SrasV1, Ncbi, Curation, bibRecord, 001149

SARS-CoV Genome Polymorphism: A Bioinformatics Study

Identifieur interne : 001149 ( Ncbi/Curation ); précédent : 001148; suivant : 001150

SARS-CoV Genome Polymorphism: A Bioinformatics Study

Auteurs : Gordana M. Pavlovi Lažeti ; Nenad S. Miti ; Andrija M. Tomovi [Suisse] ; Mirjana D. Pavlovi ; Miloš V. Beljanski

Source :

Genomics, Proteomics & Bioinformatics [ 1672-0229 ] ; 2005.

RBID : PMC:5172477

Descripteurs français

KwdFr :
- Animaux, Biologie informatique, Données de séquences moléculaires, Délétion de séquence, Génome, Humains, Mutation, Phylogénie, Polymorphisme génétique (génétique), Similitude de séquences d'acides aminés, Syndrome respiratoire aigu sévère (génétique), Séquence d'acides aminés, Taïwan, Variation génétique, Virus du SRAS (génétique), Viverridae (génétique).
MESH :
- génétique : Polymorphisme génétique, Syndrome respiratoire aigu sévère, Virus du SRAS, Viverridae.
- Animaux, Biologie informatique, Données de séquences moléculaires, Délétion de séquence, Génome, Humains, Mutation, Phylogénie, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Taïwan, Variation génétique.
Wicri :
- geographic : Taïwan.

English descriptors

KwdEn :
- Amino Acid Sequence, Animals, Computational Biology, Genetic Variation, Genome, Humans, Molecular Sequence Data, Mutation, Phylogeny, Polymorphism, Genetic (genetics), SARS Virus (genetics), Sequence Deletion, Sequence Homology, Amino Acid, Severe Acute Respiratory Syndrome (genetics), Taiwan, Viverridae (genetics).
MESH :
- geographic : Taiwan.
- genetics : Polymorphism, Genetic, SARS Virus, Severe Acute Respiratory Syndrome, Viverridae.
- Amino Acid Sequence, Animals, Computational Biology, Genetic Variation, Genome, Humans, Molecular Sequence Data, Mutation, Phylogeny, Sequence Deletion, Sequence Homology, Amino Acid.

Abstract

A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a “profile”, were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172477

DOI: 10.1016/S1672-0229(05)03004-4
PubMed: 16144519
PubMed Central: 5172477

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Gordana M. Pavlovi Lažeti

<affiliation><nlm:aff id="aff0005">Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
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Nenad S. Miti

<affiliation><nlm:aff id="aff0005">Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
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Mirjana D. Pavlovi

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Miloš V. Beljanski

<affiliation><nlm:aff id="aff0015">Institute of General and Physical Chemistry, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
<wicri:noCountry code="subfield">Serbia and Montenegro</wicri:noCountry>
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<term>Genetic Variation</term>
<term>Genome</term>
<term>Humans</term>
<term>Molecular Sequence Data</term>
<term>Mutation</term>
<term>Phylogeny</term>
<term>Polymorphism, Genetic (genetics)</term>
<term>SARS Virus (genetics)</term>
<term>Sequence Deletion</term>
<term>Sequence Homology, Amino Acid</term>
<term>Severe Acute Respiratory Syndrome (genetics)</term>
<term>Taiwan</term>
<term>Viverridae (genetics)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Biologie informatique</term>
<term>Données de séquences moléculaires</term>
<term>Délétion de séquence</term>
<term>Génome</term>
<term>Humains</term>
<term>Mutation</term>
<term>Phylogénie</term>
<term>Polymorphisme génétique (génétique)</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Syndrome respiratoire aigu sévère (génétique)</term>
<term>Séquence d'acides aminés</term>
<term>Taïwan</term>
<term>Variation génétique</term>
<term>Virus du SRAS (génétique)</term>
<term>Viverridae (génétique)</term>
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<keywords scheme="MESH" type="geographic" xml:lang="en"><term>Taiwan</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Polymorphism, Genetic</term>
<term>SARS Virus</term>
<term>Severe Acute Respiratory Syndrome</term>
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<term>Computational Biology</term>
<term>Genetic Variation</term>
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<term>Humans</term>
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<front><div type="abstract" xml:lang="en"><p>A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of <bold>genome</bold>
 polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a “profile”, were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.</p>
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   |type=    RBID
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   |texte=   SARS-CoV Genome Polymorphism: A Bioinformatics Study
}}

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HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i   -Sk "pubmed:16144519" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd   \
       | NlmPubMed2Wicri -a SrasV1

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Serveur d'exploration SRAS

SARS-CoV Genome Polymorphism: A Bioinformatics Study

SARS-CoV Genome Polymorphism: A Bioinformatics Study

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