Document Detail


GeneChip resequencing of the smallpox virus genome can identify novel strains: a biodefense application.
MedLine Citation:
PMID:  17182757     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We developed a set of seven resequencing GeneChips, based on the complete genome sequences of 24 strains of smallpox virus (variola virus), for rapid characterization of this human-pathogenic virus. Each GeneChip was designed to analyze a divergent segment of approximately 30,000 bases of the smallpox virus genome. This study includes the hybridization results of 14 smallpox virus strains. Of the 14 smallpox virus strains hybridized, only 7 had sequence information included in the design of the smallpox virus resequencing GeneChips; similar information for the remaining strains was not tiled as a reference in these GeneChips. By use of variola virus-specific primers and long-range PCR, 22 overlapping amplicons were amplified to cover nearly the complete genome and hybridized with the smallpox virus resequencing GeneChip set. These GeneChips were successful in generating nucleotide sequences for all 14 of the smallpox virus strains hybridized. Analysis of the data indicated that the GeneChip resequencing by hybridization was fast and reproducible and that the smallpox virus resequencing GeneChips could differentiate the 14 smallpox virus strains characterized. This study also suggests that high-density resequencing GeneChips have potential biodefense applications and may be used as an alternate tool for rapid identification of smallpox virus in the future.
Authors:
Irshad M Sulaiman; Kevin Tang; John Osborne; Scott Sammons; Robert M Wohlhueter
Related Documents :
21288747 - Implications of global and regional patterns of highly pathogenic avian influenza virus...
21429237 - Epstein-barr virus genetics: talking about the bac generation.
6099427 - A survey of north american migratory waterfowl for duck plague (duck virus enteritis) v...
21241537 - Transmission of swine pathogens: different means, different needs.
20852317 - Evaluation of tear samples for herpes simplex virus 1 (hsv) detection in suspected case...
18051947 - Multiplex reverse transcriptase-pcr assay for typing and subtyping of influenza a (h5 &...
Publication Detail:
Type:  Evaluation Studies; Journal Article     Date:  2006-12-20
Journal Detail:
Title:  Journal of clinical microbiology     Volume:  45     ISSN:  0095-1137     ISO Abbreviation:  J. Clin. Microbiol.     Publication Date:  2007 Feb 
Date Detail:
Created Date:  2007-02-05     Completed Date:  2007-03-29     Revised Date:  2013-06-06    
Medline Journal Info:
Nlm Unique ID:  7505564     Medline TA:  J Clin Microbiol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  358-63     Citation Subset:  IM    
Affiliation:
Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Atlanta, GA 30333, USA. ISulaiman@cdc.gov
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Bioterrorism / prevention & control*
DNA Primers
Genome, Viral / genetics*
Humans
Oligonucleotide Array Sequence Analysis / instrumentation*
Polymerase Chain Reaction
Sequence Analysis, DNA*
Variola virus / classification*,  genetics
Virology / methods
Chemical
Reg. No./Substance:
0/DNA Primers
Comments/Corrections

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


Previous Document:  Evaluation of a new selective chromogenic agar medium for detection of extended-spectrum beta-lactam...
Next Document:  Rapid and highly sensitive pathotyping of avian influenza A H5N1 virus by using real-time reverse tr...