Accumulating variation at conserved sites in potyvirus genomes is driven by species discovery and affects degenerate primer design.

ABSTRACT:

Unlabelled

Unknown and foreign viruses can be detected using degenerate primers targeted at conserved sites in the known viral gene sequences. Conserved sites are found by comparing sequences and so the usefulness of a set of primers depends crucially on how well the known sequences represent the target group including unknown sequences.

Methodology/principal findings

We developed a method for assessing the apparent stability of consensus sequences at sites over time using deposition dates from Genbank. We tested the method using 17 conserved sites in potyvirus genomes. The accumulation of knowledge of sequence variants over 20 years caused 'consensus decay' of the sites. Rates of decay were rapid at all sites but varied widely and as a result, the ranking of the most conser

SUBMITTER: Zheng L 

PROVIDER: S-EPMC2217591 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature