Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Identifieur interne : 000078 ( France/Analysis ); précédent : 000077; suivant : 000079Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Auteurs : Yee Leng Yap [Hong Kong] ; Xue Wu Zhang [Hong Kong] ; Antoine Danchin [France]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2003.
Abstract
The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (
Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (
The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.
The online version of this article (doi:10.1186/1471-2105-4-43) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2105-4-43
PubMed: 14499005
PubMed Central: 222961
Affiliations:
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PMC:222961Le document en format XML
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Man Building, 8 Sassoon Road Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Dexter H.C. Man Building, 8 Sassoon Road Pokfulam</wicri:regionArea><wicri:noRegion>8 Sassoon Road Pokfulam</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.482283.7</institution-id><institution>HKU-Pasteur Research Centre,</institution></institution-wrap>Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Dexter H.C. Man Building, 8 Sassoon Road Pokfulam</wicri:regionArea><wicri:noRegion>8 Sassoon Road Pokfulam</wicri:noRegion></affiliation></author><author><name sortKey="Danchin, Antoine" sort="Danchin, Antoine" uniqKey="Danchin A" first="Antoine" last="Danchin">Antoine Danchin</name><affiliation wicri:level="3"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.428999.7</institution-id><institution-id institution-id-type="ISNI">0000 0001 2353 6535</institution-id><institution>Institute Pasteur,</institution><institution>Unité de Génétique des Génomes Bactériens,</institution></institution-wrap>28 rue du Docteur Roux, 75724 Paris Cedex 15, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>28 rue du Docteur Roux, 75724 Paris Cedex 15</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (<italic>ss</italic> RNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern <italic>V</italic> for each virus. In approach one, a distance measure of a vector <italic>V</italic>, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses.</p></sec><sec><title>Results</title><p>Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (<italic>z</italic> = -77.31, -52.48 respectively) and selection for UpG and CpA (<italic>z</italic> = 65.79,49.99 respectively). Potential factors influencing these biases are discussed.</p></sec><sec><title>Conclusion</title><p>The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2105-4-43) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author><author><name sortKey="Kuiken, T" uniqKey="Kuiken T">T Kuiken</name></author><author><name sortKey="Schutten, M" uniqKey="Schutten M">M Schutten</name></author><author><name sortKey="Van Amerongen, G" uniqKey="Van Amerongen G">G Van Amerongen</name></author><author><name sortKey="Van Doornum, Gj" uniqKey="Van Doornum G">GJ Van Doornum</name></author><author><name sortKey="Van 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uniqKey="Koziol J">JA Koziol</name></author><author><name sortKey="Beutler, B" uniqKey="Beutler B">B Beutler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Regenmortel, Mhv" uniqKey="Regenmortel M">MHV Regenmortel</name></author><author><name sortKey="Van Fauquet, Cm" uniqKey="Van Fauquet C">CM van Fauquet</name></author><author><name sortKey="Bishop, Dhl" uniqKey="Bishop D">DHL Bishop</name></author><author><name sortKey="Carstens, Eb" uniqKey="Carstens E">EB Carstens</name></author><author><name sortKey="Estes, Mk" uniqKey="Estes M">MK Estes</name></author><author><name sortKey="Lemon, Sm" uniqKey="Lemon S">SM Lemon</name></author><author><name sortKey="Maniloff, J" uniqKey="Maniloff J">J Maniloff</name></author><author><name sortKey="Mayo, Ma" uniqKey="Mayo M">MA Mayo</name></author><author><name sortKey="Mcgeoch, Dj" uniqKey="Mcgeoch D">DJ McGeoch</name></author><author><name sortKey="Pringle, Cr" uniqKey="Pringle C">CR Pringle</name></author><author><name sortKey="Wickner, Rb" uniqKey="Wickner R">RB Wickner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bartholomew, Dj" uniqKey="Bartholomew D">DJ Bartholomew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, J" uniqKey="Kim J">J Kim</name></author><author><name sortKey="Mueller Charles, W" uniqKey="Mueller Charles W">W Mueller Charles</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bartholomew, Dj" uniqKey="Bartholomew D">DJ Bartholomew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ewens, Wj" uniqKey="Ewens W">WJ Ewens</name></author><author><name sortKey="Grant, Gr" uniqKey="Grant G">GR Grant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bronson, Ec" uniqKey="Bronson E">EC Bronson</name></author><author><name sortKey="Anderson, Jn" uniqKey="Anderson J">JN Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rocha, Ep" uniqKey="Rocha E">EP Rocha</name></author><author><name sortKey="Viari, A" uniqKey="Viari A">A Viari</name></author><author><name sortKey="Danchin, A" uniqKey="Danchin A">A Danchin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leung, My" uniqKey="Leung M">MY Leung</name></author><author><name sortKey="Marsh, Gm" uniqKey="Marsh G">GM Marsh</name></author><author><name sortKey="Speed, Tp" uniqKey="Speed T">TP Speed</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schbath, S" uniqKey="Schbath S">S Schbath</name></author><author><name sortKey="Prum, B" uniqKey="Prum B">B Prum</name></author><author><name sortKey="De Turckheim, E" uniqKey="De Turckheim E">E de Turckheim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saitou, N" uniqKey="Saitou N">N Saitou</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Hong Kong</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><country name="Hong Kong"><noRegion><name sortKey="Yap, Yee Leng" sort="Yap, Yee Leng" uniqKey="Yap Y" first="Yee Leng" last="Yap">Yee Leng Yap</name></noRegion><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name></country><country name="France"><region name="Île-de-France"><name sortKey="Danchin, Antoine" sort="Danchin, Antoine" uniqKey="Danchin A" first="Antoine" last="Danchin">Antoine Danchin</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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