Given the ultra-rapid rate of change of RNA viruses and their generally impressive level of adaptation to host-cell environments, one might expect a virus like HIV-2 to show a codon usage bias similar to that of the host. And that's approximately true.
|HIV-2 codon usage (left), in DNA format (T for U), versus overall human-cell codon usage (right).|
The above graph shows codon usage for HIV-2 on the left and codon usage for human cells on the right. (HIV is an RNA virus, but codons are shown here in DNA format, with T in place of U.) R-squared/adjusted comes to 0.2204, so we can't very well say confidently that the codon values are highly correlated. But if you look at the smaller bars (not the "peaky" ones), they tend to taper down on the left, just as on the right.
It might be instructive to go from one of the fastest-changing viruses in the biosphere (HIV) to one of the slowest, and see how its codon usage compares to that of its host. This time, we're looking at the large DNA virus known as PBCV-1 (left) versus its Chlorella host (an alga, right):
|Codon usage in Paramecium bursaria Chlorella virus 1 (PBCV-1), left, and Chlorella variabilis strain NC64A, right.|
Which brings me to the final and most intriguing (I might even say shocking) graphic, which compares codon usage in PBCV-1 virus with codon usage in Chlorella's own host, Paramecium.
|Codon usage in PBCV-1 virus (left) and Paramecium (right).|
|Paramecium filled with Chlorella cells.|
Secondly, Paramecium doesn't use the standard genetic code! It uses the Ciliate Code (Translation Table 6), in which TAA and TAG encode glutamine instead of serving as stop codons. (TGA is the one and only stop codon in Table 6.) If Paramecium used the standard genetic code, the alignment of the two organisms would be even stronger.
Also interesting is that PBCV-1 and Paramecium are quite far apart in G+C content (the former is 40%, the latter is 28%).
Perhaps at some point in its past, PBCV-1 had a wider host range, one that included Paramecium. It's possible that even today, it has hosts other than Chlorella that have yet to be observed experimentally. Certainly, the pattern of codon usage is consistent with such an idea.