Abstract: Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10(-8) to 10(-6) s/n/c for DNA viruses and from 10(-6) to 10(-4) s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut.

Abstract: We construct extensions of the Standard Model with two Higgs doublets, where there are flavour changing neutral currents both in the quark and leptonic sectors, with their strength fixed by the fermion mixing matrices V(CKM) and V(PMNS). These models are an extension to the leptonic sector of the class of models previously considered by Branco, Grimus and Lavoura, for the quark sector. We consider both the cases of Dirac and Majorana neutrinos and identify the minimal discrete symmetry required in order to implement the models in a natural way.

Abstract: We analyse the constraints and some of the phenomenological implications of a class of two Higgs doublet models where there are flavour-changing neutral currents (FCNC) at tree level but the potentially dangerous FCNC couplings are suppressed by small entries of the CKM matrix V. This class of models have the remarkable feature that, as a result of a discrete symmetry of the Lagrangian, the FCNC couplings are entirely fixed in the quark sector by V and the ratio v(2)/v(1) of the vevs of the neutral Higgs. The discrete symmetry is extended to the leptonic sector, so that there are FCNC in the leptonic sector with their flavour structure fixed by the leptonic mixing matrix. We analyse a large number of processes, including decays mediated by charged Higgs at tree level, processes involving FCNC at tree level, as well as loop induced processes. We show that in this class of models one has new physical scalars beyond the standard Higgs boson, with masses reachable at the next round of experiments.