Analysis of population structures of viral isolates using single-strand conformation polymorphism method.
The analysis of viral populations requires the use of techniques that describe characteristics of individuals. The single-strand conformation polymorphism (SSCP) makes possible the identification of genetic differences between viral sequences and constitutes an alternative to the expensive and time-consuming cloning and sequencing strategies. Applied to small genomic regions (from 100 to 500 bases in length), SSCP patterns could describe, under appropriate experimental conditions, single nucleotide variations in the studied sequence. The different steps of a complete SSCP procedure, from sampling to pattern analysis (including nucleic acid extraction, RT-PCR amplification, double-stranded DNA quantification, polyacrylamide gel preparation, electrophoresis conditions, and staining procedures), are described using a region (500 bases) of the barley yellow dwarfvirus-PAV (BYDV-PAV, Luteovirus) genome as molecular target.
Delaunay
Agnès
A
INRA, Agrocampus Rennes, Le Rheu, France.
Rolland
Mathieu
M
Jacquot
Emmanuel
E
D001483:Base Sequence; D019411:Clinical Laboratory Techniques; D004247:DNA / Q000737:chemistry; D004252:DNA Mutational Analysis; D004279:DNA, Viral / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018807:Polymorphism, Single-Stranded Conformational / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*
D004279:DNA, Viral; D004247:DNA