There is considerable uncertainty in the mutation rate estimates for HIV, ranging from 3.4 × 10−5 (Mansky and Temin 1995) to 9 × 10−5 per site and generation (O'Neil et al. 2002 for mutations in the LTR).
The implications of a new, pseudoderivative-based adaptive mutation rate are considerable.
It is now well documented that there is considerable variation in mutation rates (e.g. Hodgkinson and Eyre-Walker 2011), but we suspect that the implications of this for developmental bias are rarely appreciated.
It was recently shown that there is considerable variation in mutation rates within and between families, which in part can be attributed to the age of the father at the time of conception.
HIV-1 exhibits considerable genetic diversity resulting from the high mutation rate of reverse transcriptase, high viral turnover, viral genomic recombination, and immune and therapeutic selection pressures (1– 3).
Significantly mutated genes (SMGs) were defined as the somatic mutations with higher mutated frequency than background mutation rate.
ALV subgroups exhibit considerable genetic diversity, which results from the high mutation rate of reverse transcriptase, viral genomic recombination, and selection pressures from cell-mediated immune responses.
With a high mutation rate, the population of influenza A virus can generate considerable genetic variability and if there would be no selection it could potentially attain high levels of genetic diversity.
Our analysis, even by a conservative estimation of mutation rate, indicates that the SARS-CoV population has already harbored a considerable amount of genetic diversity.
However, assuming an average spontaneous CNV mutation rate of 1/10,000 per locus [ 5], it is expected that a considerable portion of the reported entries arise from de novo CNVs of a sporadic nature.
