Schematic representation of genomic variations and population dynamics of RNA viruses. (A) In infected hosts RNA viruses replicate as complex distributions of related genomes termed viral quasispecies. Here two out of multiple distributions are represented. Horizontal lines depict individual genomes and symbols on the lines represent different mutation types (transitions, transversions and short insertions or deletions termed indels). A distribution is defined by a consensus sequence and a mutant spectrum with a complexity given by the average pairwise genetic (also termed Hamming) distance among its components or the average mutation frequency. (B) Molecular recombination. (C) Genome segment reassortment, using influenza A virus (eight genomic segments) as an example. Reassortment (in this case the replacement of HA and NA genes) gives rise to an antigenic shift. Continued accumulation of mutations results in gradual antigenic drift. (D) A simplified view of quasispecies dynamics and fitness change. Unrestricted replication (large black arrow-head on the right, with multiple passages indicated by the dotted line) results in fitness gain, as depicted by the triangle at the bottom. Fitness gain can occur without variation of the consensus sequence (top). In contrast, repeated bottleneck transfers (left, with the dotted line representing multiple transfers) result in accumulation of mutations that modify the consensus sequences, and in fitness decrease. At low and high fitness values significant fluctuations of fitness values have been observed. This figure is based on previously published data and concepts [4, 9, 11–14, 16, 17, 19, 21, 25, 29, 31, 35, 41, 57, 59–61, 66, 71, 74].