Mutation rate in gag protein

Value 2.65e-3 substitutions/site/year Range: 0.00187 - 0.00349 substitutions/site/year
Organism HIV
Reference Novitsky V, Wang R, Lagakos S, Essex M. HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses. 2010 Jan2(1):33-54. doi: 10.3390/v2010033. p.46 top paragraphPubMed ID21994599
Method P.46 top paragraph: "Dating of HIV-1 subtype C divergence: To assess the date of the HIV-1 subtype C divergence [investigators] estimated the time to the most recent common ancestor (tMRCA) of subtype C viruses in a subset of 138 gag sequences selected by country representation (limit was set to three sequences per country per year of sampling). A relaxed clock Bayesian MCMC coalescent framework analysis was implemented in BEAST v1.4.8 [ref 42]. This approach incorporates phylogenetic uncertainty and accounts for the possibility of variable substitution rates among lineages and differences in the demographic history of the virus, sampling phylogenies and parameter estimates in proportion to their posterior probability [refs 43–46]. Substitution rates were calibrated with analyzed gag sequences with known year of sampling."
Comments P.46 top paragraph: "The median (95% highest posterior density interval, HPD, a Bayesian analog to a confidence interval) substitution rate in gag was estimated as 2.65×10^–3 (1.87x10^–3 – 3.49×10^–3) substitutions per site per year. The different demographic/coalescent models gave similar estimates for HIV-1 subtype C tMRCA. The tMRCA (95% HPD) of HIV-1 subtype C was estimated at 1950 (1930–1962) based on a constant population size model and at 1948 (1928–1962) using the Bayesian skyline plot [refs 47,48] (Figure 6), which is consistent with the estimated date of tMRCA of HIV-1 group M [ref 44]."
Entered by Uri M
ID 113337