>Medical and Health Sciences</subject><subject>Medicin och hälsovetenskap</subject><subject>Medicinska och farmaceutiska grundvetenskaper</subject><subject>Metagenome</subject><subject>Microbiology in the medical area</subject><subject>Mikrobiologi inom det medicinska området</subject><subject>multidisciplinary</subject><subject>Other Clinical Medicine</subject><subject>Papillomaviridae</subject><subject>Phylogeny</subject><subject>Polymerase chain reaction</subject><subject>Science</subject><subject>Sequence Analysis, DNA</subject><subject>Skin - 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subjects	49/23 631/326/596/2560 692/308/2778 Alphapapillomavirus - genetics Annan klinisk medicin Basic Medicine Bayes Theorem Carcinoma, Squamous Cell - virology Clinical Medicine DNA, Viral - genetics Genetic Variation Genomes High-Throughput Nucleotide Sequencing Human papillomavirus Humanities and Social Sciences Humans Keratoacanthoma - virology Keratosis, Actinic - virology Klinisk medicin Lesions Medical and Health Sciences Medicin och hälsovetenskap Medicinska och farmaceutiska grundvetenskaper Metagenome Microbiology in the medical area Mikrobiologi inom det medicinska området multidisciplinary Other Clinical Medicine Papillomaviridae Phylogeny Polymerase chain reaction Science Sequence Analysis, DNA Skin - virology Skin diseases Skin Neoplasms - virology Vaccines
title	Deep sequencing extends the diversity of human papillomaviruses in human skin
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