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 : 000A66 ( PubMed/Curation ); précédent : 000A65; suivant : 000A67Single 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.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Coronavirus bovin.
- virologie : Fosse nasale.
- Amorces ADN, Animaux, Bovins, Génome viral, Réaction de polymérisation en chaîne, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA Primers.
- genetics : Coronavirus, Bovine.
- methods : High-Throughput Nucleotide Sequencing, Polymerase Chain Reaction.
- virology : Nasal Cavity.
- Animals, Cattle, Genome, Viral.
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.
DOI: 10.1371/journal.pone.0187780
PubMed: 29112950
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Hansen</name><affiliation wicri:level="1"><nlm:affiliation>CIGENE, Norwegian University of Life Sciences, Ås, Norway.</nlm:affiliation><country xml:lang="fr">Norvège</country><wicri:regionArea>CIGENE, Norwegian University of Life Sciences, Ås</wicri:regionArea></affiliation></author><author><name sortKey="Stokstad, Maria" sort="Stokstad, Maria" uniqKey="Stokstad M" first="Maria" last="Stokstad">Maria Stokstad</name><affiliation wicri:level="1"><nlm:affiliation>Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway.</nlm:affiliation><country xml:lang="fr">Norvège</country><wicri:regionArea>Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo</wicri:regionArea></affiliation></author><author><name sortKey="Berg, Mikael" sort="Berg, Mikael" uniqKey="Berg M" first="Mikael" last="Berg">Mikael Berg</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea></affiliation></author><author><name sortKey="Blomstrom, Anne Lie" sort="Blomstrom, Anne Lie" uniqKey="Blomstrom A" first="Anne-Lie" last="Blomström">Anne-Lie Blomström</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Cattle</term><term>Coronavirus, Bovine (genetics)</term><term>DNA Primers</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Nasal Cavity (virology)</term><term>Polymerase Chain Reaction (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN</term><term>Animaux</term><term>Bovins</term><term>Coronavirus bovin (génétique)</term><term>Fosse nasale (virologie)</term><term>Génome viral</term><term>Réaction de polymérisation en chaîne ()</term><term>Séquençage nucléotidique à haut débit ()</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus, Bovine</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus bovin</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Fosse nasale</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Nasal Cavity</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cattle</term><term>Genome, Viral</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amorces ADN</term><term>Animaux</term><term>Bovins</term><term>Génome viral</term><term>Réaction de polymérisation en chaîne</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29112950</PMID><DateCompleted><Year>2017</Year><Month>11</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>11</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>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).</ArticleTitle><Pagination><MedlinePgn>e0187780</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0187780</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Myrmel</LastName><ForeName>Mette</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2794-4023</Identifier><AffiliationInfo><Affiliation>Department for Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Oma</LastName><ForeName>Veslemøy</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khatri</LastName><ForeName>Mamata</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department for Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hansen</LastName><ForeName>Hanne H</ForeName><Initials>HH</Initials><AffiliationInfo><Affiliation>CIGENE, Norwegian University of Life Sciences, Ås, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stokstad</LastName><ForeName>Maria</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berg</LastName><ForeName>Mikael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Blomström</LastName><ForeName>Anne-Lie</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002417" MajorTopicYN="N">Cattle</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017938" MajorTopicYN="N">Coronavirus, Bovine</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="Y">DNA Primers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009296" MajorTopicYN="N">Nasal Cavity</DescriptorName><QualifierName UI="Q000821" 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