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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets</title>
<author><name sortKey="Ma, Yingfei" sort="Ma, Yingfei" uniqKey="Ma Y" first="Yingfei" last="Ma">Yingfei Ma</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Madupu, Ramana" sort="Madupu, Ramana" uniqKey="Madupu R" first="Ramana" last="Madupu">Ramana Madupu</name>
<affiliation><nlm:aff id="aff2">J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Karaoz, Ulas" sort="Karaoz, Ulas" uniqKey="Karaoz U" first="Ulas" last="Karaoz">Ulas Karaoz</name>
<affiliation><nlm:aff id="aff3">Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nossa, Carlos W" sort="Nossa, Carlos W" uniqKey="Nossa C" first="Carlos W." last="Nossa">Carlos W. Nossa</name>
<affiliation><nlm:aff id="aff4">Gene by Gene, Ltd., Houston, Texas, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yang, Liying" sort="Yang, Liying" uniqKey="Yang L" first="Liying" last="Yang">Liying Yang</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yooseph, Shibu" sort="Yooseph, Shibu" uniqKey="Yooseph S" first="Shibu" last="Yooseph">Shibu Yooseph</name>
<affiliation><nlm:aff id="aff5">J. Craig Venter Institute, La Jolla, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yachimski, Patrick S" sort="Yachimski, Patrick S" uniqKey="Yachimski P" first="Patrick S." last="Yachimski">Patrick S. Yachimski</name>
<affiliation><nlm:aff id="aff6">Vanderbilt University School of Medicine, Nashville, Tennessee, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Brodie, Eoin L" sort="Brodie, Eoin L" uniqKey="Brodie E" first="Eoin L." last="Brodie">Eoin L. Brodie</name>
<affiliation><nlm:aff id="aff3">Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name>
<affiliation><nlm:aff id="aff2">J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pei, Zhiheng" sort="Pei, Zhiheng" uniqKey="Pei Z" first="Zhiheng" last="Pei">Zhiheng Pei</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff7">The Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, USA</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">24522917</idno>
<idno type="pmc">3993818</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993818</idno>
<idno type="RBID">PMC:3993818</idno>
<idno type="doi">10.1128/JVI.00093-14</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000095</idno>
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</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets</title>
<author><name sortKey="Ma, Yingfei" sort="Ma, Yingfei" uniqKey="Ma Y" first="Yingfei" last="Ma">Yingfei Ma</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Madupu, Ramana" sort="Madupu, Ramana" uniqKey="Madupu R" first="Ramana" last="Madupu">Ramana Madupu</name>
<affiliation><nlm:aff id="aff2">J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Karaoz, Ulas" sort="Karaoz, Ulas" uniqKey="Karaoz U" first="Ulas" last="Karaoz">Ulas Karaoz</name>
<affiliation><nlm:aff id="aff3">Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nossa, Carlos W" sort="Nossa, Carlos W" uniqKey="Nossa C" first="Carlos W." last="Nossa">Carlos W. Nossa</name>
<affiliation><nlm:aff id="aff4">Gene by Gene, Ltd., Houston, Texas, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yang, Liying" sort="Yang, Liying" uniqKey="Yang L" first="Liying" last="Yang">Liying Yang</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yooseph, Shibu" sort="Yooseph, Shibu" uniqKey="Yooseph S" first="Shibu" last="Yooseph">Shibu Yooseph</name>
<affiliation><nlm:aff id="aff5">J. Craig Venter Institute, La Jolla, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yachimski, Patrick S" sort="Yachimski, Patrick S" uniqKey="Yachimski P" first="Patrick S." last="Yachimski">Patrick S. Yachimski</name>
<affiliation><nlm:aff id="aff6">Vanderbilt University School of Medicine, Nashville, Tennessee, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Brodie, Eoin L" sort="Brodie, Eoin L" uniqKey="Brodie E" first="Eoin L." last="Brodie">Eoin L. Brodie</name>
<affiliation><nlm:aff id="aff3">Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name>
<affiliation><nlm:aff id="aff2">J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pei, Zhiheng" sort="Pei, Zhiheng" uniqKey="Pei Z" first="Zhiheng" last="Pei">Zhiheng Pei</name>
<affiliation><nlm:aff id="aff1">New York University, School of Medicine, New York, New York, USA</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff7">The Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, USA</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of Virology</title>
<idno type="ISSN">0022-538X</idno>
<idno type="eISSN">1098-5514</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><title>ABSTRACT</title>
<p>Human papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects.</p>
<p><bold>IMPORTANCE</bold>
This nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Virol</journal-id>
<journal-id journal-id-type="iso-abbrev">J. Virol</journal-id>
<journal-id journal-id-type="hwp">jvi</journal-id>
<journal-id journal-id-type="pmc">jvi</journal-id>
<journal-id journal-id-type="publisher-id">JVI</journal-id>
<journal-title-group><journal-title>Journal of Virology</journal-title>
</journal-title-group>
<issn pub-type="ppub">0022-538X</issn>
<issn pub-type="epub">1098-5514</issn>
<publisher><publisher-name>American Society for Microbiology</publisher-name>
<publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24522917</article-id>
<article-id pub-id-type="pmc">3993818</article-id>
<article-id pub-id-type="publisher-id">00093-14</article-id>
<article-id pub-id-type="doi">10.1128/JVI.00093-14</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Structure and Assembly</subject>
</subj-group>
</article-categories>
<title-group><article-title>Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ma</surname>
<given-names>Yingfei</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Madupu</surname>
<given-names>Ramana</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Karaoz</surname>
<given-names>Ulas</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nossa</surname>
<given-names>Carlos W.</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yang</surname>
<given-names>Liying</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yooseph</surname>
<given-names>Shibu</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yachimski</surname>
<given-names>Patrick S.</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>f</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brodie</surname>
<given-names>Eoin L.</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nelson</surname>
<given-names>Karen E.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Pei</surname>
<given-names>Zhiheng</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff7"><sup>g</sup>
</xref>
</contrib>
<aff id="aff1"><label>a</label>
New York University, School of Medicine, New York, New York, USA</aff>
<aff id="aff2"><label>b</label>
J. Craig Venter Institute, Rockville, Maryland, USA</aff>
<aff id="aff3"><label>c</label>
Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA</aff>
<aff id="aff4"><label>d</label>
Gene by Gene, Ltd., Houston, Texas, USA</aff>
<aff id="aff5"><label>e</label>
J. Craig Venter Institute, La Jolla, California, USA</aff>
<aff id="aff6"><label>f</label>
Vanderbilt University School of Medicine, Nashville, Tennessee, USA</aff>
<aff id="aff7"><label>g</label>
The Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, USA</aff>
</contrib-group>
<contrib-group><contrib contrib-type="editor"><name><surname>Imperiale</surname>
<given-names>M. J.</given-names>
</name>
<role>Editor</role>
</contrib>
</contrib-group>
<author-notes><corresp id="cor1">Address correspondence to Zhiheng Pei, <email>zhiheng.pei@nyumc.org</email>
.</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>5</month>
<year>2014</year>
</pub-date>
<volume>88</volume>
<issue>9</issue>
<fpage>4786</fpage>
<lpage>4797</lpage>
<history><date date-type="received"><day>12</day>
<month>1</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>5</day>
<month>2</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014, American Society for Microbiology. All Rights Reserved.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>American Society for Microbiology</copyright-holder>
</permissions>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zjv00914004786.pdf"></self-uri>
<abstract><title>ABSTRACT</title>
<p>Human papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects.</p>
<p><bold>IMPORTANCE</bold>
This nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections.</p>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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