Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition
Identifieur interne : 001299 ( Main/Exploration ); précédent : 001298; suivant : 001300Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition
Auteurs : Qin Tang [République populaire de Chine] ; Yulong Song [République populaire de Chine] ; Mijuan Shi [République populaire de Chine] ; Yingyin Cheng [République populaire de Chine] ; Wanting Zhang [République populaire de Chine] ; Xiao-Qin Xia [République populaire de Chine]Source :
- Scientific Reports [ 2045-2322 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Nucleotides.
- genetics : Coronavirus.
- virology : Coronavirus Infections.
- Base Composition, Host-Pathogen Interactions, Humans, Models, Statistical, Reproducibility of Results, Support Vector Machine.
Abstract
Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at
The online version of this article (doi:10.1038/srep17155) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1038/srep17155
PubMed: 26607834
PubMed Central: 4660426
Affiliations:
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when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Coronavirus (genetics)</term><term>Coronavirus Infections (virology)</term><term>Host-Pathogen Interactions</term><term>Humans</term><term>Models, Statistical</term><term>Nucleotides (genetics)</term><term>Reproducibility of Results</term><term>Support Vector Machine</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Composition en bases nucléiques</term><term>Coronavirus (génétique)</term><term>Humains</term><term>Infections à coronavirus (virologie)</term><term>Interactions hôte-pathogène</term><term>Machine à vecteur de support</term><term>Modèles statistiques</term><term>Nucléotides (génétique)</term><term>Reproductibilité des résultats</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleotides</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term><term>Nucléotides</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Host-Pathogen Interactions</term><term>Humans</term><term>Models, Statistical</term><term>Reproducibility of Results</term><term>Support Vector Machine</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Composition en bases nucléiques</term><term>Humains</term><term>Interactions hôte-pathogène</term><term>Machine à vecteur de support</term><term>Modèles statistiques</term><term>Reproductibilité des résultats</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at <ext-link ext-link-type="uri" xlink:href="http://bioinfo.ihb.ac.cn/seq2hosts">http://bioinfo.ihb.ac.cn/seq2hosts</ext-link>.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1038/srep17155) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan, Jfw" uniqKey="Chan J">JFW Chan</name></author><author><name sortKey="To, Kkw" uniqKey="To K">KKW To</name></author><author><name sortKey="Tse, H" uniqKey="Tse H">H Tse</name></author><author><name sortKey="Jin, Dy" uniqKey="Jin D">DY Jin</name></author><author><name sortKey="Yuen, Ky" uniqKey="Yuen K">KY Yuen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lau, Skp" uniqKey="Lau S">SKP 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Reuther</name></author><author><name sortKey="Schwemmle, M" uniqKey="Schwemmle M">M Schwemmle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Romero Tejeda, A" uniqKey="Romero Tejeda A">A Romero-Tejeda</name></author><author><name sortKey="Capua, I" uniqKey="Capua I">I Capua</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, Pcy" uniqKey="Woo P">PCY Woo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vijgen, L" uniqKey="Vijgen L">L Vijgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name></author><author><name sortKey="Campbell, Am" uniqKey="Campbell A">AM Campbell</name></author><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mclachlan, Gj" uniqKey="Mclachlan G">GJ McLachlan</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tang, Qin" sort="Tang, Qin" uniqKey="Tang Q" first="Qin" last="Tang">Qin Tang</name></noRegion><name sortKey="Cheng, Yingyin" sort="Cheng, Yingyin" uniqKey="Cheng Y" first="Yingyin" last="Cheng">Yingyin Cheng</name><name sortKey="Shi, Mijuan" sort="Shi, Mijuan" uniqKey="Shi M" first="Mijuan" last="Shi">Mijuan Shi</name><name sortKey="Song, Yulong" sort="Song, Yulong" uniqKey="Song Y" first="Yulong" last="Song">Yulong Song</name><name sortKey="Song, Yulong" sort="Song, Yulong" uniqKey="Song Y" first="Yulong" last="Song">Yulong Song</name><name sortKey="Tang, Qin" sort="Tang, Qin" uniqKey="Tang Q" first="Qin" last="Tang">Qin Tang</name><name sortKey="Xia, Xiao Qin" sort="Xia, Xiao Qin" uniqKey="Xia X" first="Xiao-Qin" last="Xia">Xiao-Qin Xia</name><name sortKey="Zhang, Wanting" sort="Zhang, Wanting" uniqKey="Zhang W" first="Wanting" last="Zhang">Wanting Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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