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Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling

BACKGROUND: 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 (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches...

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Autores principales: Yap, Yee Leng, Zhang, Xue Wu, Danchin, Antoine
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2003
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC222961/
https://www.ncbi.nlm.nih.gov/pubmed/14499005
http://dx.doi.org/10.1186/1471-2105-4-43
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author Yap, Yee Leng
Zhang, Xue Wu
Danchin, Antoine
author_facet Yap, Yee Leng
Zhang, Xue Wu
Danchin, Antoine
author_sort Yap, Yee Leng
collection PubMed
description BACKGROUND: 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 (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, 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. RESULTS: 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 (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: 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.
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spelling pubmed-2229612003-10-24 Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling Yap, Yee Leng Zhang, Xue Wu Danchin, Antoine BMC Bioinformatics Research Article BACKGROUND: 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 (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, 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. RESULTS: 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 (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: 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. BioMed Central 2003-09-20 /pmc/articles/PMC222961/ /pubmed/14499005 http://dx.doi.org/10.1186/1471-2105-4-43 Text en Copyright © 2003 Yap et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research Article
Yap, Yee Leng
Zhang, Xue Wu
Danchin, Antoine
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title_full Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title_fullStr Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title_full_unstemmed Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title_short Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
title_sort relationship of sars-cov to other pathogenic rna viruses explored by tetranucleotide usage profiling
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC222961/
https://www.ncbi.nlm.nih.gov/pubmed/14499005
http://dx.doi.org/10.1186/1471-2105-4-43
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