On 2017 Jan 16, Stuart RAY commented:

This is a scientifically interesting report, but the use of "mutation rate" in the title, abstract, and in some portions of the text is unfortunate, because the process being observed and measured in this report is evolutionary rate of substitution (as noted in the authors' Tables 1 and 2). The evolutionary rate of substitution results from a variety of processes that are affected by the rate mutation (determined in particular by the polymerase), positive and negative selection, and stochastic events at multiple levels (from individual cell to population). Thus, the term "mutation rate" is confusing and potentially misleading. With every RNA genome replication, there is a nonzero rate of mutation; what we estimate when we sequence virus obtained from infected individuals, sampled over a period of years, is the evolutionary rate of substitution.

On 2017 Jan 16, Stuart RAY commented:

This is a scientifically interesting report, but the use of "mutation rate" in the title, abstract, and in some portions of the text is unfortunate, because the process being observed and measured in this report is evolutionary rate of substitution (as noted in the authors' Tables 1 and 2). The evolutionary rate of substitution results from a variety of processes that are affected by the rate mutation (determined in particular by the polymerase), positive and negative selection, and stochastic events at multiple levels (from individual cell to population). Thus, the term "mutation rate" is confusing and potentially misleading. With every RNA genome replication, there is a nonzero rate of mutation; what we estimate when we sequence virus obtained from infected individuals, sampled over a period of years, is the evolutionary rate of substitution.