Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Identifieur interne : 001085 ( Main/Curation ); précédent : 001084; suivant : 001086Relationship 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.
Url:
DOI: 10.1186/1471-2105-4-43
PubMed: 14499005
PubMed Central: 222961
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PMC:222961Le document en format XML
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<author><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name>
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<author><name sortKey="Zhang, Xue Wu" sort="Zhang, Xue Wu" uniqKey="Zhang X" first="Xue Wu" last="Zhang">Xue Wu Zhang</name>
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<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>
</div>
</front>
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