Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)
Identifieur interne : 000720 ( Pmc/Checkpoint ); précédent : 000719; suivant : 000721Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)
Auteurs : Mette Myrmel [Norvège] ; Veslem Y Oma [Norvège] ; Mamata Khatri [Norvège] ; Hanne H. Hansen [Norvège] ; Maria Stokstad [Norvège] ; Mikael Berg [Suède] ; Anne-Lie Blomström [Suède]Source :
- PLoS ONE [ 1932-6203 ] ; 2017.
Abstract
Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169–284 944), only 0.07% of the SISPA reads (sequence depth of 0–249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.
Url:
DOI: 10.1371/journal.pone.0187780
PubMed: 29112950
PubMed Central: 5675387
Affiliations:
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PMC:5675387Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169–284 944), only 0.07% of the SISPA reads (sequence depth of 0–249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.</p>
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<author><name sortKey="Seelow, D" uniqKey="Seelow D">D Seelow</name>
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</author>
<author><name sortKey="Hoffmann, B" uniqKey="Hoffmann B">B Hoffmann</name>
</author>
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<article-id pub-id-type="pmc">5675387</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0187780</article-id>
<article-id pub-id-type="publisher-id">PONE-D-17-31094</article-id>
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<subj-group><subject>Organisms</subject>
<subj-group><subject>Viruses</subject>
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<subj-group><subject>Organisms</subject>
<subj-group><subject>Viruses</subject>
<subj-group><subject>RNA viruses</subject>
<subj-group><subject>Coronaviruses</subject>
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</subj-group>
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<subj-group><subject>Microbiology</subject>
<subj-group><subject>Medical Microbiology</subject>
<subj-group><subject>Microbial Pathogens</subject>
<subj-group><subject>Viral Pathogens</subject>
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<subj-group><subject>Microbial Pathogens</subject>
<subj-group><subject>Viral Pathogens</subject>
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<subj-group><subject>Organisms</subject>
<subj-group><subject>Viruses</subject>
<subj-group><subject>Viral Pathogens</subject>
<subj-group><subject>Coronaviruses</subject>
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</subj-group>
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<subj-group><subject>Molecular biology</subject>
<subj-group><subject>Molecular biology techniques</subject>
<subj-group><subject>Sequencing techniques</subject>
<subj-group><subject>RNA sequencing</subject>
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<subj-group><subject>RNA sequencing</subject>
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<subj-group><subject>Molecular Biology</subject>
<subj-group><subject>Molecular Biology Techniques</subject>
<subj-group><subject>Artificial Gene Amplification and Extension</subject>
<subj-group><subject>Polymerase Chain Reaction</subject>
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</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Molecular Biology Techniques</subject>
<subj-group><subject>Artificial Gene Amplification and Extension</subject>
<subj-group><subject>Polymerase Chain Reaction</subject>
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<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
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<subj-group><subject>Genome Analysis</subject>
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<subj-group><subject>Genetics</subject>
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<title-group><article-title>Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)</article-title>
<alt-title alt-title-type="running-head">Comparison of two sequence-independent approaches for next generation sequencing of bovine coronavirus</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><contrib-id authenticated="true" contrib-id-type="orcid">http://orcid.org/0000-0002-2794-4023</contrib-id>
<name><surname>Myrmel</surname>
<given-names>Mette</given-names>
</name>
<role content-type="http://credit.casrai.org/">Conceptualization</role>
<role content-type="http://credit.casrai.org/">Formal analysis</role>
<role content-type="http://credit.casrai.org/">Funding acquisition</role>
<role content-type="http://credit.casrai.org/">Methodology</role>
<role content-type="http://credit.casrai.org/">Supervision</role>
<role content-type="http://credit.casrai.org/">Writing – original draft</role>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Oma</surname>
<given-names>Veslemøy</given-names>
</name>
<role content-type="http://credit.casrai.org/">Methodology</role>
<role content-type="http://credit.casrai.org/">Writing – original draft</role>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="econtrib001"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Khatri</surname>
<given-names>Mamata</given-names>
</name>
<role content-type="http://credit.casrai.org/">Methodology</role>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="econtrib001"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hansen</surname>
<given-names>Hanne H.</given-names>
</name>
<role content-type="http://credit.casrai.org/">Methodology</role>
<role content-type="http://credit.casrai.org/">Writing – original draft</role>
<xref ref-type="aff" rid="aff003"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stokstad</surname>
<given-names>Maria</given-names>
</name>
<role content-type="http://credit.casrai.org/">Conceptualization</role>
<role content-type="http://credit.casrai.org/">Funding acquisition</role>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Berg</surname>
<given-names>Mikael</given-names>
</name>
<role content-type="http://credit.casrai.org/">Conceptualization</role>
<role content-type="http://credit.casrai.org/">Writing – original draft</role>
<xref ref-type="aff" rid="aff004"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Blomström</surname>
<given-names>Anne-Lie</given-names>
</name>
<role content-type="http://credit.casrai.org/">Conceptualization</role>
<role content-type="http://credit.casrai.org/">Formal analysis</role>
<role content-type="http://credit.casrai.org/">Writing – original draft</role>
<xref ref-type="aff" rid="aff004"><sup>4</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label>
<addr-line>Department for Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway</addr-line>
</aff>
<aff id="aff002"><label>2</label>
<addr-line>Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway</addr-line>
</aff>
<aff id="aff003"><label>3</label>
<addr-line>CIGENE, Norwegian University of Life Sciences, Ås, Norway</addr-line>
</aff>
<aff id="aff004"><label>4</label>
<addr-line>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Melcher</surname>
<given-names>Ulrich</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Oklahoma State University, UNITED STATES</addr-line>
</aff>
<author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="other" id="econtrib001"><p>‡ These authors also contributed equally to this work.</p>
</fn>
<corresp id="cor001">* E-mail: <email>mette.myrmel@nmbu.no</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>7</day>
<month>11</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection"><year>2017</year>
</pub-date>
<volume>12</volume>
<issue>11</issue>
<elocation-id>e0187780</elocation-id>
<history><date date-type="received"><day>23</day>
<month>8</month>
<year>2017</year>
</date>
<date date-type="accepted"><day>25</day>
<month>10</month>
<year>2017</year>
</date>
</history>
<permissions><copyright-statement>© 2017 Myrmel et al</copyright-statement>
<copyright-year>2017</copyright-year>
<copyright-holder>Myrmel et al</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="pone.0187780.pdf"></self-uri>
<abstract><p>Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169–284 944), only 0.07% of the SISPA reads (sequence depth of 0–249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.</p>
</abstract>
<funding-group><award-group id="award001"><funding-source><institution-wrap><institution-id institution-id-type="funder-id">http://dx.doi.org/10.13039/501100005416</institution-id>
<institution>Norges Forskningsråd</institution>
</institution-wrap>
</funding-source>
<award-id>224771/E40</award-id>
<principal-award-recipient><name><surname>Stokstad</surname>
<given-names>Maria</given-names>
</name>
</principal-award-recipient>
</award-group>
<award-group id="award002"><funding-source><institution-wrap><institution-id institution-id-type="funder-id">http://dx.doi.org/10.13039/501100001862</institution-id>
<institution>Svenska Forskningsrådet Formas</institution>
</institution-wrap>
</funding-source>
<award-id>Formas-2012-586</award-id>
<principal-award-recipient>Anne-Lie Blomstrøm</principal-award-recipient>
</award-group>
<funding-statement>This work was supported by Norges forskningsråd, No 224771/E40, <ext-link ext-link-type="uri" xlink:href="https://www.forskningsradet.no/no/Forsiden/1173185591033">https://www.forskningsradet.no/no/Forsiden/1173185591033</ext-link>
; Swedish research council, Formas-2012-586, <ext-link ext-link-type="uri" xlink:href="http://www.formas.se">www.formas.se</ext-link>
. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><fig-count count="1"></fig-count>
<table-count count="2"></table-count>
<page-count count="9"></page-count>
</counts>
<custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name>
<meta-value>The NGS data is deposited in SRA (NCBI); accession number SRP075933. The GenBank accession number for the bovine rhinitis B virus is KY432299.1.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes><title>Data Availability</title>
<p>The NGS data is deposited in SRA (NCBI); accession number SRP075933. The GenBank accession number for the bovine rhinitis B virus is KY432299.1.</p>
</notes>
</front>
</pmc>
<affiliations><list><country><li>Norvège</li>
<li>Suède</li>
</country>
<region><li>Østlandet</li>
</region>
<settlement><li>Oslo</li>
</settlement>
</list>
<tree><country name="Norvège"><region name="Østlandet"><name sortKey="Myrmel, Mette" sort="Myrmel, Mette" uniqKey="Myrmel M" first="Mette" last="Myrmel">Mette Myrmel</name>
</region>
<name sortKey="Hansen, Hanne H" sort="Hansen, Hanne H" uniqKey="Hansen H" first="Hanne H." last="Hansen">Hanne H. Hansen</name>
<name sortKey="Khatri, Mamata" sort="Khatri, Mamata" uniqKey="Khatri M" first="Mamata" last="Khatri">Mamata Khatri</name>
<name sortKey="Oma, Veslem Y" sort="Oma, Veslem Y" uniqKey="Oma V" first="Veslem Y" last="Oma">Veslem Y Oma</name>
<name sortKey="Stokstad, Maria" sort="Stokstad, Maria" uniqKey="Stokstad M" first="Maria" last="Stokstad">Maria Stokstad</name>
</country>
<country name="Suède"><noRegion><name sortKey="Berg, Mikael" sort="Berg, Mikael" uniqKey="Berg M" first="Mikael" last="Berg">Mikael Berg</name>
</noRegion>
<name sortKey="Blomstrom, Anne Lie" sort="Blomstrom, Anne Lie" uniqKey="Blomstrom A" first="Anne-Lie" last="Blomström">Anne-Lie Blomström</name>
</country>
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</affiliations>
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