Document Detail


SARS-CoV genome polymorphism: a bioinformatics study.
MedLine Citation:
PMID:  16144519     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Gordana M Pavlović-Lazetić; Nenad S Mitić; Andrija M Tomović; Mirjana D Pavlović; Milos V Beljanski
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Genomics, proteomics & bioinformatics     Volume:  3     ISSN:  1672-0229     ISO Abbreviation:  Genomics Proteomics Bioinformatics     Publication Date:  2005 Feb 
Date Detail:
Created Date:  2005-09-07     Completed Date:  2005-11-01     Revised Date:  2012-09-10    
Medline Journal Info:
Nlm Unique ID:  101197608     Medline TA:  Genomics Proteomics Bioinformatics     Country:  China    
Other Details:
Languages:  eng     Pagination:  18-35     Citation Subset:  IM    
Affiliation:
Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro. gordana@matf.bg.ac.yu
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MeSH Terms
Descriptor/Qualifier:
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*

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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