The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates.

ABSTRACT:

Background

Annually, rubella virus (RV) still causes severe congenital defects in around 100 000 children globally. An attempt to eradicate RV is currently underway and analytical tools to monitor the global decline of the last remaining RV lineages will be useful for assessing the effectiveness of this endeavour. RV evolves rapidly enough that much of this information might be inferable from RV genomic sequence data.

Methods

Using BEASTv1.8.0, we analysed publically available RV sequence data to estimate genome-wide and gene-specific nucleotide substitution rates to test whether current estimates of RV substitution rates are representative of the entire RV genome. We specifically accounted for possible confounders of nucleotide substitution rate estimates, such as temporall

SUBMITTER: Cloete LJ 

PROVIDER: S-EPMC4175276 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature