Figure 2. Examples of parallel adaptations following host shifts.

(A) Parallel genetic changes in five replicate lines of Hibiscus chlorotic ring spot virus. The white boxes represent the viral genome, and the coloured blocks represent mutations. The virus naturally infects Hibiscus plants, but following five passages in an alternate host, (Chenopodium quinoa) the same eight mutations repeatedly occur [57]. (B) Parallel genetic changes in codon 30 of the gag gene (Met to Arg) following three independent transfers of SIVcpz into humans [59]. When a chimp was subsequently infected with HIV-1, the residue reverted back to Met. The coloured blocks represent either a Met (yellow) or Arg (blue) at codon position 30 in the HIV gag gene. (C) Parallel changes in protein function following independent transfers of SIVs from chimpanzees (HIV-1) and sooty mangabeys (HIV-2) into humans. SIV Nef protein does not antagonise tetherin in humans, and so other HIV proteins have evolved the ability to antagonise tetherin [64]. The exception to this is HIV-1 group O viruses, which do not appear to have evolved anti-tetherin activity. In HIV-1 group N viruses the evolution of anti-tetherin activity in Vpu may have come at a cost, as Vpu no longer degrades CD4 receptors to aid the release of viral particles [61]. The coloured gene names in the schematic represent the gene that provides the anti-tetherin function in that host and viral lineage.