The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
Identifieur interne : 000373 ( Pmc/Curation ); précédent : 000372; suivant : 000374The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
Auteurs : Samia N. Naccache ; Alexander L. Greninger ; Deanna Lee ; Lark L. Coffey ; Tung Phan ; Annie Rein-Weston ; Andrew Aronsohn ; John Hackett ; Eric L. Delwart ; Charles Y. ChiuSource :
- Journal of Virology [ 0022-538X ] ; 2013.
Abstract
Next-generation sequencing was used for discovery and
Url:
DOI: 10.1128/JVI.02323-13
PubMed: 24027301
PubMed Central: 3807889
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<front><div type="abstract" xml:lang="en"><p>Next-generation sequencing was used for discovery and <italic>de novo</italic>
assembly of a novel, highly divergent DNA virus at the interface between the <named-content content-type="genus-species">Parvoviridae</named-content>
and <named-content content-type="genus-species">Circoviridae</named-content>
. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.</p>
</div>
</front>
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<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">24027301</article-id>
<article-id pub-id-type="pmc">3807889</article-id>
<article-id pub-id-type="publisher-id">02323-13</article-id>
<article-id pub-id-type="doi">10.1128/JVI.02323-13</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Genetic Diversity and Evolution</subject>
</subj-group>
</article-categories>
<title-group><article-title>The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Naccache</surname>
<given-names>Samia N.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Greninger</surname>
<given-names>Alexander L.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lee</surname>
<given-names>Deanna</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Coffey</surname>
<given-names>Lark L.</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Phan</surname>
<given-names>Tung</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rein-Weston</surname>
<given-names>Annie</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Aronsohn</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hackett</surname>
<given-names>John</given-names>
<suffix>Jr.</suffix>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Delwart</surname>
<given-names>Eric L.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Chiu</surname>
<given-names>Charles Y.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="aff" rid="aff6"><sup>f</sup>
</xref>
</contrib>
<aff id="aff1">Department of Laboratory Medicine, University of California, San Francisco, California, USA<label>a</label>
</aff>
<aff id="aff2">UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA<label>b</label>
</aff>
<aff id="aff3">Blood Systems Research Institute, San Francisco, California, USA<label>c</label>
</aff>
<aff id="aff4">Center for Liver Disease, University of Chicago Medical Center, Chicago, Illinois, USA<label>d</label>
</aff>
<aff id="aff5">Abbott Diagnostics, Abbott Park, Illinois, USA<label>e</label>
</aff>
<aff id="aff6">Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California, USA<label>f</label>
</aff>
</contrib-group>
<author-notes><corresp id="cor1">Address correspondence to Charles Y. Chiu, <email>charles.chiu@ucsf.edu</email>
.</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>11</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>15</day>
<month>11</month>
<year>2013</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>87</volume>
<issue>22</issue>
<fpage>11966</fpage>
<lpage>11977</lpage>
<history><date date-type="received"><day>15</day>
<month>8</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>28</day>
<month>8</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013, American Society for Microbiology. All Rights Reserved.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>American Society for Microbiology</copyright-holder>
<license license-type="open-access"><license-p>The authors have paid a fee to allow immediate free access to this article.</license-p>
</license>
</permissions>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zjv02213011966.pdf"></self-uri>
<abstract><p>Next-generation sequencing was used for discovery and <italic>de novo</italic>
assembly of a novel, highly divergent DNA virus at the interface between the <named-content content-type="genus-species">Parvoviridae</named-content>
and <named-content content-type="genus-species">Circoviridae</named-content>
. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.</p>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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